From 073754355af3f9774e6306ec6b8e589dafd7a8d9 Mon Sep 17 00:00:00 2001 From: kheal Date: Wed, 23 Oct 2024 23:13:34 +0000 Subject: [PATCH] =?UTF-8?q?Deploy=20preview=20for=20PR=202230=20?= =?UTF-8?q?=F0=9F=9B=AB?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pr-preview/pr-2230/add_date/index.html | 12 +- pr-preview/pr-2230/all_proteins/index.html | 10 +- .../alternative_identifiers/index.html | 210 ++++++------- .../pr-2230/analyte_category/index.html | 10 +- pr-preview/pr-2230/asm_score/index.html | 8 +- .../pr-2230/associated_studies/index.html | 16 +- pr-preview/pr-2230/best_protein/index.html | 10 +- pr-preview/pr-2230/container_size/index.html | 8 +- pr-preview/pr-2230/contig_bp/index.html | 8 +- pr-preview/pr-2230/contigs/index.html | 8 +- pr-preview/pr-2230/ctg_l50/index.html | 8 +- pr-preview/pr-2230/ctg_l90/index.html | 8 +- pr-preview/pr-2230/ctg_logsum/index.html | 8 +- pr-preview/pr-2230/ctg_max/index.html | 8 +- pr-preview/pr-2230/ctg_n50/index.html | 8 +- pr-preview/pr-2230/ctg_n90/index.html | 8 +- pr-preview/pr-2230/ctg_powsum/index.html | 8 +- pr-preview/pr-2230/cur_vegetation/index.html | 10 +- pr-preview/pr-2230/description/index.html | 212 ++++++------- pr-preview/pr-2230/duration/index.html | 16 +- pr-preview/pr-2230/elev/index.html | 10 +- pr-preview/pr-2230/end_date/index.html | 108 +++---- pr-preview/pr-2230/ended_at_time/index.html | 48 +-- .../pr-2230/execution_resource/index.html | 52 ++-- pr-preview/pr-2230/gap_pct/index.html | 8 +- pr-preview/pr-2230/gc_avg/index.html | 8 +- pr-preview/pr-2230/gc_std/index.html | 8 +- pr-preview/pr-2230/geo_loc_name/index.html | 8 +- pr-preview/pr-2230/git_url/index.html | 52 ++-- .../index.html | 8 +- .../pr-2230/gold_identifiers/index.html | 2 +- pr-preview/pr-2230/habitat/index.html | 8 +- pr-preview/pr-2230/has_calibration/index.html | 10 +- .../has_failure_categorization/index.html | 108 +++---- pr-preview/pr-2230/has_input/index.html | 130 ++++---- pr-preview/pr-2230/has_output/index.html | 128 ++++---- pr-preview/pr-2230/has_raw_value/index.html | 32 +- pr-preview/pr-2230/id/index.html | 224 +++++++------- pr-preview/pr-2230/img_identifiers/index.html | 24 +- .../insdc_assembly_identifiers/index.html | 8 +- .../insdc_experiment_identifiers/index.html | 8 +- .../pr-2230/insdc_identifiers/index.html | 4 +- pr-preview/pr-2230/instrument_used/index.html | 48 +-- pr-preview/pr-2230/lat_lon/index.html | 10 +- pr-preview/pr-2230/local_class/index.html | 8 +- pr-preview/pr-2230/mod_date/index.html | 12 +- pr-preview/pr-2230/name/index.html | 218 +++++++------- .../pr-2230/num_aligned_reads/index.html | 8 +- pr-preview/pr-2230/num_input_reads/index.html | 8 +- pr-preview/pr-2230/part_of/index.html | 8 +- .../pr-2230/principal_investigator/index.html | 12 +- .../pr-2230/processing_institution/index.html | 108 +++---- pr-preview/pr-2230/protocol_link/index.html | 118 ++++---- pr-preview/pr-2230/qc_comment/index.html | 108 +++---- pr-preview/pr-2230/qc_status/index.html | 108 +++---- pr-preview/pr-2230/scaf_bp/index.html | 8 +- pr-preview/pr-2230/scaf_l50/index.html | 8 +- pr-preview/pr-2230/scaf_l90/index.html | 8 +- pr-preview/pr-2230/scaf_l_gt50k/index.html | 8 +- pr-preview/pr-2230/scaf_logsum/index.html | 8 +- pr-preview/pr-2230/scaf_max/index.html | 8 +- pr-preview/pr-2230/scaf_n50/index.html | 8 +- pr-preview/pr-2230/scaf_n90/index.html | 8 +- pr-preview/pr-2230/scaf_n_gt50k/index.html | 8 +- pr-preview/pr-2230/scaf_pct_gt50k/index.html | 8 +- pr-preview/pr-2230/scaf_powsum/index.html | 8 +- pr-preview/pr-2230/scaffolds/index.html | 8 +- pr-preview/pr-2230/search/search_index.json | 2 +- pr-preview/pr-2230/soil_type/index.html | 8 +- pr-preview/pr-2230/start_date/index.html | 108 +++---- pr-preview/pr-2230/started_at_time/index.html | 52 ++-- pr-preview/pr-2230/substances_used/index.html | 8 +- pr-preview/pr-2230/temperature/index.html | 20 +- pr-preview/pr-2230/type/index.html | 282 +++++++++--------- pr-preview/pr-2230/url/index.html | 10 +- pr-preview/pr-2230/version/index.html | 48 +-- pr-preview/pr-2230/volume/index.html | 20 +- pr-preview/pr-2230/was_informed_by/index.html | 48 +-- 78 files changed, 1533 insertions(+), 1533 deletions(-) diff --git a/pr-preview/pr-2230/add_date/index.html b/pr-preview/pr-2230/add_date/index.html index 3c2f658638..077ad65b4d 100644 --- a/pr-preview/pr-2230/add_date/index.html +++ b/pr-preview/pr-2230/add_date/index.html @@ -497,8 +497,8 @@

Applicable Classes

-DataGeneration -The methods and processes used to generate omics data from a biosample or org... +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no @@ -507,13 +507,13 @@

Applicable Classes

no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no diff --git a/pr-preview/pr-2230/all_proteins/index.html b/pr-preview/pr-2230/all_proteins/index.html index 22ee20ef30..bbb6357a2b 100644 --- a/pr-preview/pr-2230/all_proteins/index.html +++ b/pr-preview/pr-2230/all_proteins/index.html @@ -497,15 +497,15 @@

Applicable Classes

-PeptideQuantification -This is used to link a metaproteomics analysis workflow to a specific peptide... -no - - ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes + +PeptideQuantification +This is used to link a metaproteomics analysis workflow to a specific peptide... +no +

Properties

diff --git a/pr-preview/pr-2230/alternative_identifiers/index.html b/pr-preview/pr-2230/alternative_identifiers/index.html index c66c5920c8..6f9d204ab7 100644 --- a/pr-preview/pr-2230/alternative_identifiers/index.html +++ b/pr-preview/pr-2230/alternative_identifiers/index.html @@ -511,93 +511,78 @@

Applicable Classes

-MetaproteomicsAnalysis - -no - - -MetaboliteIdentification -This is used to link a metabolomics analysis workflow to a specific metabolit... -no - - -NamedThing -a databased entity or concept/class +WorkflowExecution +Represents an instance of an execution of a particular workflow no -Extraction -A material separation in which a desired component of an input material is se... +MetatranscriptomeAnnotation + no -FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -WorkflowExecution -Represents an instance of an execution of a particular workflow +Site + no -Biosample -Biological source material which can be characterized by an experiment -yes - - -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +MaterialEntity + no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +MetatranscriptomeAssembly + no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +Configuration +A set of parameters that define the actions of a process and is shared among ... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -Configuration -A set of parameters that define the actions of a process and is shared among ... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetatranscriptomeAnnotation - +Pathway +A pathway is a sequence of steps/reactions carried out by an organism or comm... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +DataObject +An object that primarily consists of symbols that represent information no -NomAnalysis +PlannedProcess no -CollectingBiosamplesFromSite +EnvironmentalMaterialTerm no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +NamedThing +a databased entity or concept/class no @@ -606,48 +591,53 @@

Applicable Classes

no -Site +ProcessedSample no -MassSpectrometryConfiguration -A set of parameters that define and control the actions of a mass spectrometr... +ChemicalEntity +An atom or molecule that can be represented with a chemical formula no -MetabolomicsAnalysis - +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -ProcessedSample - +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected no -OntologyClass +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... +no + + +CollectingBiosamplesFromSite no -Pathway -A pathway is a sequence of steps/reactions carried out by an organism or comm... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -DataObject -An object that primarily consists of symbols that represent information +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -GeneProduct -A molecule encoded by a gene that has an evolved function +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no @@ -656,43 +646,43 @@

Applicable Classes

no -MetatranscriptomeAssembly - +InformationObject +Any data or knowledge that reduces uncertainty or enhances understanding abou... no -ChemicalEntity -An atom or molecule that can be represented with a chemical formula +MetaboliteIdentification +This is used to link a metabolomics analysis workflow to a specific metabolit... no -FiltrationProcess -The process of segregation of phases; e +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -EnvironmentalMaterialTerm - +GeneProduct +A molecule encoded by a gene that has an evolved function no -LibraryPreparation - +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -Pooling -physical combination of several instances of like material -no +Study +A study summarizes the overall goal of a research initiative and outlines the... +yes -MaterialEntity - +MassSpectrometryConfiguration +A set of parameters that define and control the actions of a mass spectrometr... no @@ -701,78 +691,88 @@

Applicable Classes

no -DissolvingProcess -A mixing step where a soluble component is mixed with a liquid component +Extraction +A material separation in which a desired component of an input material is se... no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +FunctionalAnnotationTerm +Abstract grouping class for any term/descriptor that can be applied to a func... no -FunctionalAnnotationTerm -Abstract grouping class for any term/descriptor that can be applied to a func... +Pooling +physical combination of several instances of like material no -OrthologyGroup -A set of genes or gene products in which all members are orthologous +DissolvingProcess +A mixing step where a soluble component is mixed with a liquid component no -PlannedProcess +OntologyClass no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -Study -A study summarizes the overall goal of a research initiative and outlines the... -yes +MetaproteomicsAnalysis + +no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +FiltrationProcess +The process of segregation of phases; e no -Manifest +MetabolomicsAnalysis no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +ChromatographyConfiguration +A set of parameters that define and control the actions of a chromatography p... no -InformationObject -Any data or knowledge that reduces uncertainty or enhances understanding abou... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no -ChromatographyConfiguration -A set of parameters that define and control the actions of a chromatography p... +Manifest + no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +OrthologyGroup +A set of genes or gene products in which all members are orthologous +no + + +Biosample +Biological source material which can be characterized by an experiment +yes + + +LibraryPreparation + no diff --git a/pr-preview/pr-2230/analyte_category/index.html b/pr-preview/pr-2230/analyte_category/index.html index fe75b9c9a7..231bf9540c 100644 --- a/pr-preview/pr-2230/analyte_category/index.html +++ b/pr-preview/pr-2230/analyte_category/index.html @@ -499,6 +499,11 @@

Applicable Classes

+MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... +no + + DataGeneration The methods and processes used to generate omics data from a biosample or org... no @@ -508,11 +513,6 @@

Applicable Classes

A DataGeneration in which the sequence of DNA or RNA molecules is generated no - -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... -no -

Properties

diff --git a/pr-preview/pr-2230/asm_score/index.html b/pr-preview/pr-2230/asm_score/index.html index 0db28a79bf..083db7a594 100644 --- a/pr-preview/pr-2230/asm_score/index.html +++ b/pr-preview/pr-2230/asm_score/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/associated_studies/index.html b/pr-preview/pr-2230/associated_studies/index.html index 5974b9f397..1446688cc4 100644 --- a/pr-preview/pr-2230/associated_studies/index.html +++ b/pr-preview/pr-2230/associated_studies/index.html @@ -497,9 +497,9 @@

Applicable Classes

-DataGeneration -The methods and processes used to generate omics data from a biosample or org... -yes +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... +no Biosample @@ -507,13 +507,13 @@

Applicable Classes

yes -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated -no +DataGeneration +The methods and processes used to generate omics data from a biosample or org... +yes -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no diff --git a/pr-preview/pr-2230/best_protein/index.html b/pr-preview/pr-2230/best_protein/index.html index 3116220d6f..516829b9a6 100644 --- a/pr-preview/pr-2230/best_protein/index.html +++ b/pr-preview/pr-2230/best_protein/index.html @@ -497,15 +497,15 @@

Applicable Classes

-PeptideQuantification -This is used to link a metaproteomics analysis workflow to a specific peptide... -no - - ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes + +PeptideQuantification +This is used to link a metaproteomics analysis workflow to a specific peptide... +no +

Properties

diff --git a/pr-preview/pr-2230/container_size/index.html b/pr-preview/pr-2230/container_size/index.html index 4e052e1ed3..4d30a8adee 100644 --- a/pr-preview/pr-2230/container_size/index.html +++ b/pr-preview/pr-2230/container_size/index.html @@ -497,13 +497,13 @@

Applicable Classes

-FiltrationProcess -The process of segregation of phases; e +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +FiltrationProcess +The process of segregation of phases; e no diff --git a/pr-preview/pr-2230/contig_bp/index.html b/pr-preview/pr-2230/contig_bp/index.html index 18b84bdf8f..98d9b2f851 100644 --- a/pr-preview/pr-2230/contig_bp/index.html +++ b/pr-preview/pr-2230/contig_bp/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/contigs/index.html b/pr-preview/pr-2230/contigs/index.html index 49b5f581db..cfda4ae486 100644 --- a/pr-preview/pr-2230/contigs/index.html +++ b/pr-preview/pr-2230/contigs/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/ctg_l50/index.html b/pr-preview/pr-2230/ctg_l50/index.html index 9de665ad50..048648ab34 100644 --- a/pr-preview/pr-2230/ctg_l50/index.html +++ b/pr-preview/pr-2230/ctg_l50/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/ctg_l90/index.html b/pr-preview/pr-2230/ctg_l90/index.html index bd097b3582..c8d757e15c 100644 --- a/pr-preview/pr-2230/ctg_l90/index.html +++ b/pr-preview/pr-2230/ctg_l90/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/ctg_logsum/index.html b/pr-preview/pr-2230/ctg_logsum/index.html index 64a3b18669..fcf6217dc2 100644 --- a/pr-preview/pr-2230/ctg_logsum/index.html +++ b/pr-preview/pr-2230/ctg_logsum/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/ctg_max/index.html b/pr-preview/pr-2230/ctg_max/index.html index e347534239..bcb9bf2ec7 100644 --- a/pr-preview/pr-2230/ctg_max/index.html +++ b/pr-preview/pr-2230/ctg_max/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/ctg_n50/index.html b/pr-preview/pr-2230/ctg_n50/index.html index 2a625770a3..f8e1c2fcf9 100644 --- a/pr-preview/pr-2230/ctg_n50/index.html +++ b/pr-preview/pr-2230/ctg_n50/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/ctg_n90/index.html b/pr-preview/pr-2230/ctg_n90/index.html index 3a1b9ac562..9ebc6e4c61 100644 --- a/pr-preview/pr-2230/ctg_n90/index.html +++ b/pr-preview/pr-2230/ctg_n90/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/ctg_powsum/index.html b/pr-preview/pr-2230/ctg_powsum/index.html index 675f61f446..8602895c41 100644 --- a/pr-preview/pr-2230/ctg_powsum/index.html +++ b/pr-preview/pr-2230/ctg_powsum/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/cur_vegetation/index.html b/pr-preview/pr-2230/cur_vegetation/index.html index aa2fd04331..36d02c36d9 100644 --- a/pr-preview/pr-2230/cur_vegetation/index.html +++ b/pr-preview/pr-2230/cur_vegetation/index.html @@ -538,15 +538,15 @@

Applicable Classes

-FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected -no - - Biosample Biological source material which can be characterized by an experiment yes + +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected +no +

Properties

diff --git a/pr-preview/pr-2230/description/index.html b/pr-preview/pr-2230/description/index.html index 97ba1372c7..36baa1c272 100644 --- a/pr-preview/pr-2230/description/index.html +++ b/pr-preview/pr-2230/description/index.html @@ -497,193 +497,198 @@

Applicable Classes

-MetaproteomicsAnalysis - +WorkflowExecution +Represents an instance of an execution of a particular workflow no -ImageValue -An attribute value representing an image +MetatranscriptomeAnnotation + no -Extraction -A material separation in which a desired component of an input material is se... +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -NamedThing -a databased entity or concept/class +Site + no -FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -WorkflowExecution -Represents an instance of an execution of a particular workflow +MaterialEntity + no -Biosample -Biological source material which can be characterized by an experiment +MetatranscriptomeAssembly + no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +Configuration +A set of parameters that define the actions of a process and is shared among ... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +Pathway +A pathway is a sequence of steps/reactions carried out by an organism or comm... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... -no +DataObject +An object that primarily consists of symbols that represent information +yes -Configuration -A set of parameters that define the actions of a process and is shared among ... +PlannedProcess + no -MetatranscriptomeAnnotation +EnvironmentalMaterialTerm no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +NamedThing +a databased entity or concept/class no -NomAnalysis - +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no -CollectingBiosamplesFromSite +ProcessedSample no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +ChemicalEntity +An atom or molecule that can be represented with a chemical formula no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -Site - +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected no -MassSpectrometryConfiguration -A set of parameters that define and control the actions of a mass spectrometr... -yes +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... +no -MetabolomicsAnalysis +CollectingBiosamplesFromSite no -ProcessedSample - +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -OntologyClass - +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -Pathway -A pathway is a sequence of steps/reactions carried out by an organism or comm... +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -DataObject -An object that primarily consists of symbols that represent information -yes +NomAnalysis + +no -GeneProduct -A molecule encoded by a gene that has an evolved function +Instrument +A material entity that is designed to perform a function in a scientific inve... no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +InformationObject +Any data or knowledge that reduces uncertainty or enhances understanding abou... no -Instrument -A material entity that is designed to perform a function in a scientific inve... +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetatranscriptomeAssembly - +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -ChemicalEntity -An atom or molecule that can be represented with a chemical formula +GeneProduct +A molecule encoded by a gene that has an evolved function no -FiltrationProcess -The process of segregation of phases; e +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis -no +Study +A study summarizes the overall goal of a research initiative and outlines the... +yes -EnvironmentalMaterialTerm - +MassSpectrometryConfiguration +A set of parameters that define and control the actions of a mass spectrometr... +yes + + +CalibrationInformation +A calibration object that is associated with a process no -LibraryPreparation - +Extraction +A material separation in which a desired component of an input material is se... no -Pooling -physical combination of several instances of like material +ImageValue +An attribute value representing an image no -MaterialEntity - +FunctionalAnnotationTerm +Abstract grouping class for any term/descriptor that can be applied to a func... no -CalibrationInformation -A calibration object that is associated with a process +Pooling +physical combination of several instances of like material no @@ -692,48 +697,48 @@

Applicable Classes

no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +OntologyClass + no -FunctionalAnnotationTerm -Abstract grouping class for any term/descriptor that can be applied to a func... +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -OrthologyGroup -A set of genes or gene products in which all members are orthologous +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -PlannedProcess - +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MetaproteomicsAnalysis + no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +FiltrationProcess +The process of segregation of phases; e no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetabolomicsAnalysis + no -Study -A study summarizes the overall goal of a research initiative and outlines the... +ChromatographyConfiguration +A set of parameters that define and control the actions of a chromatography p... yes -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no @@ -742,23 +747,18 @@

Applicable Classes

no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +OrthologyGroup +A set of genes or gene products in which all members are orthologous no -InformationObject -Any data or knowledge that reduces uncertainty or enhances understanding abou... +Biosample +Biological source material which can be characterized by an experiment no -ChromatographyConfiguration -A set of parameters that define and control the actions of a chromatography p... -yes - - -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + no diff --git a/pr-preview/pr-2230/duration/index.html b/pr-preview/pr-2230/duration/index.html index 0b42d94963..19afe31928 100644 --- a/pr-preview/pr-2230/duration/index.html +++ b/pr-preview/pr-2230/duration/index.html @@ -506,23 +506,23 @@

Applicable Classes

-ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MobilePhaseSegment +A fluid mixture of substances that flow though a chromatographic stationary p... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -MobilePhaseSegment -A fluid mixture of substances that flow though a chromatographic stationary p... +DissolvingProcess +A mixing step where a soluble component is mixed with a liquid component no -DissolvingProcess -A mixing step where a soluble component is mixed with a liquid component +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no diff --git a/pr-preview/pr-2230/elev/index.html b/pr-preview/pr-2230/elev/index.html index 7c1593961c..4d0915ab43 100644 --- a/pr-preview/pr-2230/elev/index.html +++ b/pr-preview/pr-2230/elev/index.html @@ -538,15 +538,15 @@

Applicable Classes

-FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected -no - - Biosample Biological source material which can be characterized by an experiment yes + +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected +no +

Properties

diff --git a/pr-preview/pr-2230/end_date/index.html b/pr-preview/pr-2230/end_date/index.html index b3742c6608..e9a7f6ffbf 100644 --- a/pr-preview/pr-2230/end_date/index.html +++ b/pr-preview/pr-2230/end_date/index.html @@ -515,58 +515,58 @@

Applicable Classes

-MetaproteomicsAnalysis - +WorkflowExecution +Represents an instance of an execution of a particular workflow no -Extraction -A material separation in which a desired component of an input material is se... +MetatranscriptomeAnnotation + no -WorkflowExecution -Represents an instance of an execution of a particular workflow +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +MetatranscriptomeAssembly + no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +PlannedProcess + no -MetatranscriptomeAnnotation - +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -NomAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no @@ -575,43 +575,43 @@

Applicable Classes

no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetabolomicsAnalysis - +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -FiltrationProcess -The process of segregation of phases; e +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -LibraryPreparation - +Extraction +A material separation in which a desired component of an input material is se... no @@ -625,43 +625,43 @@

Applicable Classes

no -PlannedProcess - +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetaproteomicsAnalysis + no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +FiltrationProcess +The process of segregation of phases; e no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetabolomicsAnalysis + no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + no diff --git a/pr-preview/pr-2230/ended_at_time/index.html b/pr-preview/pr-2230/ended_at_time/index.html index d19f52d46b..4fce147f4e 100644 --- a/pr-preview/pr-2230/ended_at_time/index.html +++ b/pr-preview/pr-2230/ended_at_time/index.html @@ -496,67 +496,67 @@

Applicable Classes

-MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +WorkflowExecution +Represents an instance of an execution of a particular workflow no -MetaproteomicsAnalysis - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -NomAnalysis +MetatranscriptomeAnnotation no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -MetabolomicsAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no -WorkflowExecution -Represents an instance of an execution of a particular workflow +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +MetatranscriptomeAssembly + no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +MetabolomicsAnalysis + no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +NomAnalysis + no -MetatranscriptomeAnnotation - +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetatranscriptomeAssembly +MetaproteomicsAnalysis no diff --git a/pr-preview/pr-2230/execution_resource/index.html b/pr-preview/pr-2230/execution_resource/index.html index 5736970ff7..9a41e61d66 100644 --- a/pr-preview/pr-2230/execution_resource/index.html +++ b/pr-preview/pr-2230/execution_resource/index.html @@ -506,67 +506,67 @@

Applicable Classes

-MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... -no +WorkflowExecution +Represents an instance of an execution of a particular workflow +yes -MetaproteomicsAnalysis - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -NomAnalysis +MetatranscriptomeAnnotation no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -MetabolomicsAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no -WorkflowExecution -Represents an instance of an execution of a particular workflow -yes +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... +no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +MetatranscriptomeAssembly + no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +MetabolomicsAnalysis + no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +NomAnalysis + no -MetatranscriptomeAnnotation - +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetatranscriptomeAssembly +MetaproteomicsAnalysis no diff --git a/pr-preview/pr-2230/gap_pct/index.html b/pr-preview/pr-2230/gap_pct/index.html index 24ec0834d0..ef85bcc3ff 100644 --- a/pr-preview/pr-2230/gap_pct/index.html +++ b/pr-preview/pr-2230/gap_pct/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/gc_avg/index.html b/pr-preview/pr-2230/gc_avg/index.html index 2b17c705f2..a87e531910 100644 --- a/pr-preview/pr-2230/gc_avg/index.html +++ b/pr-preview/pr-2230/gc_avg/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/gc_std/index.html b/pr-preview/pr-2230/gc_std/index.html index 332d1e16cd..1836b67f62 100644 --- a/pr-preview/pr-2230/gc_std/index.html +++ b/pr-preview/pr-2230/gc_std/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/geo_loc_name/index.html b/pr-preview/pr-2230/geo_loc_name/index.html index 20c756c731..2ccab6c8b3 100644 --- a/pr-preview/pr-2230/geo_loc_name/index.html +++ b/pr-preview/pr-2230/geo_loc_name/index.html @@ -538,13 +538,13 @@

Applicable Classes

-FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected +Biosample +Biological source material which can be characterized by an experiment no -Biosample -Biological source material which can be characterized by an experiment +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected no diff --git a/pr-preview/pr-2230/git_url/index.html b/pr-preview/pr-2230/git_url/index.html index 8a10ef5622..35de703c23 100644 --- a/pr-preview/pr-2230/git_url/index.html +++ b/pr-preview/pr-2230/git_url/index.html @@ -506,67 +506,67 @@

Applicable Classes

-MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... -no +WorkflowExecution +Represents an instance of an execution of a particular workflow +yes -MetaproteomicsAnalysis - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -NomAnalysis +MetatranscriptomeAnnotation no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -MetabolomicsAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no -WorkflowExecution -Represents an instance of an execution of a particular workflow -yes +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... +no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +MetatranscriptomeAssembly + no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +MetabolomicsAnalysis + no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +NomAnalysis + no -MetatranscriptomeAnnotation - +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetatranscriptomeAssembly +MetaproteomicsAnalysis no diff --git a/pr-preview/pr-2230/gold_analysis_project_identifiers/index.html b/pr-preview/pr-2230/gold_analysis_project_identifiers/index.html index c2aecf7190..f420c7ff63 100644 --- a/pr-preview/pr-2230/gold_analysis_project_identifiers/index.html +++ b/pr-preview/pr-2230/gold_analysis_project_identifiers/index.html @@ -526,13 +526,13 @@

Applicable Classes

-MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +MetatranscriptomeAnnotation + yes -MetatranscriptomeAnnotation - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... yes diff --git a/pr-preview/pr-2230/gold_identifiers/index.html b/pr-preview/pr-2230/gold_identifiers/index.html index ca4db6c366..de8dfbcd80 100644 --- a/pr-preview/pr-2230/gold_identifiers/index.html +++ b/pr-preview/pr-2230/gold_identifiers/index.html @@ -527,7 +527,7 @@

Mixin Usage

gold_analysis_project_identifiers identifiers for corresponding analysis projects in GOLD None -MetagenomeAnnotation, MetatranscriptomeAnnotation +MetatranscriptomeAnnotation, MetagenomeAnnotation diff --git a/pr-preview/pr-2230/habitat/index.html b/pr-preview/pr-2230/habitat/index.html index 44f337467c..3254e8637f 100644 --- a/pr-preview/pr-2230/habitat/index.html +++ b/pr-preview/pr-2230/habitat/index.html @@ -496,13 +496,13 @@

Applicable Classes

-FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected +Biosample +Biological source material which can be characterized by an experiment no -Biosample -Biological source material which can be characterized by an experiment +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected no diff --git a/pr-preview/pr-2230/has_calibration/index.html b/pr-preview/pr-2230/has_calibration/index.html index cfcc9da41a..04c9752139 100644 --- a/pr-preview/pr-2230/has_calibration/index.html +++ b/pr-preview/pr-2230/has_calibration/index.html @@ -497,6 +497,11 @@

Applicable Classes

+MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... +yes + + NomAnalysis no @@ -506,11 +511,6 @@

Applicable Classes

no - -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... -yes -

Properties

diff --git a/pr-preview/pr-2230/has_failure_categorization/index.html b/pr-preview/pr-2230/has_failure_categorization/index.html index 43fb42da40..d02ad878fc 100644 --- a/pr-preview/pr-2230/has_failure_categorization/index.html +++ b/pr-preview/pr-2230/has_failure_categorization/index.html @@ -496,58 +496,58 @@

Applicable Classes

-MetaproteomicsAnalysis - +WorkflowExecution +Represents an instance of an execution of a particular workflow no -Extraction -A material separation in which a desired component of an input material is se... +MetatranscriptomeAnnotation + no -WorkflowExecution -Represents an instance of an execution of a particular workflow +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +MetatranscriptomeAssembly + no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +PlannedProcess + no -MetatranscriptomeAnnotation - +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -NomAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no @@ -556,43 +556,43 @@

Applicable Classes

no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetabolomicsAnalysis - +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -FiltrationProcess -The process of segregation of phases; e +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -LibraryPreparation - +Extraction +A material separation in which a desired component of an input material is se... no @@ -606,43 +606,43 @@

Applicable Classes

no -PlannedProcess - +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetaproteomicsAnalysis + no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +FiltrationProcess +The process of segregation of phases; e no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetabolomicsAnalysis + no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + no diff --git a/pr-preview/pr-2230/has_input/index.html b/pr-preview/pr-2230/has_input/index.html index b161335ac2..5c80fdad84 100644 --- a/pr-preview/pr-2230/has_input/index.html +++ b/pr-preview/pr-2230/has_input/index.html @@ -506,28 +506,18 @@

Applicable Classes

-MetaproteomicsAnalysis - -no - - -Extraction -A material separation in which a desired component of an input material is se... -yes - - WorkflowExecution Represents an instance of an execution of a particular workflow yes -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated -no +MetatranscriptomeAnnotation + +yes -ProtocolExecution -A PlannedProces that has PlannedProcess parts +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... yes @@ -536,28 +526,38 @@

Applicable Classes

yes -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MetatranscriptomeAssembly + no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +StorageProcess +A planned process with the objective to preserve and protect material entitie... +yes + + +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetatranscriptomeAnnotation +PlannedProcess -yes +no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... yes -NomAnalysis - +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... +no + + +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no @@ -566,43 +566,43 @@

Applicable Classes

yes -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... -yes +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... +no -MetabolomicsAnalysis - -no +MetagenomeSequencing +Initial sequencing activity that precedes any analysis +yes -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... yes -FiltrationProcess -The process of segregation of phases; e -yes +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... +no -LibraryPreparation - +Extraction +A material separation in which a desired component of an input material is se... yes @@ -616,44 +616,44 @@

Applicable Classes

no -PlannedProcess - -no - - -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... yes -StorageProcess -A planned process with the objective to preserve and protect material entitie... -yes +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated +no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +MetaproteomicsAnalysis + no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +FiltrationProcess +The process of segregation of phases; e +yes + + +MetabolomicsAnalysis + no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +ProtocolExecution +A PlannedProces that has PlannedProcess parts yes -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... -no +LibraryPreparation + +yes diff --git a/pr-preview/pr-2230/has_output/index.html b/pr-preview/pr-2230/has_output/index.html index 8f5a24f145..f9db3822e3 100644 --- a/pr-preview/pr-2230/has_output/index.html +++ b/pr-preview/pr-2230/has_output/index.html @@ -506,28 +506,18 @@

Applicable Classes

-MetaproteomicsAnalysis - -no - - -Extraction -A material separation in which a desired component of an input material is se... -yes - - WorkflowExecution Represents an instance of an execution of a particular workflow yes -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated -no +MetatranscriptomeAnnotation + +yes -ProtocolExecution -A PlannedProces that has PlannedProcess parts +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... yes @@ -536,28 +526,38 @@

Applicable Classes

yes -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MetatranscriptomeAssembly + no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +StorageProcess +A planned process with the objective to preserve and protect material entitie... +yes + + +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetatranscriptomeAnnotation +PlannedProcess -yes +no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... yes -NomAnalysis - +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... +no + + +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no @@ -566,43 +566,43 @@

Applicable Classes

yes -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... -yes - - -MetabolomicsAnalysis - +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MetatranscriptomeAssembly +NomAnalysis no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -FiltrationProcess -The process of segregation of phases; e +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... yes -LibraryPreparation - +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... +no + + +Extraction +A material separation in which a desired component of an input material is se... yes @@ -616,44 +616,44 @@

Applicable Classes

no -PlannedProcess - -no - - -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... yes -StorageProcess -A planned process with the objective to preserve and protect material entitie... -yes +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated +no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +MetaproteomicsAnalysis + no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +FiltrationProcess +The process of segregation of phases; e +yes + + +MetabolomicsAnalysis + no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +ProtocolExecution +A PlannedProces that has PlannedProcess parts yes -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... -no +LibraryPreparation + +yes diff --git a/pr-preview/pr-2230/has_raw_value/index.html b/pr-preview/pr-2230/has_raw_value/index.html index d34de4b65b..1dbeb87b25 100644 --- a/pr-preview/pr-2230/has_raw_value/index.html +++ b/pr-preview/pr-2230/has_raw_value/index.html @@ -497,9 +497,9 @@

Applicable Classes

-TimestampValue -A value that is a timestamp -no +QuantityValue +A simple quantity, e +yes TextValue @@ -507,14 +507,19 @@

Applicable Classes

no +PersonValue +An attribute value representing a person +yes + + ImageValue An attribute value representing an image no -GeolocationValue -A normalized value for a location on the earth's surface -yes +AttributeValue +The value for any value of a attribute for a sample +no ControlledTermValue @@ -522,24 +527,19 @@

Applicable Classes

no -AttributeValue -The value for any value of a attribute for a sample -no - - ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no -PersonValue -An attribute value representing a person +GeolocationValue +A normalized value for a location on the earth's surface yes -QuantityValue -A simple quantity, e -yes +TimestampValue +A value that is a timestamp +no diff --git a/pr-preview/pr-2230/id/index.html b/pr-preview/pr-2230/id/index.html index 0b305c4d7f..096d4b7a22 100644 --- a/pr-preview/pr-2230/id/index.html +++ b/pr-preview/pr-2230/id/index.html @@ -506,193 +506,208 @@

Applicable Classes

-MetaproteomicsAnalysis +WorkflowExecution +Represents an instance of an execution of a particular workflow +no + + +MetatranscriptomeAnnotation yes -Extraction -A material separation in which a desired component of an input material is se... +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... yes -NamedThing -a databased entity or concept/class +Site + no -FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... yes -WorkflowExecution -Represents an instance of an execution of a particular workflow +MaterialEntity + no -Biosample -Biological source material which can be characterized by an experiment +MetatranscriptomeAssembly + yes -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated -yes +Configuration +A set of parameters that define the actions of a process and is shared among ... +no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +StorageProcess +A planned process with the objective to preserve and protect material entitie... yes -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... yes -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... -yes +Pathway +A pathway is a sequence of steps/reactions carried out by an organism or comm... +no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +DataObject +An object that primarily consists of symbols that represent information yes -Configuration -A set of parameters that define the actions of a process and is shared among ... +PlannedProcess + no -MetatranscriptomeAnnotation +EnvironmentalMaterialTerm -yes +no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +NamedThing +a databased entity or concept/class +no + + +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... yes -NomAnalysis +ProcessedSample yes -CollectingBiosamplesFromSite - +ChemicalEntity +An atom or molecule that can be represented with a chemical formula +no + + +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... yes -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected yes -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... yes -Site +CollectingBiosamplesFromSite -no +yes -MassSpectrometryConfiguration -A set of parameters that define and control the actions of a mass spectrometr... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... yes -MetabolomicsAnalysis - +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... yes -ProcessedSample - +MetagenomeSequencing +Initial sequencing activity that precedes any analysis yes -OntologyClass +NomAnalysis yes -Pathway -A pathway is a sequence of steps/reactions carried out by an organism or comm... +Instrument +A material entity that is designed to perform a function in a scientific inve... +yes + + +InformationObject +Any data or knowledge that reduces uncertainty or enhances understanding abou... no -DataObject -An object that primarily consists of symbols that represent information +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... yes +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... +no + + GeneProduct A molecule encoded by a gene that has an evolved function no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... yes -Instrument -A material entity that is designed to perform a function in a scientific inve... +Study +A study summarizes the overall goal of a research initiative and outlines the... yes -MetatranscriptomeAssembly - +MassSpectrometryConfiguration +A set of parameters that define and control the actions of a mass spectrometr... yes -ChemicalEntity -An atom or molecule that can be represented with a chemical formula -no - - -FiltrationProcess -The process of segregation of phases; e +CalibrationInformation +A calibration object that is associated with a process yes -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +Extraction +A material separation in which a desired component of an input material is se... yes -EnvironmentalMaterialTerm - +FunctionalAnnotationTerm +Abstract grouping class for any term/descriptor that can be applied to a func... no -LibraryPreparation - -yes - - Pooling physical combination of several instances of like material yes -MaterialEntity - -no +DissolvingProcess +A mixing step where a soluble component is mixed with a liquid component +yes -CalibrationInformation -A calibration object that is associated with a process +OntologyClass + yes -DissolvingProcess -A mixing step where a soluble component is mixed with a liquid component +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... yes @@ -701,43 +716,33 @@

Applicable Classes

no -FunctionalAnnotationTerm -Abstract grouping class for any term/descriptor that can be applied to a func... -no - - -OrthologyGroup -A set of genes or gene products in which all members are orthologous -no +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated +yes -PlannedProcess +MetaproteomicsAnalysis -no - - -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... yes -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... -no +FiltrationProcess +The process of segregation of phases; e +yes -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetabolomicsAnalysis + yes -Study -A study summarizes the overall goal of a research initiative and outlines the... +ChromatographyConfiguration +A set of parameters that define and control the actions of a chromatography p... yes -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +ProtocolExecution +A PlannedProces that has PlannedProcess parts yes @@ -746,23 +751,18 @@

Applicable Classes

yes -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... -yes - - -InformationObject -Any data or knowledge that reduces uncertainty or enhances understanding abou... +OrthologyGroup +A set of genes or gene products in which all members are orthologous no -ChromatographyConfiguration -A set of parameters that define and control the actions of a chromatography p... +Biosample +Biological source material which can be characterized by an experiment yes -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + yes diff --git a/pr-preview/pr-2230/img_identifiers/index.html b/pr-preview/pr-2230/img_identifiers/index.html index 3e9889f91f..9e3d7a63af 100644 --- a/pr-preview/pr-2230/img_identifiers/index.html +++ b/pr-preview/pr-2230/img_identifiers/index.html @@ -523,29 +523,29 @@

Applicable Classes

-MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +MetatranscriptomeAnnotation + yes -Biosample -Biological source material which can be characterized by an experiment -no +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... +yes -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... yes -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... yes -MetatranscriptomeAnnotation - -yes +Biosample +Biological source material which can be characterized by an experiment +no diff --git a/pr-preview/pr-2230/insdc_assembly_identifiers/index.html b/pr-preview/pr-2230/insdc_assembly_identifiers/index.html index a008f7cc43..477c4d00b5 100644 --- a/pr-preview/pr-2230/insdc_assembly_identifiers/index.html +++ b/pr-preview/pr-2230/insdc_assembly_identifiers/index.html @@ -510,13 +510,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/insdc_experiment_identifiers/index.html b/pr-preview/pr-2230/insdc_experiment_identifiers/index.html index 142711aa5d..94931a0671 100644 --- a/pr-preview/pr-2230/insdc_experiment_identifiers/index.html +++ b/pr-preview/pr-2230/insdc_experiment_identifiers/index.html @@ -513,13 +513,13 @@

Applicable Classes

-NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +DataObject +An object that primarily consists of symbols that represent information no -DataObject -An object that primarily consists of symbols that represent information +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no diff --git a/pr-preview/pr-2230/insdc_identifiers/index.html b/pr-preview/pr-2230/insdc_identifiers/index.html index 8edb231e83..dd51f5d916 100644 --- a/pr-preview/pr-2230/insdc_identifiers/index.html +++ b/pr-preview/pr-2230/insdc_identifiers/index.html @@ -552,7 +552,7 @@

Mixin Usage

insdc_experiment_identifiers None -NucleotideSequencing, DataObject +DataObject, NucleotideSequencing insdc_analysis_identifiers @@ -564,7 +564,7 @@

Mixin Usage

insdc_assembly_identifiers None -MetagenomeAssembly, MetatranscriptomeAssembly +MetatranscriptomeAssembly, MetagenomeAssembly diff --git a/pr-preview/pr-2230/instrument_used/index.html b/pr-preview/pr-2230/instrument_used/index.html index e17195bf76..bc96189c73 100644 --- a/pr-preview/pr-2230/instrument_used/index.html +++ b/pr-preview/pr-2230/instrument_used/index.html @@ -497,33 +497,33 @@

Applicable Classes

-FiltrationProcess -The process of segregation of phases; e +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -Extraction -A material separation in which a desired component of an input material is se... +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -LibraryPreparation - +FiltrationProcess +The process of segregation of phases; e no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +Extraction +A material separation in which a desired component of an input material is se... no @@ -532,33 +532,33 @@

Applicable Classes

no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +DissolvingProcess +A mixing step where a soluble component is mixed with a liquid component no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +LibraryPreparation + no -DissolvingProcess -A mixing step where a soluble component is mixed with a liquid component +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no diff --git a/pr-preview/pr-2230/lat_lon/index.html b/pr-preview/pr-2230/lat_lon/index.html index 7a3cb0f4a7..6873aaf5ed 100644 --- a/pr-preview/pr-2230/lat_lon/index.html +++ b/pr-preview/pr-2230/lat_lon/index.html @@ -538,15 +538,15 @@

Applicable Classes

-FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected -no - - Biosample Biological source material which can be characterized by an experiment yes + +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected +no +

Properties

diff --git a/pr-preview/pr-2230/local_class/index.html b/pr-preview/pr-2230/local_class/index.html index d9ce37ec7e..39702c87f3 100644 --- a/pr-preview/pr-2230/local_class/index.html +++ b/pr-preview/pr-2230/local_class/index.html @@ -538,13 +538,13 @@

Applicable Classes

-FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected +Biosample +Biological source material which can be characterized by an experiment no -Biosample -Biological source material which can be characterized by an experiment +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected no diff --git a/pr-preview/pr-2230/mod_date/index.html b/pr-preview/pr-2230/mod_date/index.html index 3499745fbf..f7fded260d 100644 --- a/pr-preview/pr-2230/mod_date/index.html +++ b/pr-preview/pr-2230/mod_date/index.html @@ -497,8 +497,8 @@

Applicable Classes

-DataGeneration -The methods and processes used to generate omics data from a biosample or org... +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no @@ -507,13 +507,13 @@

Applicable Classes

no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no diff --git a/pr-preview/pr-2230/name/index.html b/pr-preview/pr-2230/name/index.html index 615b867368..70be947c8c 100644 --- a/pr-preview/pr-2230/name/index.html +++ b/pr-preview/pr-2230/name/index.html @@ -497,43 +497,28 @@

Applicable Classes

-MetaproteomicsAnalysis - -no - - -Extraction -A material separation in which a desired component of an input material is se... -no - - -NamedThing -a databased entity or concept/class -no - - -FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected -no - - WorkflowExecution Represents an instance of an execution of a particular workflow no -Biosample -Biological source material which can be characterized by an experiment +MetatranscriptomeAnnotation + no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +PersonValue +An attribute value representing a person +yes + + +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +Site + no @@ -542,13 +527,13 @@

Applicable Classes

no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MaterialEntity + no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +MetatranscriptomeAssembly + no @@ -557,33 +542,38 @@

Applicable Classes

no -PersonValue -An attribute value representing a person -yes +StorageProcess +A planned process with the objective to preserve and protect material entitie... +no -MetatranscriptomeAnnotation - +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +Pathway +A pathway is a sequence of steps/reactions carried out by an organism or comm... no -NomAnalysis +DataObject +An object that primarily consists of symbols that represent information +yes + + +PlannedProcess no -CollectingBiosamplesFromSite +EnvironmentalMaterialTerm no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +NamedThing +a databased entity or concept/class no @@ -592,48 +582,53 @@

Applicable Classes

no -Site +ProcessedSample no -MassSpectrometryConfiguration -A set of parameters that define and control the actions of a mass spectrometr... -yes +ChemicalEntity +An atom or molecule that can be represented with a chemical formula +no -MetabolomicsAnalysis - +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -ProcessedSample - +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected no -OntologyClass +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... +no + + +CollectingBiosamplesFromSite no -Pathway -A pathway is a sequence of steps/reactions carried out by an organism or comm... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -DataObject -An object that primarily consists of symbols that represent information -yes +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... +no -GeneProduct -A molecule encoded by a gene that has an evolved function +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no @@ -642,48 +637,63 @@

Applicable Classes

no -MetatranscriptomeAssembly - +InformationObject +Any data or knowledge that reduces uncertainty or enhances understanding abou... no -ChemicalEntity -An atom or molecule that can be represented with a chemical formula +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -FiltrationProcess -The process of segregation of phases; e +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +GeneProduct +A molecule encoded by a gene that has an evolved function no -EnvironmentalMaterialTerm - +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -LibraryPreparation - +Study +A study summarizes the overall goal of a research initiative and outlines the... +yes + + +MassSpectrometryConfiguration +A set of parameters that define and control the actions of a mass spectrometr... +yes + + +CalibrationInformation +A calibration object that is associated with a process no -Pooling -physical combination of several instances of like material +Extraction +A material separation in which a desired component of an input material is se... no -MaterialEntity +FunctionalAnnotationTerm +Abstract grouping class for any term/descriptor that can be applied to a func... +no + + +Protocol no -CalibrationInformation -A calibration object that is associated with a process +Pooling +physical combination of several instances of like material no @@ -692,53 +702,48 @@

Applicable Classes

no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +OntologyClass + no -FunctionalAnnotationTerm -Abstract grouping class for any term/descriptor that can be applied to a func... +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -OrthologyGroup -A set of genes or gene products in which all members are orthologous +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -PlannedProcess - +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -Protocol +MetaproteomicsAnalysis no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... -no - - -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +FiltrationProcess +The process of segregation of phases; e no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetabolomicsAnalysis + no -Study -A study summarizes the overall goal of a research initiative and outlines the... +ChromatographyConfiguration +A set of parameters that define and control the actions of a chromatography p... yes -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no @@ -747,23 +752,18 @@

Applicable Classes

no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +OrthologyGroup +A set of genes or gene products in which all members are orthologous no -InformationObject -Any data or knowledge that reduces uncertainty or enhances understanding abou... +Biosample +Biological source material which can be characterized by an experiment no -ChromatographyConfiguration -A set of parameters that define and control the actions of a chromatography p... -yes - - -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + no diff --git a/pr-preview/pr-2230/num_aligned_reads/index.html b/pr-preview/pr-2230/num_aligned_reads/index.html index e28476601e..3fdd3330e7 100644 --- a/pr-preview/pr-2230/num_aligned_reads/index.html +++ b/pr-preview/pr-2230/num_aligned_reads/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/num_input_reads/index.html b/pr-preview/pr-2230/num_input_reads/index.html index 6664a9b9b3..29020d5366 100644 --- a/pr-preview/pr-2230/num_input_reads/index.html +++ b/pr-preview/pr-2230/num_input_reads/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/part_of/index.html b/pr-preview/pr-2230/part_of/index.html index 2c25d0e4fe..4b77ba6477 100644 --- a/pr-preview/pr-2230/part_of/index.html +++ b/pr-preview/pr-2230/part_of/index.html @@ -506,13 +506,13 @@

Applicable Classes

-FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected +Study +A study summarizes the overall goal of a research initiative and outlines the... yes -Study -A study summarizes the overall goal of a research initiative and outlines the... +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected yes diff --git a/pr-preview/pr-2230/principal_investigator/index.html b/pr-preview/pr-2230/principal_investigator/index.html index 13cb983d7c..56bdc7bcc0 100644 --- a/pr-preview/pr-2230/principal_investigator/index.html +++ b/pr-preview/pr-2230/principal_investigator/index.html @@ -506,8 +506,8 @@

Applicable Classes

-DataGeneration -The methods and processes used to generate omics data from a biosample or org... +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no @@ -516,13 +516,13 @@

Applicable Classes

no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no diff --git a/pr-preview/pr-2230/processing_institution/index.html b/pr-preview/pr-2230/processing_institution/index.html index c9467c1e1c..f3a9aeae86 100644 --- a/pr-preview/pr-2230/processing_institution/index.html +++ b/pr-preview/pr-2230/processing_institution/index.html @@ -497,58 +497,58 @@

Applicable Classes

-MetaproteomicsAnalysis - +WorkflowExecution +Represents an instance of an execution of a particular workflow no -Extraction -A material separation in which a desired component of an input material is se... +MetatranscriptomeAnnotation + no -WorkflowExecution -Represents an instance of an execution of a particular workflow +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +MetatranscriptomeAssembly + no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +PlannedProcess + no -MetatranscriptomeAnnotation - +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -NomAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no @@ -557,43 +557,43 @@

Applicable Classes

no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetabolomicsAnalysis - +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -FiltrationProcess -The process of segregation of phases; e +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -LibraryPreparation - +Extraction +A material separation in which a desired component of an input material is se... no @@ -607,43 +607,43 @@

Applicable Classes

no -PlannedProcess - +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetaproteomicsAnalysis + no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +FiltrationProcess +The process of segregation of phases; e no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetabolomicsAnalysis + no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + no diff --git a/pr-preview/pr-2230/protocol_link/index.html b/pr-preview/pr-2230/protocol_link/index.html index a84c1a6fb6..c27e81f0ae 100644 --- a/pr-preview/pr-2230/protocol_link/index.html +++ b/pr-preview/pr-2230/protocol_link/index.html @@ -496,58 +496,58 @@

Applicable Classes

-MetaproteomicsAnalysis - +WorkflowExecution +Represents an instance of an execution of a particular workflow no -Extraction -A material separation in which a desired component of an input material is se... +MetatranscriptomeAnnotation + no -WorkflowExecution -Represents an instance of an execution of a particular workflow +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +MetatranscriptomeAssembly + no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +PlannedProcess + no -MetatranscriptomeAnnotation - +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -NomAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no @@ -556,43 +556,48 @@

Applicable Classes

no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetabolomicsAnalysis - +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -FiltrationProcess -The process of segregation of phases; e +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -LibraryPreparation - +Study +A study summarizes the overall goal of a research initiative and outlines the... +yes + + +Extraction +A material separation in which a desired component of an input material is se... no @@ -606,48 +611,43 @@

Applicable Classes

no -PlannedProcess - +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -Study -A study summarizes the overall goal of a research initiative and outlines the... -yes - - -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetaproteomicsAnalysis + no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +FiltrationProcess +The process of segregation of phases; e no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetabolomicsAnalysis + no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + no diff --git a/pr-preview/pr-2230/qc_comment/index.html b/pr-preview/pr-2230/qc_comment/index.html index 1a71232318..cefea5d12f 100644 --- a/pr-preview/pr-2230/qc_comment/index.html +++ b/pr-preview/pr-2230/qc_comment/index.html @@ -497,58 +497,58 @@

Applicable Classes

-MetaproteomicsAnalysis - +WorkflowExecution +Represents an instance of an execution of a particular workflow no -Extraction -A material separation in which a desired component of an input material is se... +MetatranscriptomeAnnotation + no -WorkflowExecution -Represents an instance of an execution of a particular workflow +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +MetatranscriptomeAssembly + no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +PlannedProcess + no -MetatranscriptomeAnnotation - +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -NomAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no @@ -557,43 +557,43 @@

Applicable Classes

no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetabolomicsAnalysis - +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -FiltrationProcess -The process of segregation of phases; e +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -LibraryPreparation - +Extraction +A material separation in which a desired component of an input material is se... no @@ -607,43 +607,43 @@

Applicable Classes

no -PlannedProcess - +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetaproteomicsAnalysis + no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +FiltrationProcess +The process of segregation of phases; e no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetabolomicsAnalysis + no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + no diff --git a/pr-preview/pr-2230/qc_status/index.html b/pr-preview/pr-2230/qc_status/index.html index 1ee6de546f..dc1af2fa69 100644 --- a/pr-preview/pr-2230/qc_status/index.html +++ b/pr-preview/pr-2230/qc_status/index.html @@ -497,58 +497,58 @@

Applicable Classes

-MetaproteomicsAnalysis - +WorkflowExecution +Represents an instance of an execution of a particular workflow no -Extraction -A material separation in which a desired component of an input material is se... +MetatranscriptomeAnnotation + no -WorkflowExecution -Represents an instance of an execution of a particular workflow +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +MetatranscriptomeAssembly + no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +PlannedProcess + no -MetatranscriptomeAnnotation - +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -NomAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no @@ -557,43 +557,43 @@

Applicable Classes

no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetabolomicsAnalysis - +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -FiltrationProcess -The process of segregation of phases; e +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -LibraryPreparation - +Extraction +A material separation in which a desired component of an input material is se... no @@ -607,43 +607,43 @@

Applicable Classes

no -PlannedProcess - +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetaproteomicsAnalysis + no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +FiltrationProcess +The process of segregation of phases; e no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetabolomicsAnalysis + no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + no diff --git a/pr-preview/pr-2230/scaf_bp/index.html b/pr-preview/pr-2230/scaf_bp/index.html index 79b52ea4ed..4698fc983a 100644 --- a/pr-preview/pr-2230/scaf_bp/index.html +++ b/pr-preview/pr-2230/scaf_bp/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_l50/index.html b/pr-preview/pr-2230/scaf_l50/index.html index d8478be7b7..7116ceab54 100644 --- a/pr-preview/pr-2230/scaf_l50/index.html +++ b/pr-preview/pr-2230/scaf_l50/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_l90/index.html b/pr-preview/pr-2230/scaf_l90/index.html index 95d3856bd1..11fd8dfe24 100644 --- a/pr-preview/pr-2230/scaf_l90/index.html +++ b/pr-preview/pr-2230/scaf_l90/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_l_gt50k/index.html b/pr-preview/pr-2230/scaf_l_gt50k/index.html index d26fb5a5d6..5d62877f83 100644 --- a/pr-preview/pr-2230/scaf_l_gt50k/index.html +++ b/pr-preview/pr-2230/scaf_l_gt50k/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_logsum/index.html b/pr-preview/pr-2230/scaf_logsum/index.html index 2da7d83ef2..02a89e979d 100644 --- a/pr-preview/pr-2230/scaf_logsum/index.html +++ b/pr-preview/pr-2230/scaf_logsum/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_max/index.html b/pr-preview/pr-2230/scaf_max/index.html index 3c34d87dd0..378db60859 100644 --- a/pr-preview/pr-2230/scaf_max/index.html +++ b/pr-preview/pr-2230/scaf_max/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_n50/index.html b/pr-preview/pr-2230/scaf_n50/index.html index d130498f9f..5f625d97b4 100644 --- a/pr-preview/pr-2230/scaf_n50/index.html +++ b/pr-preview/pr-2230/scaf_n50/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_n90/index.html b/pr-preview/pr-2230/scaf_n90/index.html index b80bd0a745..43eefe1432 100644 --- a/pr-preview/pr-2230/scaf_n90/index.html +++ b/pr-preview/pr-2230/scaf_n90/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_n_gt50k/index.html b/pr-preview/pr-2230/scaf_n_gt50k/index.html index 043131b831..e7c7fd8529 100644 --- a/pr-preview/pr-2230/scaf_n_gt50k/index.html +++ b/pr-preview/pr-2230/scaf_n_gt50k/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_pct_gt50k/index.html b/pr-preview/pr-2230/scaf_pct_gt50k/index.html index 5acbdee411..05ebdb01ff 100644 --- a/pr-preview/pr-2230/scaf_pct_gt50k/index.html +++ b/pr-preview/pr-2230/scaf_pct_gt50k/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaf_powsum/index.html b/pr-preview/pr-2230/scaf_powsum/index.html index 34372bf6ff..9f110ba6c5 100644 --- a/pr-preview/pr-2230/scaf_powsum/index.html +++ b/pr-preview/pr-2230/scaf_powsum/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/scaffolds/index.html b/pr-preview/pr-2230/scaffolds/index.html index b7a6bcaab5..59a0fd08d3 100644 --- a/pr-preview/pr-2230/scaffolds/index.html +++ b/pr-preview/pr-2230/scaffolds/index.html @@ -511,13 +511,13 @@

Applicable Classes

-MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetatranscriptomeAssembly + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no diff --git a/pr-preview/pr-2230/search/search_index.json b/pr-preview/pr-2230/search/search_index.json index 3f29c0c986..097559a396 100644 --- a/pr-preview/pr-2230/search/search_index.json +++ b/pr-preview/pr-2230/search/search_index.json @@ -1 +1 @@ -{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"NMDC","text":"

Schema for National Microbiome Data Collaborative (NMDC). This schema is organized into multiple modules, such as:

URI: https://w3id.org/nmdc/nmdc

"},{"location":"#classes","title":"Classes","text":"Class Description AttributeValue The value for any value of a attribute for a sample ControlledTermValue A controlled term or class from an ontology ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... GeolocationValue A normalized value for a location on the earth's surface ImageValue An attribute value representing an image PersonValue An attribute value representing a person QuantityValue A simple quantity, e TextValue A basic string value TimestampValue A value that is a timestamp CreditAssociation This class supports binding associated researchers to studies Database An abstract holder for any set of metadata and data Doi A centrally registered identifier symbol used to uniquely identify objects gi... EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... FailureCategorization FunctionalAnnotation An assignment of a function term (e FunctionalAnnotationAggMember GenomeFeature A feature localized to an interval along a genome MagBin MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... NamedThing a databased entity or concept/class GeneProduct A molecule encoded by a gene that has an evolved function InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... CalibrationInformation A calibration object that is associated with a process Configuration A set of parameters that define the actions of a process and is shared among ... ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... DataObject An object that primarily consists of symbols that represent information Manifest MaterialEntity Biosample Biological source material which can be characterized by an experiment Instrument A material entity that is designed to perform a function in a scientific inve... ProcessedSample Site FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected OntologyClass ChemicalEntity An atom or molecule that can be represented with a chemical formula EnvironmentalMaterialTerm FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... OrthologyGroup A set of genes or gene products in which all members are orthologous Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... PlannedProcess CollectingBiosamplesFromSite DataGeneration The methods and processes used to generate omics data from a biosample or org... MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... DissolvingProcess A mixing step where a soluble component is mixed with a liquid component Extraction A material separation in which a desired component of an input material is se... FiltrationProcess The process of segregation of phases; e LibraryPreparation MixingProcess The combining of components, particles or layers into a more homogeneous stat... Pooling physical combination of several instances of like material SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... ProtocolExecution A PlannedProces that has PlannedProcess parts StorageProcess A planned process with the objective to preserve and protect material entitie... WorkflowExecution Represents an instance of an execution of a particular workflow MagsAnalysis A workflow execution activity that uses computational binning tools to group ... MetabolomicsAnalysis MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... MetagenomeSequencing Initial sequencing activity that precedes any analysis MetaproteomicsAnalysis MetatranscriptomeAnnotation MetatranscriptomeAssembly MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... NomAnalysis ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... Study A study summarizes the overall goal of a research initiative and outlines the... PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein Protocol"},{"location":"#slots","title":"Slots","text":"Slot Description abs_air_humidity Actual mass of water vapor - mh20 - present in the air water vapor mixture add_date The date on which the information was added to the database add_recov_method Additional (i additional_info Information that doesn't fit anywhere else address The street name and building number where the sampling occurred adj_room List of rooms (room number, room name) immediately adjacent to the sampling r... aero_struc Aerospace structures typically consist of thin plates with stiffeners for the... agrochem_addition Addition of fertilizers, pesticides, etc air_PM_concen Concentration of substances that remain suspended in the air, and comprise mi... air_temp Temperature of the air at the time of sampling air_temp_regm Information about treatment involving an exposure to varying temperatures; sh... al_sat Aluminum saturation (esp al_sat_meth Reference or method used in determining Al saturation alkalinity Alkalinity, the ability of a solution to neutralize acids to the equivalence ... alkalinity_method Method used for alkalinity measurement alkyl_diethers Concentration of alkyl diethers all_proteins the list of protein identifiers that are associated with the peptide sequence alt Altitude is a term used to identify heights of objects such as airplanes, spa... alternative_descriptions A list of alternative descriptions for the entity alternative_identifiers A list of alternative identifiers for the entity alternative_names A list of alternative names used to refer to the entity alternative_titles A list of alternative titles for the entity aminopept_act Measurement of aminopeptidase activity ammonium Concentration of ammonium in the sample ammonium_nitrogen Concentration of ammonium nitrogen in the sample amount_light The unit of illuminance and luminous emittance, measuring luminous flux per u... analysis_identifiers analysis_type Select all the data types associated or available for this biosample analyte_category The type of analyte(s) that were measured in the data generation process and ... ances_data Information about either pedigree or other ancestral information description ... annual_precpt The average of all annual precipitation values known, or an estimated equival... annual_temp Mean annual temperature antibiotic_regm Information about treatment involving antibiotic administration; should inclu... api API gravity is a measure of how heavy or light a petroleum liquid is compared... applied_roles applies_to_person arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c... aromatics_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... asm_score A score for comparing metagenomic assembly quality from same sample asphaltenes_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... assembly_identifiers associated_dois A list of DOIs associated with a resource, such as a list of DOIS associated ... associated_studies The study associated with a resource atmospheric_data Measurement of atmospheric data; can include multiple data avg_dew_point The average of dew point measures taken at the beginning of every hour over a... avg_occup Daily average occupancy of room avg_temp The average of temperatures taken at the beginning of every hour over a 24 ho... bac_prod Bacterial production in the water column measured by isotope uptake bac_resp Measurement of bacterial respiration in the water column bacteria_carb_prod Measurement of bacterial carbon production barometric_press Force per unit area exerted against a surface by the weight of air above that... basin Name of the basin (e bathroom_count The number of bathrooms in the building bedroom_count The number of bedrooms in the building benzene Concentration of benzene in the sample best_protein the specific protein identifier most correctly associated with the peptide se... bin_name bin_quality binned_contig_num biochem_oxygen_dem Amount of dissolved oxygen needed by aerobic biological organisms in a body o... biocide List of biocides (commercial name of product and supplier) and date of admini... biocide_admin_method Method of biocide administration (dose, frequency, duration, time elapsed bet... biogas_retention_time biogas_temperature biol_stat The level of genome modification biomass Amount of biomass; should include the name for the part of biomass measured, ... biomaterial_purity biosample_categories biosample_identifiers biosample_set This property links a database object to the set of samples within it biotic_regm Information about treatment(s) involving use of biotic factors, such as bacte... biotic_relationship Description of relationship(s) between the subject organism and other organis... bishomohopanol Concentration of bishomohopanol blood_press_diast Resting diastolic blood pressure, measured as mm mercury blood_press_syst Resting systolic blood pressure, measured as mm mercury bromide Concentration of bromide build_docs The building design, construction and operation documents build_occup_type The primary function for which a building or discrete part of a building is i... building_setting A location (geography) where a building is set built_struc_age The age of the built structure since construction built_struc_set The characterization of the location of the built structure as high or low hu... built_struc_type A physical structure that is a body or assemblage of bodies in space to form ... bulk_elect_conductivity Electrical conductivity is a measure of the ability to carry electric current... calcium Concentration of calcium in the sample calibration_object the file containing calibration data object calibration_set This property links a database object to the set of calibrations within it calibration_standard the reference standard(s) used for calibration calibration_target the target measurement of the calibration carb_dioxide Carbon dioxide (gas) amount or concentration at the time of sampling carb_monoxide Carbon monoxide (gas) amount or concentration at the time of sampling carb_nitro_ratio Ratio of amount or concentrations of carbon to nitrogen ceil_area The area of the ceiling space within the room ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide... ceil_finish_mat The type of material used to finish a ceiling ceil_struc The construction format of the ceiling ceil_texture The feel, appearance, or consistency of a ceiling surface ceil_thermal_mass The ability of the ceiling to provide inertia against temperature fluctuation... ceil_type The type of ceiling according to the ceiling's appearance or construction ceil_water_mold Signs of the presence of mold or mildew on the ceiling chem_administration List of chemical compounds administered to the host or site where sampling oc... chem_mutagen Treatment involving use of mutagens; should include the name of mutagen, amou... chem_oxygen_dem A measure of the capacity of water to consume oxygen during the decomposition... chem_treat_method Method of chemical administration(dose, frequency, duration, time elapsed bet... chem_treatment List of chemical compounds administered upstream the sampling location where ... chemical_conversion_category The type of chemical conversion process chemical_entity_set This property links a database object to the set of chemical entities within ... chemical_formula A generic grouping for molecular formulae and empirical formulae chimera_check Tool(s) used for chimera checking, including version number and parameters, t... chloride Concentration of chloride in the sample chlorophyll Concentration of chlorophyll chromatographic_category The type of chromatography used in a process climate_environment Treatment involving an exposure to a particular climate; treatment regimen in... collected_from The Site from which a Biosample was collected collecting_biosamples_from_site_set collection_date The time of sampling, either as an instance (single point in time) or interva... collection_date_inc Date the incubation was harvested/collected/ended collection_time The time of sampling, either as an instance (single point) or interval collection_time_inc Time the incubation was harvested/collected/ended community completeness completion_date compression_type If provided, specifies the compression type concentration The concentration of a substance used in a process conditionings Preliminary treatment of either phase with a suitable solution of the other p... conduc Electrical conductivity of water configuration_set This property links a database object to the set of configurations within it contained_in A type of container container_size The volume of the container an analyte is stored in or an activity takes plac... contamination contig_bp Total size in bp of all contigs contigs The sum of the (length*log(length)) of all contigs, times some constant cool_syst_id The cooling system identifier core_field basic fields count crop_rotation Whether or not crop is rotated, and if yes, rotation schedule ctg_l50 Given a set of contigs, the L50 is defined as the sequence length of the shor... ctg_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... ctg_logsum Maximum contig length ctg_max Maximum contig length ctg_n50 Given a set of contigs, each with its own length, the N50 count is defined as... ctg_n90 Given a set of contigs, each with its own length, the N90 count is defined as... ctg_powsum Powersum of all contigs is the same as logsum except that it uses the sum of ... cult_root_med Name or reference for the hydroponic or in vitro culture rooting medium; can ... cur_land_use Present state of sample site cur_vegetation Vegetation classification from one or more standard classification systems, o... cur_vegetation_meth Reference or method used in vegetation classification data_category The category of the file, such as instrument data from data generation or pro... data_generation_set This property links a database object to the set of data generations within i... data_object_set This property links a database object to the set of data objects within it data_object_type The type of file represented by the data object date_created from database class date_last_rain The date of the last time it rained density Density of the sample, which is its mass per unit volume (aka volumetric mass... depos_env Main depositional environment (https://en depth The vertical distance below local surface, e description a human-readable description of a thing dew_point The temperature to which a given parcel of humid air must be cooled, at const... diether_lipids Concentration of diether lipids; can include multiple types of diether lipids direct_infusion_category used when a processed sample is introduced into a mass spectrometer without c... display_order When rendering information, this attribute to specify the order in which the ... diss_carb_dioxide Concentration of dissolved carbon dioxide in the sample or liquid portion of ... diss_hydrogen Concentration of dissolved hydrogen diss_inorg_carb Dissolved inorganic carbon concentration in the sample, typically measured af... diss_inorg_nitro Concentration of dissolved inorganic nitrogen diss_inorg_phosp Concentration of dissolved inorganic phosphorus in the sample diss_iron Concentration of dissolved iron in the sample diss_org_carb Concentration of dissolved organic carbon in the sample, liquid portion of th... diss_org_nitro Dissolved organic nitrogen concentration measured as; total dissolved nitroge... diss_oxygen Concentration of dissolved oxygen diss_oxygen_fluid Concentration of dissolved oxygen in the oil field produced fluids as it cont... dna_absorb1 260/280 measurement of DNA sample purity dna_absorb2 260/230 measurement of DNA sample purity dna_collect_site Provide information on the site your DNA sample was collected from dna_concentration dna_cont_type Tube or plate (96-well) dna_cont_well dna_container_id dna_dnase dna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA dna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... dna_project_contact dna_samp_id dna_sample_format Solution in which the DNA sample has been suspended dna_sample_name Give the DNA sample a name that is meaningful to you dna_seq_project dna_seq_project_name dna_seq_project_pi dna_volume dnase_rna doi_category The resource type the corresponding doi resolves to doi_provider The authority, or organization, the DOI is associated with doi_value A digital object identifier, which is intended to persistantly identify some ... door_comp_type The composite type of the door door_cond The phsical condition of the door door_direct The direction the door opens door_loc The relative location of the door in the room door_mat The material the door is composed of door_move The type of movement of the door door_size The size of the door door_type The type of door material door_type_metal The type of metal door door_type_wood The type of wood door door_water_mold Signs of the presence of mold or mildew on a door down_par Visible waveband radiance and irradiance measurements in the water column drainage_class Drainage classification from a standard system such as the USDA system drawings The buildings architectural drawings; if design is chosen, indicate phase-con... duration The elapsed time of an activity ecosystem An ecosystem is a combination of a physical environment (abiotic factors) and... ecosystem_category Ecosystem categories represent divisions within the ecosystem based on specif... ecosystem_path_id A unique id representing the GOLD classifiers associated with a sample ecosystem_subtype Ecosystem subtypes represent further subdivision of Ecosystem types into more... ecosystem_type Ecosystem types represent things having common characteristics within the Eco... efficiency_percent Percentage of volatile solids removed from the anaerobic digestor elev Elevation of the sampling site is its height above a fixed reference point, m... elevator The number of elevators within the built structure eluent_introduction_category A high-level categorization for how the processed sample is introduced into a... email An email address for an entity such as a person embargoed If true, the data are embargoed and not available for public access emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database emsl_identifiers emsl_project_identifiers Identifiers that link a NMDC study to the EMSL user facility website hosting ... emsl_store_temp The temperature at which the sample should be stored upon delivery to EMSL emulsions Amount or concentration of substances such as paints, adhesives, mayonnaise, ... encodes The gene product encoded by this feature end The end of the feature in positive 1-based integer coordinates end_date The date on which any process or activity was ended ended_at_time env_broad_scale Report the major environmental system the sample or specimen came from env_local_scale Report the entity or entities which are in the sample or specimen\u2019s local vic... env_medium Report the environmental material(s) immediately surrounding the sample or sp... env_package MIxS extension for reporting of measurements and observations obtained from o... environment_field field describing environmental aspect of a sample escalator The number of escalators within the built structure ethylbenzene Concentration of ethylbenzene in the sample etl_software_version from database class eukaryotic_evaluation Contains results from evaluating if a Metagenome-Assembled Genome is of eukar... execution_resource The computing resource or facility where the workflow was executed exp_duct The amount of exposed ductwork in the room exp_pipe The number of exposed pipes in the room experimental_factor Experimental factors are essentially the variable aspects of an experiment de... experimental_factor_other Other details about your sample that you feel can't be accurately represented... ext_door The number of exterior doors in the built structure ext_wall_orient The orientation of the exterior wall ext_window_orient The compass direction the exterior window of the room is facing external_database_identifiers Link to corresponding identifier in external database extraction_targets Provides the target biomolecule that has been separated from a sample during ... extreme_event Unusual physical events that may have affected microbial populations fao_class Soil classification from the FAO World Reference Database for Soil Resources feature_category A Sequence Ontology term that describes the category of a feature feature_type TODO: Yuri to write fertilizer_regm Information about treatment involving the use of fertilizers; should include ... field Name of the hydrocarbon field (e field_research_site_set file_size_bytes Size of the file in bytes filter_material A porous material on which solid particles present in air or other fluid whic... filter_method Type of filter used or how the sample was filtered filter_pore_size A quantitative or qualitative measurement of the physical dimensions of the p... filter_type A device which removes solid particulates or airborne molecular contaminants filtration_category The type of conditioning applied to a filter, device, etc final_concentration When solutions A (containing substance X) and B are combined together, this s... fire Historical and/or physical evidence of fire fireplace_type A firebox with chimney flooding Historical and/or physical evidence of flooding floor_age The time period since installment of the carpet or flooring floor_area The area of the floor space within the room floor_cond The physical condition of the floor at the time of sampling; photos or video ... floor_count The number of floors in the building, including basements and mechanical pent... floor_finish_mat The floor covering type; the finished surface that is walked on floor_struc Refers to the structural elements and subfloor upon which the finish flooring... floor_thermal_mass The ability of the floor to provide inertia against temperature fluctuations floor_water_mold Signs of the presence of mold or mildew in a room fluor Raw or converted fluorescence of water freq_clean The number of times the sample location is cleaned freq_cook The number of times a meal is cooked per week functional_annotation_agg functional_annotation_set This property links a database object to the set of all functional annotation... funding_sources A list of organizations, along with the award numbers, that underwrite financ... fungicide_regm Information about treatment involving use of fungicides; should include the n... furniture The types of furniture present in the sampled room gap_pct The gap size percentage of all scaffolds gaseous_environment Use of conditions with differing gaseous environments; should include the nam... gaseous_substances Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... gc_avg Average of GC content of all contigs gc_std Standard deviation of GC content of all contigs gender_restroom The gender type of the restroom gene_count gene_function_id The identifier for the gene function genetic_mod Genetic modifications of the genome of an organism, which may occur naturally... genome_feature_set This property links a database object to the set of all features geo_loc_name The geographical origin of the sample as defined by the country or sea name f... gff_coordinate A positive 1-based integer coordinate indicating start or end git_url The url that points to the exact github location of a workflow glucosidase_act Measurement of glucosidase activity gnps_identifiers gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... gold_analysis_project_identifiers identifiers for corresponding analysis projects in GOLD gold_biosample_identifiers identifiers for corresponding sample in GOLD gold_identifiers gold_path_field This is a grouping for any of the gold path fields gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD gold_study_identifiers identifiers for corresponding project(s) in GOLD gravidity Whether or not subject is gravid, and if yes date due or date post-conception... gravity Information about treatment involving use of gravity factor to study various ... growth_facil Type of facility where the sampled plant was grown; controlled vocabulary: gr... growth_habit Characteristic shape, appearance or growth form of a plant species growth_hormone_regm Information about treatment involving use of growth hormones; should include ... gtdbtk_class gtdbtk_domain gtdbtk_family gtdbtk_genus gtdbtk_order gtdbtk_phylum gtdbtk_species habitat hall_count The total count of hallways and cooridors in the built structure handidness The handidness of the individual sampled has_boolean_value Links a quantity value to a boolean has_calibration a calibration instance associated with a process has_chromatography_configuration The identifier of the associated ChromatographyConfiguration, providing infor... has_credit_associations This slot links a study to a credit association has_failure_categorization has_function has_input An input to a process has_mass_spectrometry_configuration The identifier of the associated MassSpectrometryConfiguration has_maximum_numeric_value The maximum value part, expressed as number, of the quantity value when the v... has_metabolite_identifications has_minimum_numeric_value The minimum value part, expressed as number, of the quantity value when the v... has_numeric_value Links a quantity value to a number has_output An output from a process has_peptide_quantifications has_process_parts A list of process parts that make up a protocol has_raw_value The value that was specified for an annotation in raw form, i has_unit Links a QuantityValue to a unit hc_produced Main hydrocarbon type produced from resource (i hcr Main Hydrocarbon Resource type hcr_fw_salinity Original formation water salinity (prior to secondary recovery e hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en hcr_pressure Original pressure of the hydrocarbon resource hcr_temp Original temperature of the hydrocarbon resource heat_cool_type Methods of conditioning or heating a room or building heat_deliv_loc The location of heat delivery within the room heat_sys_deliv_meth The method by which the heat is delivered through the system heat_system_id The heating system identifier heavy_metals Heavy metals present in the sequenced sample and their concentrations heavy_metals_meth Reference or method used in determining heavy metals height_carper_fiber The average carpet fiber height in the indoor environment herbicide_regm Information about treatment involving use of herbicides; information about tr... highest_similarity_score homepage_website The website address (URL) of an entity's homepage horizon_meth Reference or method used in determining the horizon host_age Age of host at the time of sampling; relevant scale depends on species and st... host_body_habitat Original body habitat where the sample was obtained from host_body_product Substance produced by the body, e host_body_site Name of body site where the sample was obtained from, such as a specific orga... host_body_temp Core body temperature of the host when sample was collected host_color The color of host host_common_name Common name of the host host_diet Type of diet depending on the host, for animals omnivore, herbivore etc host_disease_stat List of diseases with which the host has been diagnosed; can include multiple... host_dry_mass Measurement of dry mass host_family_relation Familial relationships to other hosts in the same study; can include multiple... host_genotype Observed genotype host_growth_cond Literature reference giving growth conditions of the host host_height The height of subject host_last_meal Content of last meal and time since feeding; can include multiple values host_length The length of subject host_life_stage Description of life stage of host host_name host_phenotype Phenotype of human or other host host_sex Gender or physical sex of the host host_shape Morphological shape of host host_subject_id A unique identifier by which each subject can be referred to, de-identified host_subspecf_genlin Information about the genetic distinctness of the host organism below the sub... host_substrate The growth substrate of the host host_symbiont The taxonomic name of the organism(s) found living in mutualistic, commensali... host_taxid NCBI taxon id of the host, e host_tot_mass Total mass of the host at collection, the unit depends on host host_wet_mass Measurement of wet mass humidity Amount of water vapour in the air, at the time of sampling humidity_regm Information about treatment involving an exposure to varying degree of humidi... id A unique identifier for a thing igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database igsn_identifiers img_identifiers A list of identifiers that relate the biosample to records in the IMG databas... in_manifest inchi inchi_key indoor_space A distinguishable space within a structure, the purpose for which discrete ar... indoor_surf Type of indoor surface indust_eff_percent Percentage of industrial effluents received by wastewater treatment plant infiltrations The amount of time it takes to complete each infiltration activity inorg_particles Concentration of particles such as sand, grit, metal particles, ceramics, etc input_base_count The nucleotide base count number of input reads for QC analysis input_contig_num input_mass Total mass of sample used in activity input_read_bases TODO input_read_count The sequence count number of input reads for QC analysis input_volume The volume of the input sample insdc_analysis_identifiers insdc_assembly_identifiers insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject insdc_biosample_identifiers identifiers for corresponding sample in INSDC insdc_experiment_identifiers insdc_identifiers Any identifier covered by the International Nucleotide Sequence Database Coll... insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA inside_lux The recorded value at sampling time (power density) instrument_set This property links a database object to the set of instruments within it instrument_used What instrument was used during DataGeneration or MaterialProcessing int_wall_cond The physical condition of the wall at the time of sampling; photos or video p... internal_calibration whether internal calibration was used, if false, external calibration was use... investigation_field field describing aspect of the investigation/study to which the sample belong... ionization_source The ionization source used to introduce processed samples into a mass spectro... is_pressurized Whether or not pressure was applied to a thing or process is_stranded Is the (RNA) library stranded or non-stranded (unstranded) isotope_exposure List isotope exposure or addition applied to your sample iw_bt_date_well Injection water breakthrough date per well following a secondary and/or terti... iwf Proportion of the produced fluids derived from injected water at the time of ... jgi_portal_analysis_project_identifiers identifiers for corresponding analysis projects in JGI Portal jgi_portal_identifiers identifiers for entities according to JGI Portal jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... known_as language Should use ISO 639-1 code e last_clean The last time the floor was cleaned (swept, mopped, vacuumed) lat_lon The geographical origin of the sample as defined by latitude and longitude latitude latitude lbc_thirty lime buffer capacity, determined after 30 minute incubation lbceq lime buffer capacity, determined at equilibrium after 5 day incubation library_preparation_kit library_type light_intensity Measurement of light intensity light_regm Information about treatment(s) involving exposure to light, including both li... light_type Application of light to achieve some practical or aesthetic effect link_addit_analys Link to additional analysis results performed on the sample link_class_info Link to digitized soil maps or other soil classification information link_climate_info Link to climate resource lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki local_class Soil classification based on local soil classification system local_class_meth Reference or method used in determining the local soil classification location longitude longitude low_depth_contig_num magnesium Concentration of magnesium in the sample mags_list manganese Concentration of manganese in the sample manifest_category The type of collection that describes the data in the collection manifest_set This property links a database object to the set of manifests within it mass A physical quality that inheres in a bearer by virtue of the proportion of th... mass_analyzers The kind of mass analyzer(s) used during the spectra collection mass_spectrometry_acquisition_strategy Mode of running a mass spectrometer method by which m/z ranges are selected a... mass_spectrum_collection_modes Indicates whether mass spectra were collected in full profile, reduced profil... material_component_separation A material processing in which components of an input material become segrega... material_processing_set This property links a database object to the set of material processing withi... max_occup The maximum amount of people allowed in the indoor environment md5_checksum MD5 checksum of file (pre-compressed) mean_frict_vel Measurement of mean friction velocity mean_peak_frict_vel Measurement of mean peak friction velocity mech_struc mechanical structure: a moving structure mechanical_damage Information about any mechanical damage exerted on the plant; can include mul... members_id metabolite_identified the specific metabolite identifier metagenome_annotation_id The identifier for the analysis activity that generated the functional annota... metagenome_assembly_parameter methane Methane (gas) amount or concentration at the time of sampling mgnify_analysis_identifiers mgnify_identifiers mgnify_project_identifiers identifiers for corresponding project in MGnify micro_biomass_c_meth Reference or method used in determining microbial biomass carbon micro_biomass_meth Reference or method used in determining microbial biomass micro_biomass_n_meth Reference or method used in determining microbial biomass nitrogen microbial_biomass The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_c The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_n The part of the organic matter in the soil that constitutes living microorgan... min_q_value smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... mineral_nutr_regm Information about treatment involving the use of mineral supplements; should ... misc_param Any other measurement performed or parameter collected, that is not listed he... mod_date The last date on which the database information was modified model modifier_substance The type of modification being done n_alkanes Concentration of n-alkanes; can include multiple n-alkanes name A human readable label for an entity ncbi_lineage Comma delimited ordered list of NCBI taxonomy names ncbi_lineage_tax_ids Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId) ncbi_project_name ncbi_taxonomy_name neon_biosample_identifiers neon_identifiers identifiers for entities according to NEON neon_study_identifiers nitrate Concentration of nitrate in the sample nitrate_nitrogen Concentration of nitrate nitrogen in the sample nitrite Concentration of nitrite in the sample nitrite_nitrogen Concentration of nitrite nitrogen in the sample nitro Concentration of nitrogen (total) non_microb_biomass Amount of biomass; should include the name for the part of biomass measured, ... non_microb_biomass_method Reference or method used in determining biomass non_min_nutr_regm Information about treatment involving the exposure of plant to non-mineral nu... notes nucl_acid_amp A link to a literature reference, electronic resource or a standard operating... nucl_acid_ext A link to a literature reference, electronic resource or a standard operating... nucleic_acid_sequence_source_field num_16s num_23s num_5s num_aligned_reads The sequence count number of input reads aligned to assembled contigs num_input_reads The sequence count number of input reads for assembly num_t_rna number_of_contig number_pets The number of pets residing in the sampled space number_plants The number of plant(s) in the sampling space number_resident The number of individuals currently occupying in the sampling location object_set Applies to a property that links a database object to a set of objects objective The scientific objectives associated with the entity occup_density_samp Average number of occupants at time of sampling per square footage occup_document The type of documentation of occupancy occup_samp Number of occupants present at time of sample within the given space omics_processing_identifiers omics_type The type of omics data orcid The ORCID of a person ordered_mobile_phases The solution(s) that moves through a chromatography column org_carb Concentration of organic carbon org_count_qpcr_info If qpcr was used for the cell count, the target gene name, the primer sequenc... org_matter Concentration of organic matter org_nitro Concentration of organic nitrogen org_nitro_method Method used for obtaining organic nitrogen org_particles Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... organism_count Total cell count of any organism (or group of organisms) per gram, volume or ... other_treatment Other treatments applied to your samples that are not applicable to the provi... output_base_count After QC analysis nucleotide base count number output_read_bases TODO output_read_count After QC analysis sequence count number owc_tvdss Depth of the original oil water contact (OWC) zone (average) (m TVDSS) oxy_stat_samp Oxygenation status of sample oxygen Oxygen (gas) amount or concentration at the time of sampling part_of Links a resource to another resource that either logically or physically incl... part_org_carb Concentration of particulate organic carbon part_org_nitro Concentration of particulate organic nitrogen particle_class Particles are classified, based on their size, into six general categories:cl... pcr_cond Description of reaction conditions and components of PCR in the form of 'init... pcr_cycles pcr_primers PCR primers that were used to amplify the sequence of the targeted gene, locu... peptide_sequence peptide_sequence_count count of peptide sequences grouped to the best_protein peptide_spectral_count sum of filter passing MS2 spectra associated with the peptide sequence within... peptide_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... permeability Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... perturbation Type of perturbation, e pesticide_regm Information about treatment involving use of insecticides; should include the... petroleum_hydrocarb Concentration of petroleum hydrocarbon ph Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... ph_meth Reference or method used in determining ph ph_regm Information about treatment involving exposure of plants to varying levels of... phaeopigments Concentration of phaeopigments; can include multiple phaeopigments phase The phase for a coding sequence entity phosphate Concentration of phosphate phosplipid_fatt_acid Concentration of phospholipid fatty acids; can include multiple values photon_flux Measurement of photon flux plant_growth_med Specification of the media for growing the plants or tissue cultured samples,... plant_product Substance produced by the plant, where the sample was obtained from plant_sex Sex of the reproductive parts on the whole plant, e plant_struc Name of plant structure the sample was obtained from; for Plant Ontology (PO)... polarity_mode the polarity of which ions are generated and detected pollutants Pollutant types and, amount or concentrations measured at the time of samplin... pool_dna_extracts Indicate whether multiple DNA extractions were mixed porosity Porosity of deposited sediment is volume of voids divided by the total volume... potassium Concentration of potassium in the sample pour_point Temperature at which a liquid becomes semi solid and loses its flow character... pre_treatment The process of pre-treatment removes materials that can be easily collected f... pres_animal_insect The type and number of animals or insects present in the sampling space pressure Pressure to which the sample is subject to, in atmospheres prev_land_use_meth Reference or method used in determining previous land use and dates previous_land_use Previous land use and dates primary_prod Measurement of primary production, generally measured as isotope uptake primary_treatment The process to produce both a generally homogeneous liquid capable of being t... principal_investigator Principal Investigator who led the study and/or generated the dataset processed_sample_set This property links a database object to the set of processed samples within ... processing_institution The organization that processed the sample prod_rate Oil and/or gas production rates per well (e prod_start_date Date of field's first production profile_image_url A url that points to an image of a person profile_position Cross-sectional position in the hillslope where sample was collected project_id Proposal IDs or names associated with dataset proport_woa_temperature proposal_dna proposal_rna protein_spectral_count sum of filter passing MS2 spectra associated with the best protein within a g... protein_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... protocol_execution_category protocol_execution_set This property links a database object to the set of protocol executions withi... protocol_link qc_comment Slot to store additional comments about laboratory or workflow output qc_failure_what Provides a summary about what caused a lab or workflow process to fail qc_failure_where Describes the nmdc schema class that corresonds to where the failure occurred qc_status Stores information about the result of a process (ie the process of sequencin... quad_pos The quadrant position of the sampling room within the building radiation_regm Information about treatment involving exposure of plant or a plant part to a ... rainfall_regm Information about treatment involving an exposure to a given amount of rainfa... reactor_type Anaerobic digesters can be designed and engineered to operate using a number ... read_qc_analysis_statistic redox_potential Redox potential, measured relative to a hydrogen cell, indicating oxidation o... rel_air_humidity Partial vapor and air pressure, density of the vapor and air, or by the actua... rel_humidity_out The recorded outside relative humidity value at the time of sampling rel_samp_loc The sampling location within the train car related_identifiers Identifiers assigned to a thing that is similar to that which is represented ... replicate_number If sending biological replicates, indicate the rep number here reservoir Name of the reservoir (e resins_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... resolution_categories The relative resolution at which spectra were collected rna_absorb1 260/280 measurement of RNA sample purity rna_absorb2 260/230 measurement of RNA sample purity rna_collect_site Provide information on the site your RNA sample was collected from rna_concentration rna_cont_type Tube or plate (96-well) rna_cont_well rna_container_id rna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA rna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... rna_project_contact rna_samp_id rna_sample_format Solution in which the RNA sample has been suspended rna_sample_name Give the RNA sample a name that is meaningful to you rna_seq_project rna_seq_project_name rna_seq_project_pi rna_volume room_air_exch_rate The rate at which outside air replaces indoor air in a given space room_architec_elem The unique details and component parts that, together, form the architecture ... room_condt The condition of the room at the time of sampling room_connected List of rooms connected to the sampling room by a doorway room_count The total count of rooms in the built structure including all room types room_dim The length, width and height of sampling room room_door_dist Distance between doors (meters) in the hallway between the sampling room and ... room_door_share List of room(s) (room number, room name) sharing a door with the sampling roo... room_hallway List of room(s) (room number, room name) located in the same hallway as sampl... room_loc The position of the room within the building room_moist_dam_hist The history of moisture damage or mold in the past 12 months room_net_area The net floor area of sampling room room_occup Count of room occupancy at time of sampling room_samp_pos The horizontal sampling position in the room relative to architectural elemen... room_type The main purpose or activity of the sampling room room_vol Volume of sampling room room_wall_share List of room(s) (room number, room name) sharing a wall with the sampling roo... room_window_count Number of windows in the room root_cond Relevant rooting conditions such as field plot size, sowing density, containe... root_med_carbon Source of organic carbon in the culture rooting medium; e root_med_macronutr Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... root_med_micronutr Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... root_med_ph pH measurement of the culture rooting medium; e root_med_regl Growth regulators in the culture rooting medium such as cytokinins, auxins, g... root_med_solid Specification of the solidifying agent in the culture rooting medium; e root_med_suppl Organic supplements of the culture rooting medium, such as vitamins, amino ac... salinity The total concentration of all dissolved salts in a liquid or solid sample salinity_category Categorical description of the sample's salinity salinity_meth Reference or method used in determining salinity salt_regm Information about treatment involving use of salts as supplement to liquid an... samp_capt_status Reason for the sample samp_collec_device The device used to collect an environmental sample samp_collec_method The method employed for collecting the sample samp_collect_point Sampling point on the asset were sample was collected (e samp_dis_stage Stage of the disease at the time of sample collection, e samp_floor The floor of the building, where the sampling room is located samp_loc_corr_rate Metal corrosion rate is the speed of metal deterioration due to environmental... samp_mat_process A brief description of any processing applied to the sample during or after r... samp_md In non deviated well, measured depth is equal to the true vertical depth, TVD... samp_name A local identifier or name that for the material sample used for extracting n... samp_preserv Preservative added to the sample (e samp_room_id Sampling room number samp_size The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... samp_sort_meth Method by which samples are sorted; open face filter collecting total suspend... samp_store_dur Duration for which the sample was stored samp_store_loc Location at which sample was stored, usually name of a specific freezer/room samp_store_temp Temperature at which sample was stored, e samp_subtype Name of sample sub-type samp_taxon_id NCBI taxon id of the sample samp_time_out The recent and long term history of outside sampling samp_transport_cond Sample transport duration (in days or hrs) and temperature the sample was exp... samp_tvdss Depth of the sample i samp_type The type of material from which the sample was obtained samp_vol_we_dna_ext Volume (ml) or mass (g) of total collected sample processed for DNA extractio... samp_weather The weather on the sampling day samp_well_name Name of the well (e sample_collection_day sample_collection_hour sample_collection_minute sample_collection_month sample_collection_site sample_collection_year sample_link A unique identifier to assign parent-child, subsample, or sibling samples sample_shipped The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... sample_state_information The chemical phase of a pure sample, or the state of a mixed sample sample_type Type of sample being submitted sampled_portion The portion of the sample that is taken for downstream activity saturates_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... scaf_bp Total size in bp of all scaffolds scaf_l50 Given a set of scaffolds, the L50 is defined as the sequence length of the sh... scaf_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... scaf_l_gt50k Total size in bp of all scaffolds greater than 50 KB scaf_logsum The sum of the (length*log(length)) of all scaffolds, times some constant scaf_max Maximum scaffold length scaf_n50 Given a set of scaffolds, each with its own length, the N50 count is defined ... scaf_n90 Given a set of scaffolds, each with its own length, the N90 count is defined ... scaf_n_gt50k Total sequence count of scaffolds greater than 50 KB scaf_pct_gt50k Total sequence size percentage of scaffolds greater than 50 KB scaf_powsum Powersum of all scaffolds is the same as logsum except that it uses the sum o... scaffolds Total sequence count of all scaffolds season The season when sampling occurred season_environment Treatment involving an exposure to a particular season (e season_precpt The average of all seasonal precipitation values known, or an estimated equiv... season_temp Mean seasonal temperature season_use The seasons the space is occupied secondary_treatment The process for substantially degrading the biological content of the sewage sediment_type Information about the sediment type based on major constituents separation_method The method that was used to separate a substance from a solution or mixture seq_meth Sequencing machine used seq_quality_check Indicate if the sequence has been called by automatic systems (none) or under... seqid The ID of the landmark used to establish the coordinate system for the curren... sequencing_field sewage_type Type of wastewater treatment plant as municipial or industrial shad_dev_water_mold Signs of the presence of mold or mildew on the shading device shading_device_cond The physical condition of the shading device at the time of sampling shading_device_loc The location of the shading device in relation to the built structure shading_device_mat The material the shading device is composed of shading_device_type The type of shading device sieving Collection design of pooled samples and/or sieve size and amount of sample si... silicate Concentration of silicate size_frac Filtering pore size used in sample preparation size_frac_low Refers to the mesh/pore size used to pre-filter/pre-sort the sample size_frac_up Refers to the mesh/pore size used to retain the sample slope_aspect The direction a slope faces slope_gradient Commonly called 'slope' sludge_retent_time The time activated sludge remains in reactor smiles A string encoding of a molecular graph, no chiral or isotopic information sodium Sodium concentration in the sample soil_annual_season_temp soil_horizon Specific layer in the land area which measures parallel to the soil surface a... soil_text_measure The relative proportion of different grain sizes of mineral particles in a so... soil_texture_meth Reference or method used in determining soil texture soil_type Description of the soil type or classification soil_type_meth Reference or method used in determining soil series name or other lower-level... solar_irradiance The amount of solar energy that arrives at a specific area of a surface durin... soluble_inorg_mat Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... soluble_iron_micromol soluble_org_mat Concentration of substances such as urea, fruit sugars, soluble proteins, dru... soluble_react_phosp Concentration of soluble reactive phosphorus source_concentration When solutions A (containing substance X) and B are combined together, this s... source_mat_id A unique identifier assigned to a material sample (as defined by http://rs space_typ_state Customary or normal state of the space specific The building specifications specific_ecosystem Specific ecosystems represent specific features of the environment like aphot... specific_humidity The mass of water vapour in a unit mass of moist air, usually expressed as gr... sr_dep_env Source rock depositional environment (https://en sr_geol_age Geological age of source rock (Additional info: https://en sr_kerog_type Origin of kerogen sr_lithology Lithology of source rock (https://en standing_water_regm Treatment involving an exposure to standing water during a plant's life span,... start The start of the feature in positive 1-based integer coordinates start_date The date on which any process or activity was started start_date_inc Date the incubation was started start_time_inc Time the incubation was started started_at_time stationary_phase The material the stationary phase is comprised of used in chromatography storage_process_set This property links a database object to the set of storage processes within ... store_cond Explain how and for how long the soil sample was stored before DNA extraction... strand The strand on which a feature is located stranded_orientation Lists the strand orientiation for a stranded RNA library preparation study_category The type of research initiative study_identifiers study_image Links a study to one or more images study_set This property links a database object to the set of studies within it subject substance_role The role of a substance in a process substances_used The substances that are combined to enable a ChemicalConversionProcess substances_volume The volume of the combined substances that was included in a ChemicalConversi... substructure_type The substructure or under building is that largely hidden section of the buil... subsurface_depth sulfate Concentration of sulfate in the sample sulfate_fw Original sulfate concentration in the hydrocarbon resource sulfide Concentration of sulfide in the sample surf_air_cont Contaminant identified on surface surf_humidity Surfaces: water activity as a function of air and material moisture surf_material Surface materials at the point of sampling surf_moisture Water held on a surface surf_moisture_ph ph measurement of surface surf_temp Temperature of the surface at the time of sampling suspend_part_matter Concentration of suspended particulate matter suspend_solids Concentration of substances including a wide variety of material, such as sil... tan Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by th... target_gene Targeted gene or locus name for marker gene studies target_subfragment Name of subfragment of a gene or locus technical_reps If sending technical replicates of the same sample, indicate the replicate co... temp Temperature of the sample at the time of sampling temp_out The recorded temperature value at sampling time outside temperature The value of a temperature measurement or temperature used in a process term pointer to an ontology class tertiary_treatment The process providing a final treatment stage to raise the effluent quality b... tidal_stage Stage of tide tillage Note method(s) used for tilling tiss_cult_growth_med Description of plant tissue culture growth media used title A name given to the entity that differs from the name/label programmatically ... toluene Concentration of toluene in the sample too_short_contig_num tot_carb Total carbon content tot_depth_water_col Measurement of total depth of water column tot_diss_nitro Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... tot_inorg_nitro Total inorganic nitrogen content tot_iron Concentration of total iron in the sample tot_nitro Total nitrogen concentration of water samples, calculated by: total nitrogen ... tot_nitro_cont_meth Reference or method used in determining the total nitrogen tot_nitro_content Total nitrogen content of the sample tot_org_c_meth Reference or method used in determining total organic carbon tot_org_carb Definition for soil: total organic carbon content of the soil, definition oth... tot_part_carb Total particulate carbon content tot_phosp Total phosphorus concentration in the sample, calculated by: total phosphorus... tot_phosphate Total amount or concentration of phosphate tot_sulfur Concentration of total sulfur in the sample total_bases train_line The subway line name train_stat_loc The train station collection location train_stop_loc The train stop collection location turbidity Measure of the amount of cloudiness or haziness in water caused by individual... tvdss_of_hcr_press True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... tvdss_of_hcr_temp True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... typ_occup_density Customary or normal density of occupants type the class_uri of the class that has been instantiated unbinned_contig_num url value vendor ventilation_rate Ventilation rate of the system in the sampled premises ventilation_type Ventilation system used in the sampled premises version vfa Concentration of Volatile Fatty Acids in the sample vfa_fw Original volatile fatty acid concentration in the hydrocarbon resource vis_media The building visual media viscosity A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020t... volatile_org_comp Concentration of carbon-based chemicals that easily evaporate at room tempera... volume The volume of a substance wall_area The total area of the sampled room's walls wall_const_type The building class of the wall defined by the composition of the building ele... wall_finish_mat The material utilized to finish the outer most layer of the wall wall_height The average height of the walls in the sampled room wall_loc The relative location of the wall within the room wall_surf_treatment The surface treatment of interior wall wall_texture The feel, appearance, or consistency of a wall surface wall_thermal_mass The ability of the wall to provide inertia against temperature fluctuations wall_water_mold Signs of the presence of mold or mildew on a wall was_generated_by was_informed_by wastewater_type The origin of wastewater such as human waste, rainfall, storm drains, etc water_cont_soil_meth Reference or method used in determining the water content of soil water_content Water content measurement water_current Measurement of magnitude and direction of flow within a fluid water_cut Current amount of water (%) in a produced fluid stream; or the average of the... water_feat_size The size of the water feature water_feat_type The type of water feature present within the building being sampled water_prod_rate Water production rates per well (e water_temp_regm Information about treatment involving an exposure to water with varying degre... watering_regm Information about treatment involving an exposure to watering frequencies, tr... websites A list of websites that are associated with the entity weekday The day of the week when sampling occurred win A unique identifier of a well or wellbore wind_direction Wind direction is the direction from which a wind originates wind_speed Speed of wind measured at the time of sampling window_cond The physical condition of the window at the time of sampling window_cover The type of window covering window_horiz_pos The horizontal position of the window on the wall window_loc The relative location of the window within the room window_mat The type of material used to finish a window window_open_freq The number of times windows are opened per week window_size The window's length and width window_status Defines whether the windows were open or closed during environmental testing window_type The type of windows window_vert_pos The vertical position of the window on the wall window_water_mold Signs of the presence of mold or mildew on the window workflow_execution_set This property links a database object to the set of workflow executions xylene Concentration of xylene in the sample zinc Concentration of zinc in the sample"},{"location":"#enumerations","title":"Enumerations","text":"Enumeration Description AnalysisTypeEnum AnalyteCategoryEnum ArchStrucEnum BiolStatEnum BiosampleCategoryEnum Funding-based, sample location-based, or experimental method-based defined ca... BioticRelationshipEnum BuildDocsEnum BuildOccupTypeEnum BuildingSettingEnum CalibrationStandardEnum CalibrationTargetEnum CeilCondEnum CeilFinishMatEnum CeilTextureEnum CeilTypeEnum ChemicalConversionCategoryEnum ChromatographicCategoryEnum ContainerCategoryEnum The permitted types of containers used in processing metabolomic samples CreditEnum CurLandUseEnum DataCategoryEnum DeposEnvEnum DirectInfusionEnum DNASampleFormatEnum DoiCategoryEnum DoiProviderEnum DoorCompTypeEnum DoorCondEnum DoorDirectEnum DoorLocEnum DoorMatEnum DoorMoveEnum DoorTypeEnum DoorTypeMetalEnum DoorTypeWoodEnum DrainageClassEnum DrawingsEnum EluentIntroductionCategoryEnum ExecutionResourceEnum ExtWallOrientEnum ExtWindowOrientEnum ExtractionTargetEnum FailureWhatEnum The permitted values for describing where a failure occurred during processin... FailureWhereEnum The permitted values for describing where in the process, either a lab or ana... FaoClassEnum FileTypeEnum FilterTypeEnum FloorCondEnum FloorFinishMatEnum FloorStrucEnum FloorWaterMoldEnum FreqCleanEnum FurnitureEnum GenderRestroomEnum GrowthHabitEnum HandidnessEnum HcProducedEnum HcrEnum HcrGeolAgeEnum HeatCoolTypeEnum HeatDelivLocEnum HostSexEnum IndoorSpaceEnum IndoorSurfEnum InstrumentModelEnum InstrumentVendorEnum IntWallCondEnum IonizationSourceEnum JgiContTypeEnum LibraryTypeEnum LightTypeEnum LithologyEnum ManifestCategoryEnum MassAnalyzerEnum MassSpectrometryAcquisitionStrategyEnum MassSpectrumCollectionModeEnum MechStrucEnum OccupDocumentEnum OrganismCountEnum OxyStatSampEnum PlantGrowthMedEnum PlantSexEnum PolarityModeEnum ProcessingInstitutionEnum ProfilePositionEnum ProtocolCategoryEnum The possible protocols that may be followed for an assay QuadPosEnum RelSampLocEnum ResolutionCategoryEnum RNASampleFormatEnum RoomCondtEnum RoomConnectedEnum RoomLocEnum RoomSampPosEnum RoomTypeEnum SampCaptStatusEnum SampCollectPointEnum SampDisStageEnum SampFloorEnum SampMdEnum SampSubtypeEnum SampWeatherEnum SamplePortionEnum SampleStateEnum SampleTypeEnum SeasonUseEnum SedimentTypeEnum SeparationMethodEnum The tool/substance used to separate or filter a solution or mixture ShadingDeviceCondEnum ShadingDeviceTypeEnum SoilHorizonEnum SpecificEnum SrDepEnvEnum SrGeolAgeEnum SrKerogTypeEnum SrLithologyEnum StationaryPhaseEnum The type of stationary phase used in a chromatography process StatusEnum StrandedOrientationEnum This enumeration specifies information about stranded RNA library preparation... StudyCategoryEnum SubstanceRoleEnum SubstructureTypeEnum SurfAirContEnum SurfMaterialEnum TidalStageEnum TillageEnum TrainLineEnum TrainStatLocEnum TrainStopLocEnum VisMediaEnum WallConstTypeEnum WallFinishMatEnum WallLocEnum WallSurfTreatmentEnum WallTextureEnum WaterFeatTypeEnum WeekdayEnum WindowCondEnum WindowCoverEnum WindowHorizPosEnum WindowLocEnum WindowMatEnum WindowTypeEnum WindowVertPosEnum YesNoEnum replaces DnaDnaseEnum and DnaseRnaEnum"},{"location":"#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Bytes An integer value that corresponds to a size in bytes Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... DecimalDegree A decimal degree expresses latitude or longitude as decimal fractions Double A real number that conforms to the xsd:double specification ExternalIdentifier A CURIE representing an external identifier Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer LanguageCode A language code conforming to ISO_639-1 Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Unit Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"#subsets","title":"Subsets","text":"Subset Description Checklist A MIxS checklist ChecklistPackageCombination A combination of a checklist and a package DataObjectSubset Subset consisting of the data objects that either inputs or outputs of proces... DataPortalSubset Subset consisting of entities that Kitware/nmdc-server use to populate the da... Environment Investigation MixsExtension MixsEnvironmentalTriad NucleicAcidSequenceSource Package A MIxS package Proteases SampleSubset Subset consisting of entities linked to the processing of samples Sequencing WorkflowSubset Subset consisting of just the workflow execution activities"},{"location":"AnalysisTypeEnum/","title":"Enum: AnalysisTypeEnum","text":"

URI: AnalysisTypeEnum

"},{"location":"AnalysisTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metabolomics None metagenomics None Standard short-read metagenomic sequencing metagenomics_long_read None Long-read metagenomic sequencing metaproteomics None metatranscriptomics None natural organic matter None bulk chemistry None"},{"location":"AnalysisTypeEnum/#slots","title":"Slots","text":"Name Description analysis_type Select all the data types associated or available for this biosample"},{"location":"AnalysisTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AnalysisTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"AnalysisTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: AnalysisTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  metabolomics:\n    text: metabolomics\n  metagenomics:\n    text: metagenomics\n    description: Standard short-read metagenomic sequencing\n    title: Metagenomics\n  metagenomics_long_read:\n    text: metagenomics_long_read\n    description: Long-read metagenomic sequencing\n    title: Metagenomics (long read)\n  metaproteomics:\n    text: metaproteomics\n  metatranscriptomics:\n    text: metatranscriptomics\n  natural organic matter:\n    text: natural organic matter\n  bulk chemistry:\n    text: bulk chemistry\n\n
"},{"location":"AnalyteCategoryEnum/","title":"Enum: AnalyteCategoryEnum","text":"

URI: AnalyteCategoryEnum

"},{"location":"AnalyteCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metagenome None metatranscriptome None metaproteome None metabolome None lipidome None nom None"},{"location":"AnalyteCategoryEnum/#slots","title":"Slots","text":"Name Description analyte_category The type of analyte(s) that were measured in the data generation process and ..."},{"location":"AnalyteCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AnalyteCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"AnalyteCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: AnalyteCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  metagenome:\n    text: metagenome\n    aliases:\n    - metaG\n  metatranscriptome:\n    text: metatranscriptome\n    aliases:\n    - metaT\n  metaproteome:\n    text: metaproteome\n    aliases:\n    - metaP\n  metabolome:\n    text: metabolome\n    aliases:\n    - metaB\n  lipidome:\n    text: lipidome\n  nom:\n    text: nom\n    aliases:\n    - natural organic matter\n\n
"},{"location":"ArchStrucEnum/","title":"Enum: ArchStrucEnum","text":"

URI: ArchStrucEnum

"},{"location":"ArchStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building None shed None home None"},{"location":"ArchStrucEnum/#slots","title":"Slots","text":"Name Description arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c..."},{"location":"ArchStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ArchStrucEnum/#schema-source","title":"Schema Source","text":""},{"location":"ArchStrucEnum/#linkml-source","title":"LinkML Source","text":"
name: arch_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  building:\n    text: building\n  shed:\n    text: shed\n  home:\n    text: home\n\n
"},{"location":"AttributeValue/","title":"Class: AttributeValue","text":"

The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:AttributeValue

classDiagram\n  class AttributeValue\n  click AttributeValue href \"../AttributeValue\"\n    AttributeValue <|-- QuantityValue\n      click QuantityValue href \"../QuantityValue\"\n    AttributeValue <|-- ImageValue\n      click ImageValue href \"../ImageValue\"\n    AttributeValue <|-- PersonValue\n      click PersonValue href \"../PersonValue\"\n    AttributeValue <|-- TextValue\n      click TextValue href \"../TextValue\"\n    AttributeValue <|-- TimestampValue\n      click TimestampValue href \"../TimestampValue\"\n    AttributeValue <|-- ControlledTermValue\n      click ControlledTermValue href \"../ControlledTermValue\"\n    AttributeValue <|-- GeolocationValue\n      click GeolocationValue href \"../GeolocationValue\"\n\n\n\n  AttributeValue : has_raw_value\n\n  AttributeValue : type\n\n\n\n
"},{"location":"AttributeValue/#inheritance","title":"Inheritance","text":""},{"location":"AttributeValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_raw_value 0..1 String The value that was specified for an annotation in raw form, i direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"AttributeValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AttributeValue/#schema-source","title":"Schema Source","text":""},{"location":"AttributeValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:AttributeValue native nmdc:AttributeValue"},{"location":"AttributeValue/#linkml-source","title":"LinkML Source","text":""},{"location":"AttributeValue/#direct","title":"Direct","text":"
name: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n  hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- has_raw_value\n- type\nclass_uri: nmdc:AttributeValue\n\n
"},{"location":"AttributeValue/#induced","title":"Induced","text":"
name: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n  hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: AttributeValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: AttributeValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:AttributeValue\n\n
"},{"location":"BiolStatEnum/","title":"Enum: BiolStatEnum","text":"

URI: BiolStatEnum

"},{"location":"BiolStatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description wild None natural None semi-natural None inbred line None breeder's line None hybrid None clonal selection None mutant None"},{"location":"BiolStatEnum/#slots","title":"Slots","text":"Name Description biol_stat The level of genome modification"},{"location":"BiolStatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BiolStatEnum/#schema-source","title":"Schema Source","text":""},{"location":"BiolStatEnum/#linkml-source","title":"LinkML Source","text":"
name: biol_stat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  wild:\n    text: wild\n  natural:\n    text: natural\n  semi-natural:\n    text: semi-natural\n  inbred line:\n    text: inbred line\n  breeder's line:\n    text: breeder's line\n  hybrid:\n    text: hybrid\n  clonal selection:\n    text: clonal selection\n  mutant:\n    text: mutant\n\n
"},{"location":"Biosample/","title":"Class: Biosample","text":"

Biological source material which can be characterized by an experiment.

URI: nmdc:Biosample

Note

Mermaid class diagram too large to render.

"},{"location":"Biosample/#inheritance","title":"Inheritance","text":""},{"location":"Biosample/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance associated_studies 1..* Study The study associated with a resource direct biosample_categories * BiosampleCategoryEnum direct collected_from 0..1 FieldResearchSite The Site from which a Biosample was collected direct embargoed 0..1 recommended Boolean If true, the data are embargoed and not available for public access direct host_disease_stat 0..1 TextValue List of diseases with which the host has been diagnosed; can include multiple... direct host_taxid 0..1 ControlledIdentifiedTermValue NCBI taxon id of the host, e direct img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct neon_biosample_identifiers * ExternalIdentifier direct samp_name 0..1 String A local identifier or name that for the material sample used for extracting n... direct gold_biosample_identifiers * Uriorcurie Unique identifier for a biosample submitted to GOLD that matches the NMDC sub... direct insdc_biosample_identifiers * ExternalIdentifier identifiers for corresponding sample in INSDC direct emsl_biosample_identifiers * ExternalIdentifier A list of identifiers for the biosample from the EMSL database direct igsn_biosample_identifiers * ExternalIdentifier A list of identifiers for the biosample from the IGSN database direct abs_air_humidity 0..1 QuantityValue Actual mass of water vapor - mh20 - present in the air water vapor mixture direct add_recov_method 0..1 TextValue Additional (i direct additional_info 0..1 TextValue Information that doesn't fit anywhere else direct address 0..1 TextValue The street name and building number where the sampling occurred direct adj_room 0..1 TextValue List of rooms (room number, room name) immediately adjacent to the sampling r... direct aero_struc 0..1 TextValue Aerospace structures typically consist of thin plates with stiffeners for the... direct agrochem_addition * TextValue Addition of fertilizers, pesticides, etc direct air_PM_concen * TextValue Concentration of substances that remain suspended in the air, and comprise mi... direct air_temp 0..1 QuantityValue Temperature of the air at the time of sampling direct air_temp_regm * TextValue Information about treatment involving an exposure to varying temperatures; sh... direct al_sat 0..1 QuantityValue The relative abundance of aluminum in the sample direct al_sat_meth 0..1 TextValue Reference or method used in determining Aluminum saturation direct alkalinity 0..1 QuantityValue Alkalinity, the ability of a solution to neutralize acids to the equivalence ... direct alkalinity_method 0..1 TextValue Method used for alkalinity measurement direct alkyl_diethers 0..1 QuantityValue Concentration of alkyl diethers direct alt 0..1 QuantityValue Altitude is a term used to identify heights of objects such as airplanes, spa... direct aminopept_act 0..1 QuantityValue Measurement of aminopeptidase activity direct ammonium 0..1 QuantityValue Concentration of ammonium in the sample direct ammonium_nitrogen 0..1 QuantityValue Concentration of ammonium nitrogen in the sample direct amount_light 0..1 QuantityValue The unit of illuminance and luminous emittance, measuring luminous flux per u... direct ances_data 0..1 TextValue Information about either pedigree or other ancestral information description ... direct annual_precpt 0..1 QuantityValue The average of all annual precipitation values known, or an estimated equival... direct annual_temp 0..1 QuantityValue Mean annual temperature direct antibiotic_regm * TextValue Information about treatment involving antibiotic administration; should inclu... direct api 0..1 QuantityValue API gravity is a measure of how heavy or light a petroleum liquid is compared... direct arch_struc 0..1 ArchStrucEnum An architectural structure is a human-made, free-standing, immobile outdoor c... direct aromatics_pc 0..1 TextValue Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... direct asphaltenes_pc 0..1 TextValue Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... direct atmospheric_data * TextValue Measurement of atmospheric data; can include multiple data direct avg_dew_point 0..1 QuantityValue The average of dew point measures taken at the beginning of every hour over a... direct avg_occup 0..1 TextValue Daily average occupancy of room direct avg_temp 0..1 QuantityValue The average of temperatures taken at the beginning of every hour over a 24 ho... direct bac_prod 0..1 QuantityValue Bacterial production in the water column measured by isotope uptake direct bac_resp 0..1 QuantityValue Measurement of bacterial respiration in the water column direct bacteria_carb_prod 0..1 QuantityValue Measurement of bacterial carbon production direct barometric_press 0..1 QuantityValue Force per unit area exerted against a surface by the weight of air above that... direct basin 0..1 TextValue Name of the basin (e direct bathroom_count 0..1 TextValue The number of bathrooms in the building direct bedroom_count 0..1 TextValue The number of bedrooms in the building direct benzene 0..1 QuantityValue Concentration of benzene in the sample direct biochem_oxygen_dem 0..1 QuantityValue Amount of dissolved oxygen needed by aerobic biological organisms in a body o... direct biocide 0..1 TextValue List of biocides (commercial name of product and supplier) and date of admini... direct biocide_admin_method 0..1 TextValue Method of biocide administration (dose, frequency, duration, time elapsed bet... direct biol_stat 0..1 BiolStatEnum The level of genome modification direct biomass * TextValue Amount of biomass; should include the name for the part of biomass measured, ... direct biotic_regm 0..1 TextValue Information about treatment(s) involving use of biotic factors, such as bacte... direct biotic_relationship 0..1 BioticRelationshipEnum Description of relationship(s) between the subject organism and other organis... direct bishomohopanol 0..1 QuantityValue Concentration of bishomohopanol direct blood_press_diast 0..1 QuantityValue Resting diastolic blood pressure, measured as mm mercury direct blood_press_syst 0..1 QuantityValue Resting systolic blood pressure, measured as mm mercury direct bromide 0..1 QuantityValue Concentration of bromide direct build_docs 0..1 BuildDocsEnum The building design, construction and operation documents direct build_occup_type * BuildOccupTypeEnum The primary function for which a building or discrete part of a building is i... direct building_setting 0..1 BuildingSettingEnum A location (geography) where a building is set direct built_struc_age 0..1 QuantityValue The age of the built structure since construction direct built_struc_set 0..1 TextValue The characterization of the location of the built structure as high or low hu... direct built_struc_type 0..1 TextValue A physical structure that is a body or assemblage of bodies in space to form ... direct calcium 0..1 QuantityValue Concentration of calcium in the sample direct carb_dioxide 0..1 QuantityValue Carbon dioxide (gas) amount or concentration at the time of sampling direct carb_monoxide 0..1 QuantityValue Carbon monoxide (gas) amount or concentration at the time of sampling direct carb_nitro_ratio 0..1 QuantityValue Ratio of amount or concentrations of carbon to nitrogen direct ceil_area 0..1 QuantityValue The area of the ceiling space within the room direct ceil_cond 0..1 CeilCondEnum The physical condition of the ceiling at the time of sampling; photos or vide... direct ceil_finish_mat 0..1 CeilFinishMatEnum The type of material used to finish a ceiling direct ceil_struc 0..1 TextValue The construction format of the ceiling direct ceil_texture 0..1 CeilTextureEnum The feel, appearance, or consistency of a ceiling surface direct ceil_thermal_mass 0..1 QuantityValue The ability of the ceiling to provide inertia against temperature fluctuation... direct ceil_type 0..1 CeilTypeEnum The type of ceiling according to the ceiling's appearance or construction direct ceil_water_mold 0..1 TextValue Signs of the presence of mold or mildew on the ceiling direct chem_administration * ControlledTermValue List of chemical compounds administered to the host or site where sampling oc... direct chem_mutagen * TextValue Treatment involving use of mutagens; should include the name of mutagen, amou... direct chem_oxygen_dem 0..1 QuantityValue A measure of the capacity of water to consume oxygen during the decomposition... direct chem_treat_method 0..1 String Method of chemical administration(dose, frequency, duration, time elapsed bet... direct chem_treatment 0..1 TextValue List of chemical compounds administered upstream the sampling location where ... direct chloride 0..1 QuantityValue Concentration of chloride in the sample direct chlorophyll 0..1 QuantityValue Concentration of chlorophyll direct climate_environment * TextValue Treatment involving an exposure to a particular climate; treatment regimen in... direct collection_date 0..1 TimestampValue The time of sampling, either as an instance (single point in time) or interva... direct conduc 0..1 QuantityValue Electrical conductivity of water direct cool_syst_id 0..1 TextValue The cooling system identifier direct core_field 0..1 String basic fields direct crop_rotation 0..1 TextValue Whether or not crop is rotated, and if yes, rotation schedule direct cult_root_med 0..1 TextValue Name or reference for the hydroponic or in vitro culture rooting medium; can ... direct cur_land_use 0..1 CurLandUseEnum Present state of sample site direct cur_vegetation 0..1 TextValue Vegetation classification from one or more standard classification systems, o... direct cur_vegetation_meth 0..1 TextValue Reference or method used in vegetation classification direct date_last_rain 0..1 TimestampValue The date of the last time it rained direct density 0..1 QuantityValue Density of the sample, which is its mass per unit volume (aka volumetric mass... direct depos_env 0..1 DeposEnvEnum Main depositional environment (https://en direct depth 0..1 QuantityValue The vertical distance below local surface, e direct dew_point 0..1 QuantityValue The temperature to which a given parcel of humid air must be cooled, at const... direct diether_lipids * TextValue Concentration of diether lipids; can include multiple types of diether lipids direct diss_carb_dioxide 0..1 QuantityValue Concentration of dissolved carbon dioxide in the sample or liquid portion of ... direct diss_hydrogen 0..1 QuantityValue Concentration of dissolved hydrogen direct diss_inorg_carb 0..1 QuantityValue Dissolved inorganic carbon concentration in the sample, typically measured af... direct diss_inorg_nitro 0..1 QuantityValue Concentration of dissolved inorganic nitrogen direct diss_inorg_phosp 0..1 QuantityValue Concentration of dissolved inorganic phosphorus in the sample direct diss_iron 0..1 QuantityValue Concentration of dissolved iron in the sample direct diss_org_carb 0..1 QuantityValue Concentration of dissolved organic carbon in the sample, liquid portion of th... direct diss_org_nitro 0..1 QuantityValue Dissolved organic nitrogen concentration measured as; total dissolved nitroge... direct diss_oxygen 0..1 QuantityValue Concentration of dissolved oxygen direct diss_oxygen_fluid 0..1 QuantityValue Concentration of dissolved oxygen in the oil field produced fluids as it cont... direct dna_cont_well 0..1 recommended String direct door_comp_type 0..1 DoorCompTypeEnum The composite type of the door direct door_cond 0..1 DoorCondEnum The phsical condition of the door direct door_direct 0..1 DoorDirectEnum The direction the door opens direct door_loc 0..1 DoorLocEnum The relative location of the door in the room direct door_mat 0..1 DoorMatEnum The material the door is composed of direct door_move 0..1 DoorMoveEnum The type of movement of the door direct door_size 0..1 QuantityValue The size of the door direct door_type 0..1 DoorTypeEnum The type of door material direct door_type_metal 0..1 DoorTypeMetalEnum The type of metal door direct door_type_wood 0..1 DoorTypeWoodEnum The type of wood door direct door_water_mold 0..1 TextValue Signs of the presence of mold or mildew on a door direct down_par 0..1 QuantityValue Visible waveband radiance and irradiance measurements in the water column direct drainage_class 0..1 DrainageClassEnum Drainage classification from a standard system such as the USDA system direct drawings 0..1 DrawingsEnum The buildings architectural drawings; if design is chosen, indicate phase-con... direct ecosystem 0..1 String An ecosystem is a combination of a physical environment (abiotic factors) and... direct ecosystem_category 0..1 String Ecosystem categories represent divisions within the ecosystem based on specif... direct ecosystem_subtype 0..1 String Ecosystem subtypes represent further subdivision of Ecosystem types into more... direct ecosystem_type 0..1 String Ecosystem types represent things having common characteristics within the Eco... direct efficiency_percent 0..1 QuantityValue Percentage of volatile solids removed from the anaerobic digestor direct elev 0..1 Float Elevation of the sampling site is its height above a fixed reference point, m... direct elevator 0..1 TextValue The number of elevators within the built structure direct emulsions * TextValue Amount or concentration of substances such as paints, adhesives, mayonnaise, ... direct env_broad_scale 1 ControlledIdentifiedTermValue Report the major environmental system the sample or specimen came from direct env_local_scale 1 ControlledIdentifiedTermValue Report the entity or entities which are in the sample or specimen\u2019s local vic... direct env_medium 1 ControlledIdentifiedTermValue Report the environmental material(s) immediately surrounding the sample or sp... direct env_package 0..1 TextValue MIxS extension for reporting of measurements and observations obtained from o... direct environment_field 0..1 String field describing environmental aspect of a sample direct escalator 0..1 TextValue The number of escalators within the built structure direct ethylbenzene 0..1 QuantityValue Concentration of ethylbenzene in the sample direct exp_duct 0..1 QuantityValue The amount of exposed ductwork in the room direct exp_pipe 0..1 QuantityValue The number of exposed pipes in the room direct experimental_factor 0..1 ControlledTermValue Experimental factors are essentially the variable aspects of an experiment de... direct ext_door 0..1 TextValue The number of exterior doors in the built structure direct ext_wall_orient 0..1 ExtWallOrientEnum The orientation of the exterior wall direct ext_window_orient 0..1 ExtWindowOrientEnum The compass direction the exterior window of the room is facing direct extreme_event 0..1 String Unusual physical events that may have affected microbial populations direct fao_class 0..1 FaoClassEnum Soil classification from the FAO World Reference Database for Soil Resources direct fertilizer_regm * TextValue Information about treatment involving the use of fertilizers; should include ... direct field 0..1 TextValue Name of the hydrocarbon field (e direct filter_type * FilterTypeEnum A device which removes solid particulates or airborne molecular contaminants direct fire 0..1 String Historical and/or physical evidence of fire direct fireplace_type 0..1 TextValue A firebox with chimney direct flooding 0..1 String Historical and/or physical evidence of flooding direct floor_age 0..1 QuantityValue The time period since installment of the carpet or flooring direct floor_area 0..1 QuantityValue The area of the floor space within the room direct floor_cond 0..1 FloorCondEnum The physical condition of the floor at the time of sampling; photos or video ... direct floor_count 0..1 TextValue The number of floors in the building, including basements and mechanical pent... direct floor_finish_mat 0..1 FloorFinishMatEnum The floor covering type; the finished surface that is walked on direct floor_struc 0..1 FloorStrucEnum Refers to the structural elements and subfloor upon which the finish flooring... direct floor_thermal_mass 0..1 QuantityValue The ability of the floor to provide inertia against temperature fluctuations direct floor_water_mold 0..1 FloorWaterMoldEnum Signs of the presence of mold or mildew in a room direct fluor 0..1 QuantityValue Raw or converted fluorescence of water direct freq_clean 0..1 QuantityValue The number of times the sample location is cleaned direct freq_cook 0..1 QuantityValue The number of times a meal is cooked per week direct fungicide_regm * TextValue Information about treatment involving use of fungicides; should include the n... direct furniture 0..1 FurnitureEnum The types of furniture present in the sampled room direct gaseous_environment * TextValue Use of conditions with differing gaseous environments; should include the nam... direct gaseous_substances * TextValue Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... direct gender_restroom 0..1 GenderRestroomEnum The gender type of the restroom direct genetic_mod 0..1 TextValue Genetic modifications of the genome of an organism, which may occur naturally... direct geo_loc_name 0..1 TextValue The geographical origin of the sample as defined by the country or sea name f... direct glucosidase_act 0..1 QuantityValue Measurement of glucosidase activity direct gravidity 0..1 TextValue Whether or not subject is gravid, and if yes date due or date post-conception... direct gravity * TextValue Information about treatment involving use of gravity factor to study various ... direct growth_facil 0..1 ControlledTermValue Type of facility where the sampled plant was grown; controlled vocabulary: gr... direct growth_habit 0..1 GrowthHabitEnum Characteristic shape, appearance or growth form of a plant species direct growth_hormone_regm * TextValue Information about treatment involving use of growth hormones; should include ... direct hall_count 0..1 TextValue The total count of hallways and cooridors in the built structure direct handidness 0..1 HandidnessEnum The handidness of the individual sampled direct hc_produced 0..1 HcProducedEnum Main hydrocarbon type produced from resource (i direct hcr 0..1 HcrEnum Main Hydrocarbon Resource type direct hcr_fw_salinity 0..1 QuantityValue Original formation water salinity (prior to secondary recovery e direct hcr_geol_age 0..1 HcrGeolAgeEnum Geological age of hydrocarbon resource (Additional info: https://en direct hcr_pressure 0..1 TextValue Original pressure of the hydrocarbon resource direct hcr_temp 0..1 TextValue Original temperature of the hydrocarbon resource direct heat_cool_type * HeatCoolTypeEnum Methods of conditioning or heating a room or building direct heat_deliv_loc 0..1 HeatDelivLocEnum The location of heat delivery within the room direct heat_sys_deliv_meth 0..1 String The method by which the heat is delivered through the system direct heat_system_id 0..1 TextValue The heating system identifier direct heavy_metals * TextValue Heavy metals present in the sample and their concentrations direct heavy_metals_meth * TextValue Reference or method used in determining heavy metals direct height_carper_fiber 0..1 QuantityValue The average carpet fiber height in the indoor environment direct herbicide_regm * TextValue Information about treatment involving use of herbicides; information about tr... direct horizon_meth 0..1 TextValue Reference or method used in determining the horizon direct host_age 0..1 QuantityValue Age of host at the time of sampling; relevant scale depends on species and st... direct host_body_habitat 0..1 TextValue Original body habitat where the sample was obtained from direct host_body_product 0..1 ControlledTermValue Substance produced by the body, e direct host_body_site 0..1 ControlledTermValue Name of body site where the sample was obtained from, such as a specific orga... direct host_body_temp 0..1 QuantityValue Core body temperature of the host when sample was collected direct host_color 0..1 TextValue The color of host direct host_common_name 0..1 TextValue Common name of the host direct host_diet * TextValue Type of diet depending on the host, for animals omnivore, herbivore etc direct host_dry_mass 0..1 QuantityValue Measurement of dry mass direct host_family_relation * String Familial relationships to other hosts in the same study; can include multiple... direct host_genotype 0..1 TextValue Observed genotype direct host_growth_cond 0..1 TextValue Literature reference giving growth conditions of the host direct host_height 0..1 QuantityValue The height of subject direct host_last_meal * TextValue Content of last meal and time since feeding; can include multiple values direct host_length 0..1 QuantityValue The length of subject direct host_life_stage 0..1 TextValue Description of life stage of host direct host_phenotype 0..1 ControlledTermValue Phenotype of human or other host direct host_sex 0..1 HostSexEnum Gender or physical sex of the host direct host_shape 0..1 TextValue Morphological shape of host direct host_subject_id 0..1 TextValue A unique identifier by which each subject can be referred to, de-identified direct host_subspecf_genlin * String Information about the genetic distinctness of the host organism below the sub... direct host_substrate 0..1 TextValue The growth substrate of the host direct host_symbiont * String The taxonomic name of the organism(s) found living in mutualistic, commensali... direct host_taxid 0..1 ControlledIdentifiedTermValue NCBI taxon id of the host, e direct host_tot_mass 0..1 QuantityValue Total mass of the host at collection, the unit depends on host direct host_wet_mass 0..1 QuantityValue Measurement of wet mass direct humidity 0..1 QuantityValue Amount of water vapour in the air, at the time of sampling direct humidity_regm * TextValue Information about treatment involving an exposure to varying degree of humidi... direct indoor_space 0..1 IndoorSpaceEnum A distinguishable space within a structure, the purpose for which discrete ar... direct indoor_surf 0..1 IndoorSurfEnum Type of indoor surface direct indust_eff_percent 0..1 QuantityValue Percentage of industrial effluents received by wastewater treatment plant direct inorg_particles * TextValue Concentration of particles such as sand, grit, metal particles, ceramics, etc direct inside_lux 0..1 QuantityValue The recorded value at sampling time (power density) direct int_wall_cond 0..1 IntWallCondEnum The physical condition of the wall at the time of sampling; photos or video p... direct investigation_field 0..1 String field describing aspect of the investigation/study to which the sample belong... direct iw_bt_date_well 0..1 TimestampValue Injection water breakthrough date per well following a secondary and/or terti... direct iwf 0..1 QuantityValue Proportion of the produced fluids derived from injected water at the time of ... direct last_clean 0..1 TimestampValue The last time the floor was cleaned (swept, mopped, vacuumed) direct lat_lon 0..1 GeolocationValue The geographical origin of the sample as defined by latitude and longitude direct lbc_thirty 0..1 QuantityValue lime buffer capacity, determined after 30 minute incubation direct lbceq 0..1 QuantityValue lime buffer capacity, determined at equilibrium after 5 day incubation direct light_intensity 0..1 QuantityValue Measurement of light intensity direct light_regm 0..1 TextValue Information about treatment(s) involving exposure to light, including both li... direct light_type * LightTypeEnum Application of light to achieve some practical or aesthetic effect direct link_addit_analys 0..1 TextValue Link to additional analysis results performed on the sample direct link_class_info 0..1 TextValue Link to digitized soil maps or other soil classification information direct link_climate_info 0..1 TextValue Link to climate resource direct lithology 0..1 LithologyEnum Hydrocarbon resource main lithology (Additional information: http://petrowiki direct local_class 0..1 TextValue Soil classification based on local soil classification system direct local_class_meth 0..1 TextValue Reference or method used in determining the local soil classification direct magnesium 0..1 QuantityValue Concentration of magnesium in the sample direct manganese 0..1 QuantityValue Concentration of manganese in the sample direct max_occup 0..1 QuantityValue The maximum amount of people allowed in the indoor environment direct mean_frict_vel 0..1 QuantityValue Measurement of mean friction velocity direct mean_peak_frict_vel 0..1 QuantityValue Measurement of mean peak friction velocity direct mech_struc 0..1 MechStrucEnum mechanical structure: a moving structure direct mechanical_damage * TextValue Information about any mechanical damage exerted on the plant; can include mul... direct methane 0..1 QuantityValue Methane (gas) amount or concentration at the time of sampling direct micro_biomass_meth 0..1 String Reference or method used in determining microbial biomass direct microbial_biomass 0..1 QuantityValue The part of the organic matter in the soil that constitutes living microorgan... direct mineral_nutr_regm * TextValue Information about treatment involving the use of mineral supplements; should ... direct misc_param * TextValue Any other measurement performed or parameter collected, that is not listed he... direct n_alkanes * TextValue Concentration of n-alkanes; can include multiple n-alkanes direct nitrate 0..1 QuantityValue Concentration of nitrate in the sample direct nitrate_nitrogen 0..1 QuantityValue Concentration of nitrate nitrogen in the sample direct nitrite 0..1 QuantityValue Concentration of nitrite in the sample direct nitrite_nitrogen 0..1 QuantityValue Concentration of nitrite nitrogen in the sample direct nitro 0..1 QuantityValue Concentration of nitrogen (total) direct non_min_nutr_regm * String Information about treatment involving the exposure of plant to non-mineral nu... direct nucleic_acid_sequence_source_field 0..1 String direct number_pets 0..1 QuantityValue The number of pets residing in the sampled space direct number_plants 0..1 QuantityValue The number of plant(s) in the sampling space direct number_resident 0..1 QuantityValue The number of individuals currently occupying in the sampling location direct occup_density_samp 0..1 QuantityValue Average number of occupants at time of sampling per square footage direct occup_document 0..1 OccupDocumentEnum The type of documentation of occupancy direct occup_samp 0..1 QuantityValue Number of occupants present at time of sample within the given space direct org_carb 0..1 QuantityValue Concentration of organic carbon direct org_count_qpcr_info 0..1 String If qpcr was used for the cell count, the target gene name, the primer sequenc... direct org_matter 0..1 QuantityValue Concentration of organic matter direct org_nitro 0..1 QuantityValue Concentration of organic nitrogen direct org_particles * TextValue Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... direct organism_count * QuantityValue Total cell count of any organism (or group of organisms) per gram, volume or ... direct owc_tvdss 0..1 QuantityValue Depth of the original oil water contact (OWC) zone (average) (m TVDSS) direct oxy_stat_samp 0..1 OxyStatSampEnum Oxygenation status of sample direct oxygen 0..1 QuantityValue Oxygen (gas) amount or concentration at the time of sampling direct part_org_carb 0..1 QuantityValue Concentration of particulate organic carbon direct part_org_nitro 0..1 QuantityValue Concentration of particulate organic nitrogen direct particle_class * TextValue Particles are classified, based on their size, into six general categories:cl... direct permeability 0..1 TextValue Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... direct perturbation * TextValue Type of perturbation, e direct pesticide_regm * TextValue Information about treatment involving use of insecticides; should include the... direct petroleum_hydrocarb 0..1 QuantityValue Concentration of petroleum hydrocarbon direct ph 0..1 Double Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... direct ph_meth 0..1 TextValue Reference or method used in determining ph direct ph_regm * TextValue Information about treatment involving exposure of plants to varying levels of... direct phaeopigments * TextValue Concentration of phaeopigments; can include multiple phaeopigments direct phosphate 0..1 QuantityValue Concentration of phosphate direct phosplipid_fatt_acid * TextValue Concentration of phospholipid fatty acids; can include multiple values direct photon_flux 0..1 QuantityValue Measurement of photon flux direct plant_growth_med 0..1 ControlledTermValue Specification of the media for growing the plants or tissue cultured samples,... direct plant_product 0..1 TextValue Substance produced by the plant, where the sample was obtained from direct plant_sex 0..1 PlantSexEnum Sex of the reproductive parts on the whole plant, e direct plant_struc 0..1 ControlledTermValue Name of plant structure the sample was obtained from; for Plant Ontology (PO)... direct pollutants * TextValue Pollutant types and, amount or concentrations measured at the time of samplin... direct porosity 0..1 TextValue Porosity of deposited sediment is volume of voids divided by the total volume... direct potassium 0..1 QuantityValue Concentration of potassium in the sample direct pour_point 0..1 QuantityValue Temperature at which a liquid becomes semi solid and loses its flow character... direct pre_treatment 0..1 TextValue The process of pre-treatment removes materials that can be easily collected f... direct pres_animal_insect 0..1 String The type and number of animals or insects present in the sampling space direct pressure 0..1 QuantityValue Pressure to which the sample is subject to, in atmospheres direct prev_land_use_meth 0..1 String Reference or method used in determining previous land use and dates direct previous_land_use 0..1 TextValue Previous land use and dates direct primary_prod 0..1 QuantityValue Measurement of primary production, generally measured as isotope uptake direct primary_treatment 0..1 TextValue The process to produce both a generally homogeneous liquid capable of being t... direct prod_rate 0..1 QuantityValue Oil and/or gas production rates per well (e direct prod_start_date 0..1 TimestampValue Date of field's first production direct profile_position 0..1 ProfilePositionEnum Cross-sectional position in the hillslope where sample was collected direct quad_pos 0..1 QuadPosEnum The quadrant position of the sampling room within the building direct radiation_regm * TextValue Information about treatment involving exposure of plant or a plant part to a ... direct rainfall_regm * TextValue Information about treatment involving an exposure to a given amount of rainfa... direct reactor_type 0..1 TextValue Anaerobic digesters can be designed and engineered to operate using a number ... direct redox_potential 0..1 QuantityValue Redox potential, measured relative to a hydrogen cell, indicating oxidation o... direct rel_air_humidity 0..1 QuantityValue Partial vapor and air pressure, density of the vapor and air, or by the actua... direct rel_humidity_out 0..1 QuantityValue The recorded outside relative humidity value at the time of sampling direct rel_samp_loc 0..1 RelSampLocEnum The sampling location within the train car direct reservoir 0..1 TextValue Name of the reservoir (e direct resins_pc 0..1 TextValue Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... direct room_air_exch_rate 0..1 QuantityValue The rate at which outside air replaces indoor air in a given space direct room_architec_elem 0..1 String The unique details and component parts that, together, form the architecture ... direct room_condt 0..1 RoomCondtEnum The condition of the room at the time of sampling direct room_connected 0..1 RoomConnectedEnum List of rooms connected to the sampling room by a doorway direct room_count 0..1 TextValue The total count of rooms in the built structure including all room types direct room_dim 0..1 TextValue The length, width and height of sampling room direct room_door_dist 0..1 TextValue Distance between doors (meters) in the hallway between the sampling room and ... direct room_door_share 0..1 TextValue List of room(s) (room number, room name) sharing a door with the sampling roo... direct room_hallway 0..1 TextValue List of room(s) (room number, room name) located in the same hallway as sampl... direct room_loc 0..1 RoomLocEnum The position of the room within the building direct room_moist_dam_hist 0..1 Integer The history of moisture damage or mold in the past 12 months direct room_net_area 0..1 TextValue The net floor area of sampling room direct room_occup 0..1 QuantityValue Count of room occupancy at time of sampling direct room_samp_pos 0..1 RoomSampPosEnum The horizontal sampling position in the room relative to architectural elemen... direct room_type 0..1 RoomTypeEnum The main purpose or activity of the sampling room direct room_vol 0..1 TextValue Volume of sampling room direct room_wall_share 0..1 TextValue List of room(s) (room number, room name) sharing a wall with the sampling roo... direct room_window_count 0..1 Integer Number of windows in the room direct root_cond 0..1 TextValue Relevant rooting conditions such as field plot size, sowing density, containe... direct root_med_carbon 0..1 TextValue Source of organic carbon in the culture rooting medium; e direct root_med_macronutr 0..1 TextValue Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... direct root_med_micronutr 0..1 TextValue Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... direct root_med_ph 0..1 QuantityValue pH measurement of the culture rooting medium; e direct root_med_regl 0..1 TextValue Growth regulators in the culture rooting medium such as cytokinins, auxins, g... direct root_med_solid 0..1 TextValue Specification of the solidifying agent in the culture rooting medium; e direct root_med_suppl 0..1 TextValue Organic supplements of the culture rooting medium, such as vitamins, amino ac... direct salinity 0..1 QuantityValue The total concentration of all dissolved salts in a liquid or solid sample direct salinity_meth 0..1 TextValue Reference or method used in determining salinity direct salt_regm * TextValue Information about treatment involving use of salts as supplement to liquid an... direct samp_capt_status 0..1 SampCaptStatusEnum Reason for the sample direct samp_collec_device 0..1 String The device used to collect an environmental sample direct samp_collec_method 0..1 String The method employed for collecting the sample direct samp_collect_point 0..1 SampCollectPointEnum Sampling point on the asset were sample was collected (e direct samp_dis_stage 0..1 SampDisStageEnum Stage of the disease at the time of sample collection, e direct samp_floor 0..1 SampFloorEnum The floor of the building, where the sampling room is located direct samp_loc_corr_rate 0..1 TextValue Metal corrosion rate is the speed of metal deterioration due to environmental... direct samp_mat_process 0..1 ControlledTermValue A brief description of any processing applied to the sample during or after r... direct samp_md 0..1 QuantityValue In non deviated well, measured depth is equal to the true vertical depth, TVD... direct samp_name 0..1 String A local identifier or name that for the material sample used for extracting n... direct samp_preserv 0..1 TextValue Preservative added to the sample (e direct samp_room_id 0..1 TextValue Sampling room number direct samp_size 0..1 QuantityValue The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... direct samp_sort_meth * TextValue Method by which samples are sorted; open face filter collecting total suspend... direct samp_store_dur 0..1 TextValue Duration for which the sample was stored direct samp_store_loc 0..1 TextValue Location at which sample was stored, usually name of a specific freezer/room direct samp_store_temp 0..1 QuantityValue Temperature at which sample was stored, e direct samp_subtype 0..1 SampSubtypeEnum Name of sample sub-type direct samp_taxon_id 0..1 ControlledIdentifiedTermValue NCBI taxon id of the sample direct samp_time_out 0..1 TextValue The recent and long term history of outside sampling direct samp_transport_cond 0..1 TextValue Sample transport duration (in days or hrs) and temperature the sample was exp... direct samp_tvdss 0..1 TextValue Depth of the sample i direct samp_type 0..1 TextValue The type of material from which the sample was obtained direct samp_weather 0..1 SampWeatherEnum The weather on the sampling day direct samp_well_name 0..1 TextValue Name of the well (e direct saturates_pc 0..1 TextValue Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... direct season 0..1 TextValue The season when sampling occurred direct season_environment * TextValue Treatment involving an exposure to a particular season (e direct season_precpt 0..1 QuantityValue The average of all seasonal precipitation values known, or an estimated equiv... direct season_temp 0..1 QuantityValue Mean seasonal temperature direct season_use 0..1 SeasonUseEnum The seasons the space is occupied direct secondary_treatment 0..1 TextValue The process for substantially degrading the biological content of the sewage direct sediment_type 0..1 SedimentTypeEnum Information about the sediment type based on major constituents direct sequencing_field 0..1 String direct sewage_type 0..1 TextValue Type of wastewater treatment plant as municipial or industrial direct shad_dev_water_mold 0..1 String Signs of the presence of mold or mildew on the shading device direct shading_device_cond 0..1 ShadingDeviceCondEnum The physical condition of the shading device at the time of sampling direct shading_device_loc 0..1 TextValue The location of the shading device in relation to the built structure direct shading_device_mat 0..1 TextValue The material the shading device is composed of direct shading_device_type 0..1 ShadingDeviceTypeEnum The type of shading device direct sieving 0..1 TextValue Collection design of pooled samples and/or sieve size and amount of sample si... direct silicate 0..1 QuantityValue Concentration of silicate direct size_frac 0..1 TextValue Filtering pore size used in sample preparation direct size_frac_low 0..1 QuantityValue Refers to the mesh/pore size used to pre-filter/pre-sort the sample direct size_frac_up 0..1 QuantityValue Refers to the mesh/pore size used to retain the sample direct slope_aspect 0..1 QuantityValue The direction a slope faces direct slope_gradient 0..1 QuantityValue Commonly called 'slope' direct sludge_retent_time 0..1 QuantityValue The time activated sludge remains in reactor direct sodium 0..1 QuantityValue Sodium concentration in the sample direct soil_horizon 0..1 SoilHorizonEnum Specific layer in the land area which measures parallel to the soil surface a... direct soil_text_measure 0..1 QuantityValue The relative proportion of different grain sizes of mineral particles in a so... direct soil_texture_meth 0..1 String Reference or method used in determining soil texture direct soil_type 0..1 TextValue Description of the soil type or classification direct soil_type_meth 0..1 TextValue Reference or method used in determining soil series name or other lower-level... direct solar_irradiance 0..1 QuantityValue The amount of solar energy that arrives at a specific area of a surface durin... direct soluble_inorg_mat * TextValue Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... direct soluble_org_mat * TextValue Concentration of substances such as urea, fruit sugars, soluble proteins, dru... direct soluble_react_phosp 0..1 QuantityValue Concentration of soluble reactive phosphorus direct source_mat_id 0..1 TextValue A globally unique identifier assigned to the biological sample direct space_typ_state 0..1 TextValue Customary or normal state of the space direct specific 0..1 SpecificEnum The building specifications direct specific_ecosystem 0..1 String Specific ecosystems represent specific features of the environment like aphot... direct specific_humidity 0..1 QuantityValue The mass of water vapour in a unit mass of moist air, usually expressed as gr... direct sr_dep_env 0..1 SrDepEnvEnum Source rock depositional environment (https://en direct sr_geol_age 0..1 SrGeolAgeEnum Geological age of source rock (Additional info: https://en direct sr_kerog_type 0..1 SrKerogTypeEnum Origin of kerogen direct sr_lithology 0..1 SrLithologyEnum Lithology of source rock (https://en direct standing_water_regm * TextValue Treatment involving an exposure to standing water during a plant's life span,... direct store_cond 0..1 TextValue Explain how and for how long the soil sample was stored before DNA extraction... direct substructure_type * SubstructureTypeEnum The substructure or under building is that largely hidden section of the buil... direct sulfate 0..1 QuantityValue Concentration of sulfate in the sample direct sulfate_fw 0..1 QuantityValue Original sulfate concentration in the hydrocarbon resource direct sulfide 0..1 QuantityValue Concentration of sulfide in the sample direct surf_air_cont * SurfAirContEnum Contaminant identified on surface direct surf_humidity 0..1 QuantityValue Surfaces: water activity as a function of air and material moisture direct surf_material 0..1 SurfMaterialEnum Surface materials at the point of sampling direct surf_moisture 0..1 QuantityValue Water held on a surface direct surf_moisture_ph 0..1 Double ph measurement of surface direct surf_temp 0..1 QuantityValue Temperature of the surface at the time of sampling direct suspend_part_matter 0..1 QuantityValue Concentration of suspended particulate matter direct suspend_solids * TextValue Concentration of substances including a wide variety of material, such as sil... direct tan 0..1 QuantityValue Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by th... direct temp 0..1 QuantityValue Temperature of the sample at the time of sampling direct temp_out 0..1 QuantityValue The recorded temperature value at sampling time outside direct tertiary_treatment 0..1 TextValue The process providing a final treatment stage to raise the effluent quality b... direct tidal_stage 0..1 TidalStageEnum Stage of tide direct tillage * TillageEnum Note method(s) used for tilling direct tiss_cult_growth_med 0..1 TextValue Description of plant tissue culture growth media used direct toluene 0..1 QuantityValue Concentration of toluene in the sample direct tot_carb 0..1 QuantityValue Total carbon content direct tot_depth_water_col 0..1 QuantityValue Measurement of total depth of water column direct tot_diss_nitro 0..1 QuantityValue Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... direct tot_inorg_nitro 0..1 QuantityValue Total inorganic nitrogen content direct tot_iron 0..1 QuantityValue Concentration of total iron in the sample direct tot_nitro 0..1 QuantityValue Total nitrogen concentration of water samples, calculated by: total nitrogen ... direct tot_nitro_cont_meth 0..1 String Reference or method used in determining the total nitrogen direct tot_nitro_content 0..1 QuantityValue Total nitrogen content of the sample direct tot_org_c_meth 0..1 TextValue Reference or method used in determining total organic carbon direct tot_org_carb 0..1 QuantityValue Definition for soil: total organic carbon content of the soil, definition oth... direct tot_part_carb 0..1 QuantityValue Total particulate carbon content direct tot_phosp 0..1 QuantityValue Total phosphorus concentration in the sample, calculated by: total phosphorus... direct tot_phosphate 0..1 QuantityValue Total amount or concentration of phosphate direct tot_sulfur 0..1 QuantityValue Concentration of total sulfur in the sample direct train_line 0..1 TrainLineEnum The subway line name direct train_stat_loc 0..1 TrainStatLocEnum The train station collection location direct train_stop_loc 0..1 TrainStopLocEnum The train stop collection location direct turbidity 0..1 QuantityValue Measure of the amount of cloudiness or haziness in water caused by individual... direct tvdss_of_hcr_press 0..1 QuantityValue True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... direct tvdss_of_hcr_temp 0..1 QuantityValue True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... direct typ_occup_density 0..1 Double Customary or normal density of occupants direct ventilation_rate 0..1 QuantityValue Ventilation rate of the system in the sampled premises direct ventilation_type 0..1 TextValue Ventilation system used in the sampled premises direct vfa 0..1 QuantityValue Concentration of Volatile Fatty Acids in the sample direct vfa_fw 0..1 QuantityValue Original volatile fatty acid concentration in the hydrocarbon resource direct vis_media 0..1 VisMediaEnum The building visual media direct viscosity 0..1 TextValue A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020t... direct volatile_org_comp * TextValue Concentration of carbon-based chemicals that easily evaporate at room tempera... direct wall_area 0..1 QuantityValue The total area of the sampled room's walls direct wall_const_type 0..1 WallConstTypeEnum The building class of the wall defined by the composition of the building ele... direct wall_finish_mat 0..1 WallFinishMatEnum The material utilized to finish the outer most layer of the wall direct wall_height 0..1 QuantityValue The average height of the walls in the sampled room direct wall_loc 0..1 WallLocEnum The relative location of the wall within the room direct wall_surf_treatment 0..1 WallSurfTreatmentEnum The surface treatment of interior wall direct wall_texture 0..1 WallTextureEnum The feel, appearance, or consistency of a wall surface direct wall_thermal_mass 0..1 QuantityValue The ability of the wall to provide inertia against temperature fluctuations direct wall_water_mold 0..1 TextValue Signs of the presence of mold or mildew on a wall direct wastewater_type 0..1 TextValue The origin of wastewater such as human waste, rainfall, storm drains, etc direct water_cont_soil_meth 0..1 String Reference or method used in determining the water content of soil direct water_content * String Water content measurement direct water_current 0..1 QuantityValue Measurement of magnitude and direction of flow within a fluid direct water_cut 0..1 QuantityValue Current amount of water (%) in a produced fluid stream; or the average of the... direct water_feat_size 0..1 QuantityValue The size of the water feature direct water_feat_type 0..1 WaterFeatTypeEnum The type of water feature present within the building being sampled direct water_prod_rate 0..1 QuantityValue Water production rates per well (e direct water_temp_regm * TextValue Information about treatment involving an exposure to water with varying degre... direct watering_regm * TextValue Information about treatment involving an exposure to watering frequencies, tr... direct weekday 0..1 WeekdayEnum The day of the week when sampling occurred direct win 0..1 TextValue A unique identifier of a well or wellbore direct wind_direction 0..1 TextValue Wind direction is the direction from which a wind originates direct wind_speed 0..1 QuantityValue Speed of wind measured at the time of sampling direct window_cond 0..1 WindowCondEnum The physical condition of the window at the time of sampling direct window_cover 0..1 WindowCoverEnum The type of window covering direct window_horiz_pos 0..1 WindowHorizPosEnum The horizontal position of the window on the wall direct window_loc 0..1 WindowLocEnum The relative location of the window within the room direct window_mat 0..1 WindowMatEnum The type of material used to finish a window direct window_open_freq 0..1 TextValue The number of times windows are opened per week direct window_size 0..1 TextValue The window's length and width direct window_status 0..1 TextValue Defines whether the windows were open or closed during environmental testing direct window_type 0..1 WindowTypeEnum The type of windows direct window_vert_pos 0..1 WindowVertPosEnum The vertical position of the window on the wall direct window_water_mold 0..1 TextValue Signs of the presence of mold or mildew on the window direct xylene 0..1 QuantityValue Concentration of xylene in the sample direct zinc 0..1 QuantityValue Concentration of zinc in the sample direct ecosystem 0..1 String An ecosystem is a combination of a physical environment (abiotic factors) and... direct ecosystem_category 0..1 String Ecosystem categories represent divisions within the ecosystem based on specif... direct ecosystem_type 0..1 String Ecosystem types represent things having common characteristics within the Eco... direct ecosystem_subtype 0..1 String Ecosystem subtypes represent further subdivision of Ecosystem types into more... direct specific_ecosystem 0..1 String Specific ecosystems represent specific features of the environment like aphot... direct add_date 0..1 String The date on which the information was added to the database direct community 0..1 String direct habitat 0..1 String direct host_name 0..1 String direct location 0..1 String direct mod_date 0..1 String The last date on which the database information was modified direct ncbi_taxonomy_name 0..1 String direct proport_woa_temperature 0..1 String direct salinity_category 0..1 String Categorical description of the sample's salinity direct sample_collection_site 0..1 String direct soluble_iron_micromol 0..1 String direct subsurface_depth 0..1 QuantityValue direct air_temp_regm * TextValue Information about treatment involving an exposure to varying temperatures; sh... direct biotic_regm 0..1 TextValue Information about treatment(s) involving use of biotic factors, such as bacte... direct biotic_relationship 0..1 BioticRelationshipEnum Description of relationship(s) between the subject organism and other organis... direct climate_environment * TextValue Treatment involving an exposure to a particular climate; treatment regimen in... direct experimental_factor 0..1 ControlledTermValue Experimental factors are essentially the variable aspects of an experiment de... direct gaseous_environment * TextValue Use of conditions with differing gaseous environments; should include the nam... direct growth_facil 0..1 ControlledTermValue Type of facility where the sampled plant was grown; controlled vocabulary: gr... direct humidity_regm * TextValue Information about treatment involving an exposure to varying degree of humidi... direct light_regm 0..1 TextValue Information about treatment(s) involving exposure to light, including both li... direct phosphate 0..1 QuantityValue Concentration of phosphate direct samp_collec_method 0..1 String The method employed for collecting the sample direct samp_size 0..1 QuantityValue The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... direct source_mat_id 0..1 TextValue A globally unique identifier assigned to the biological sample direct watering_regm * TextValue Information about treatment involving an exposure to watering frequencies, tr... direct dna_absorb1 0..1 recommended Float 260/280 measurement of DNA sample purity direct dna_absorb2 0..1 recommended Float 260/230 measurement of DNA sample purity direct dna_collect_site 0..1 recommended String Provide information on the site your DNA sample was collected from direct dna_concentration 0..1 recommended Float direct dna_cont_type 0..1 recommended JgiContTypeEnum Tube or plate (96-well) direct dna_cont_well 0..1 recommended String direct dna_container_id 0..1 recommended String direct dna_dnase 0..1 recommended YesNoEnum direct dna_isolate_meth 0..1 recommended String Describe the method/protocol/kit used to extract DNA/RNA direct dna_organisms 0..1 recommended String List any organisms known or suspected to grow in co-culture, as well as estim... direct dna_project_contact 0..1 recommended String direct dna_samp_id 0..1 recommended String direct dna_sample_format 0..1 recommended DNASampleFormatEnum Solution in which the DNA sample has been suspended direct dna_sample_name 0..1 recommended String Give the DNA sample a name that is meaningful to you direct dna_seq_project 0..1 recommended String direct dna_seq_project_pi 0..1 recommended String direct dna_seq_project_name 0..1 recommended String direct dna_volume 0..1 recommended Float direct proposal_dna 0..1 recommended String direct dnase_rna 0..1 recommended YesNoEnum direct proposal_rna 0..1 recommended String direct rna_absorb1 0..1 recommended Float 260/280 measurement of RNA sample purity direct rna_absorb2 0..1 recommended Float 260/230 measurement of RNA sample purity direct rna_collect_site 0..1 recommended String Provide information on the site your RNA sample was collected from direct rna_concentration 0..1 recommended Float direct rna_cont_type 0..1 recommended JgiContTypeEnum Tube or plate (96-well) direct rna_cont_well 0..1 recommended String direct rna_container_id 0..1 recommended String direct rna_isolate_meth 0..1 recommended String Describe the method/protocol/kit used to extract DNA/RNA direct rna_organisms 0..1 recommended String List any organisms known or suspected to grow in co-culture, as well as estim... direct rna_project_contact 0..1 recommended String direct rna_samp_id 0..1 recommended String direct rna_sample_format 0..1 recommended RNASampleFormatEnum Solution in which the RNA sample has been suspended direct rna_sample_name 0..1 recommended String Give the RNA sample a name that is meaningful to you direct rna_seq_project 0..1 recommended String direct rna_seq_project_pi 0..1 recommended String direct rna_seq_project_name 0..1 recommended String direct rna_volume 0..1 recommended Float direct collection_date_inc 0..1 recommended String Date the incubation was harvested/collected/ended direct collection_time 0..1 recommended String The time of sampling, either as an instance (single point) or interval direct collection_time_inc 0..1 recommended String Time the incubation was harvested/collected/ended direct experimental_factor_other 0..1 recommended String Other details about your sample that you feel can't be accurately represented... direct filter_method 0..1 recommended String Type of filter used or how the sample was filtered direct isotope_exposure 0..1 recommended String List isotope exposure or addition applied to your sample direct micro_biomass_c_meth 0..1 recommended String Reference or method used in determining microbial biomass carbon direct micro_biomass_n_meth 0..1 String Reference or method used in determining microbial biomass nitrogen direct microbial_biomass_c 0..1 String The part of the organic matter in the soil that constitutes living microorgan... direct microbial_biomass_n 0..1 String The part of the organic matter in the soil that constitutes living microorgan... direct non_microb_biomass 0..1 String Amount of biomass; should include the name for the part of biomass measured, ... direct non_microb_biomass_method 0..1 String Reference or method used in determining biomass direct org_nitro_method 0..1 String Method used for obtaining organic nitrogen direct other_treatment 0..1 recommended String Other treatments applied to your samples that are not applicable to the provi... direct start_date_inc 0..1 recommended String Date the incubation was started direct start_time_inc 0..1 recommended String Time the incubation was started direct project_id 0..1 recommended String Proposal IDs or names associated with dataset direct replicate_number 0..1 recommended String If sending biological replicates, indicate the rep number here direct sample_shipped 0..1 recommended String The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... direct sample_type 0..1 recommended SampleTypeEnum Type of sample being submitted direct technical_reps 0..1 recommended String If sending technical replicates of the same sample, indicate the replicate co... direct analysis_type * recommended AnalysisTypeEnum Select all the data types associated or available for this biosample direct sample_link * recommended String A unique identifier to assign parent-child, subsample, or sibling samples direct bulk_elect_conductivity 0..1 QuantityValue Electrical conductivity is a measure of the ability to carry electric current... direct infiltrations * String The amount of time it takes to complete each infiltration activity direct zinc 0..1 QuantityValue Concentration of zinc in the sample direct manganese 0..1 QuantityValue Concentration of manganese in the sample direct ammonium_nitrogen 0..1 QuantityValue Concentration of ammonium nitrogen in the sample direct nitrate_nitrogen 0..1 QuantityValue Concentration of nitrate nitrogen in the sample direct nitrite_nitrogen 0..1 QuantityValue Concentration of nitrite nitrogen in the sample direct lbc_thirty 0..1 QuantityValue lime buffer capacity, determined after 30 minute incubation direct lbceq 0..1 QuantityValue lime buffer capacity, determined at equilibrium after 5 day incubation direct id 1 Uriorcurie An NMDC assigned unique identifier for a biosample submitted to NMDC NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie Unique identifier for a biosample submitted to additional resources NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Biosample/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_input any_of[range] Biosample MassSpectrometry has_input any_of[range] Biosample Database biosample_set range Biosample Pooling has_input any_of[range] Biosample Extraction has_input any_of[range] Biosample LibraryPreparation has_input any_of[range] Biosample CollectingBiosamplesFromSite has_output range Biosample SubSamplingProcess has_input any_of[range] Biosample MixingProcess has_input any_of[range] Biosample FiltrationProcess has_input any_of[range] Biosample ChromatographicSeparationProcess has_input any_of[range] Biosample DissolvingProcess has_input any_of[range] Biosample ChemicalConversionProcess has_input any_of[range] Biosample MaterialProcessing has_input any_of[range] Biosample DataGeneration has_input any_of[range] Biosample"},{"location":"Biosample/#aliases","title":"Aliases","text":""},{"location":"Biosample/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Biosample/#schema-source","title":"Schema Source","text":""},{"location":"Biosample/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Biosample native nmdc:Biosample exact OBI:0000747, NCIT:C43412, http://purl.obolibrary.org/obo/FBcv_0003024"},{"location":"Biosample/#linkml-source","title":"LinkML Source","text":""},{"location":"Biosample/#direct","title":"Direct","text":"
name: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: A sample contains information about the sequenced source material.\n      Samples are associated with checklists, which define the fields used to annotate\n      the samples. Samples are always associated with a taxon.\nnotes:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: MaterialEntity\nslots:\n- associated_studies\n- biosample_categories\n- collected_from\n- embargoed\n- host_disease_stat\n- host_taxid\n- img_identifiers\n- neon_biosample_identifiers\n- samp_name\n- gold_biosample_identifiers\n- insdc_biosample_identifiers\n- emsl_biosample_identifiers\n- igsn_biosample_identifiers\n- abs_air_humidity\n- add_recov_method\n- additional_info\n- address\n- adj_room\n- aero_struc\n- agrochem_addition\n- air_PM_concen\n- air_temp\n- air_temp_regm\n- al_sat\n- al_sat_meth\n- alkalinity\n- alkalinity_method\n- alkyl_diethers\n- alt\n- aminopept_act\n- ammonium\n- ammonium_nitrogen\n- amount_light\n- ances_data\n- annual_precpt\n- annual_temp\n- antibiotic_regm\n- api\n- arch_struc\n- aromatics_pc\n- asphaltenes_pc\n- atmospheric_data\n- avg_dew_point\n- avg_occup\n- avg_temp\n- bac_prod\n- bac_resp\n- bacteria_carb_prod\n- barometric_press\n- basin\n- bathroom_count\n- bedroom_count\n- benzene\n- biochem_oxygen_dem\n- biocide\n- biocide_admin_method\n- biol_stat\n- biomass\n- biotic_regm\n- biotic_relationship\n- bishomohopanol\n- blood_press_diast\n- blood_press_syst\n- bromide\n- build_docs\n- build_occup_type\n- building_setting\n- built_struc_age\n- built_struc_set\n- built_struc_type\n- calcium\n- carb_dioxide\n- carb_monoxide\n- carb_nitro_ratio\n- ceil_area\n- ceil_cond\n- ceil_finish_mat\n- ceil_struc\n- ceil_texture\n- ceil_thermal_mass\n- ceil_type\n- ceil_water_mold\n- chem_administration\n- chem_mutagen\n- chem_oxygen_dem\n- chem_treat_method\n- chem_treatment\n- chloride\n- chlorophyll\n- climate_environment\n- collection_date\n- conduc\n- cool_syst_id\n- core field\n- crop_rotation\n- cult_root_med\n- cur_land_use\n- cur_vegetation\n- cur_vegetation_meth\n- date_last_rain\n- density\n- depos_env\n- depth\n- dew_point\n- diether_lipids\n- diss_carb_dioxide\n- diss_hydrogen\n- diss_inorg_carb\n- diss_inorg_nitro\n- diss_inorg_phosp\n- diss_iron\n- diss_org_carb\n- diss_org_nitro\n- diss_oxygen\n- diss_oxygen_fluid\n- dna_cont_well\n- door_comp_type\n- door_cond\n- door_direct\n- door_loc\n- door_mat\n- door_move\n- door_size\n- door_type\n- door_type_metal\n- door_type_wood\n- door_water_mold\n- down_par\n- drainage_class\n- drawings\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- efficiency_percent\n- elev\n- elevator\n- emulsions\n- env_broad_scale\n- env_local_scale\n- env_medium\n- env_package\n- environment field\n- escalator\n- ethylbenzene\n- exp_duct\n- exp_pipe\n- experimental_factor\n- ext_door\n- ext_wall_orient\n- ext_window_orient\n- extreme_event\n- fao_class\n- fertilizer_regm\n- field\n- filter_type\n- fire\n- fireplace_type\n- flooding\n- floor_age\n- floor_area\n- floor_cond\n- floor_count\n- floor_finish_mat\n- floor_struc\n- floor_thermal_mass\n- floor_water_mold\n- fluor\n- freq_clean\n- freq_cook\n- fungicide_regm\n- furniture\n- gaseous_environment\n- gaseous_substances\n- gender_restroom\n- genetic_mod\n- geo_loc_name\n- glucosidase_act\n- gravidity\n- gravity\n- growth_facil\n- growth_habit\n- growth_hormone_regm\n- hall_count\n- handidness\n- hc_produced\n- hcr\n- hcr_fw_salinity\n- hcr_geol_age\n- hcr_pressure\n- hcr_temp\n- heat_cool_type\n- heat_deliv_loc\n- heat_sys_deliv_meth\n- heat_system_id\n- heavy_metals\n- heavy_metals_meth\n- height_carper_fiber\n- herbicide_regm\n- horizon_meth\n- host_age\n- host_body_habitat\n- host_body_product\n- host_body_site\n- host_body_temp\n- host_color\n- host_common_name\n- host_diet\n- host_dry_mass\n- host_family_relation\n- host_genotype\n- host_growth_cond\n- host_height\n- host_last_meal\n- host_length\n- host_life_stage\n- host_phenotype\n- host_sex\n- host_shape\n- host_subject_id\n- host_subspecf_genlin\n- host_substrate\n- host_symbiont\n- host_taxid\n- host_tot_mass\n- host_wet_mass\n- humidity\n- humidity_regm\n- indoor_space\n- indoor_surf\n- indust_eff_percent\n- inorg_particles\n- inside_lux\n- int_wall_cond\n- investigation field\n- iw_bt_date_well\n- iwf\n- last_clean\n- lat_lon\n- lbc_thirty\n- lbceq\n- light_intensity\n- light_regm\n- light_type\n- link_addit_analys\n- link_class_info\n- link_climate_info\n- lithology\n- local_class\n- local_class_meth\n- magnesium\n- manganese\n- max_occup\n- mean_frict_vel\n- mean_peak_frict_vel\n- mech_struc\n- mechanical_damage\n- methane\n- micro_biomass_meth\n- microbial_biomass\n- mineral_nutr_regm\n- misc_param\n- n_alkanes\n- nitrate\n- nitrate_nitrogen\n- nitrite\n- nitrite_nitrogen\n- nitro\n- non_min_nutr_regm\n- nucleic acid sequence source field\n- number_pets\n- number_plants\n- number_resident\n- occup_density_samp\n- occup_document\n- occup_samp\n- org_carb\n- org_count_qpcr_info\n- org_matter\n- org_nitro\n- org_particles\n- organism_count\n- owc_tvdss\n- oxy_stat_samp\n- oxygen\n- part_org_carb\n- part_org_nitro\n- particle_class\n- permeability\n- perturbation\n- pesticide_regm\n- petroleum_hydrocarb\n- ph\n- ph_meth\n- ph_regm\n- phaeopigments\n- phosphate\n- phosplipid_fatt_acid\n- photon_flux\n- plant_growth_med\n- plant_product\n- plant_sex\n- plant_struc\n- pollutants\n- porosity\n- potassium\n- pour_point\n- pre_treatment\n- pres_animal_insect\n- pressure\n- prev_land_use_meth\n- previous_land_use\n- primary_prod\n- primary_treatment\n- prod_rate\n- prod_start_date\n- profile_position\n- quad_pos\n- radiation_regm\n- rainfall_regm\n- reactor_type\n- redox_potential\n- rel_air_humidity\n- rel_humidity_out\n- rel_samp_loc\n- reservoir\n- resins_pc\n- room_air_exch_rate\n- room_architec_elem\n- room_condt\n- room_connected\n- room_count\n- room_dim\n- room_door_dist\n- room_door_share\n- room_hallway\n- room_loc\n- room_moist_dam_hist\n- room_net_area\n- room_occup\n- room_samp_pos\n- room_type\n- room_vol\n- room_wall_share\n- room_window_count\n- root_cond\n- root_med_carbon\n- root_med_macronutr\n- root_med_micronutr\n- root_med_ph\n- root_med_regl\n- root_med_solid\n- root_med_suppl\n- salinity\n- salinity_meth\n- salt_regm\n- samp_capt_status\n- samp_collec_device\n- samp_collec_method\n- samp_collect_point\n- samp_dis_stage\n- samp_floor\n- samp_loc_corr_rate\n- samp_mat_process\n- samp_md\n- samp_name\n- samp_preserv\n- samp_room_id\n- samp_size\n- samp_sort_meth\n- samp_store_dur\n- samp_store_loc\n- samp_store_temp\n- samp_subtype\n- samp_taxon_id\n- samp_time_out\n- samp_transport_cond\n- samp_tvdss\n- samp_type\n- samp_weather\n- samp_well_name\n- saturates_pc\n- season\n- season_environment\n- season_precpt\n- season_temp\n- season_use\n- secondary_treatment\n- sediment_type\n- sequencing field\n- sewage_type\n- shad_dev_water_mold\n- shading_device_cond\n- shading_device_loc\n- shading_device_mat\n- shading_device_type\n- sieving\n- silicate\n- size_frac\n- size_frac_low\n- size_frac_up\n- slope_aspect\n- slope_gradient\n- sludge_retent_time\n- sodium\n- soil_horizon\n- soil_text_measure\n- soil_texture_meth\n- soil_type\n- soil_type_meth\n- solar_irradiance\n- soluble_inorg_mat\n- soluble_org_mat\n- soluble_react_phosp\n- source_mat_id\n- space_typ_state\n- specific\n- specific_ecosystem\n- specific_humidity\n- sr_dep_env\n- sr_geol_age\n- sr_kerog_type\n- sr_lithology\n- standing_water_regm\n- store_cond\n- substructure_type\n- sulfate\n- sulfate_fw\n- sulfide\n- surf_air_cont\n- surf_humidity\n- surf_material\n- surf_moisture\n- surf_moisture_ph\n- surf_temp\n- suspend_part_matter\n- suspend_solids\n- tan\n- temp\n- temp_out\n- tertiary_treatment\n- tidal_stage\n- tillage\n- tiss_cult_growth_med\n- toluene\n- tot_carb\n- tot_depth_water_col\n- tot_diss_nitro\n- tot_inorg_nitro\n- tot_iron\n- tot_nitro\n- tot_nitro_cont_meth\n- tot_nitro_content\n- tot_org_c_meth\n- tot_org_carb\n- tot_part_carb\n- tot_phosp\n- tot_phosphate\n- tot_sulfur\n- train_line\n- train_stat_loc\n- train_stop_loc\n- turbidity\n- tvdss_of_hcr_press\n- tvdss_of_hcr_temp\n- typ_occup_density\n- ventilation_rate\n- ventilation_type\n- vfa\n- vfa_fw\n- vis_media\n- viscosity\n- volatile_org_comp\n- wall_area\n- wall_const_type\n- wall_finish_mat\n- wall_height\n- wall_loc\n- wall_surf_treatment\n- wall_texture\n- wall_thermal_mass\n- wall_water_mold\n- wastewater_type\n- water_cont_soil_meth\n- water_content\n- water_current\n- water_cut\n- water_feat_size\n- water_feat_type\n- water_prod_rate\n- water_temp_regm\n- watering_regm\n- weekday\n- win\n- wind_direction\n- wind_speed\n- window_cond\n- window_cover\n- window_horiz_pos\n- window_loc\n- window_mat\n- window_open_freq\n- window_size\n- window_status\n- window_type\n- window_vert_pos\n- window_water_mold\n- xylene\n- zinc\n- ecosystem\n- ecosystem_category\n- ecosystem_type\n- ecosystem_subtype\n- specific_ecosystem\n- add_date\n- community\n- habitat\n- host_name\n- location\n- mod_date\n- ncbi_taxonomy_name\n- proport_woa_temperature\n- salinity_category\n- sample_collection_site\n- soluble_iron_micromol\n- subsurface_depth\n- air_temp_regm\n- biotic_regm\n- biotic_relationship\n- climate_environment\n- experimental_factor\n- gaseous_environment\n- growth_facil\n- humidity_regm\n- light_regm\n- phosphate\n- samp_collec_method\n- samp_size\n- source_mat_id\n- watering_regm\n- dna_absorb1\n- dna_absorb2\n- dna_collect_site\n- dna_concentration\n- dna_cont_type\n- dna_cont_well\n- dna_container_id\n- dna_dnase\n- dna_isolate_meth\n- dna_organisms\n- dna_project_contact\n- dna_samp_id\n- dna_sample_format\n- dna_sample_name\n- dna_seq_project\n- dna_seq_project_pi\n- dna_seq_project_name\n- dna_volume\n- proposal_dna\n- dnase_rna\n- proposal_rna\n- rna_absorb1\n- rna_absorb2\n- rna_collect_site\n- rna_concentration\n- rna_cont_type\n- rna_cont_well\n- rna_container_id\n- rna_isolate_meth\n- rna_organisms\n- rna_project_contact\n- rna_samp_id\n- rna_sample_format\n- rna_sample_name\n- rna_seq_project\n- rna_seq_project_pi\n- rna_seq_project_name\n- rna_volume\n- collection_date_inc\n- collection_time\n- collection_time_inc\n- experimental_factor_other\n- filter_method\n- isotope_exposure\n- micro_biomass_c_meth\n- micro_biomass_n_meth\n- microbial_biomass_c\n- microbial_biomass_n\n- non_microb_biomass\n- non_microb_biomass_method\n- org_nitro_method\n- other_treatment\n- start_date_inc\n- start_time_inc\n- project_id\n- replicate_number\n- sample_shipped\n- sample_type\n- technical_reps\n- analysis_type\n- sample_link\n- bulk_elect_conductivity\n- infiltrations\n- zinc\n- manganese\n- ammonium_nitrogen\n- nitrate_nitrogen\n- nitrite_nitrogen\n- lbc_thirty\n- lbceq\nslot_usage:\n  collected_from:\n    name: collected_from\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  elev:\n    name: elev\n    title: elevation, meters\n    comments:\n    - All elevations must be reported in meters. Provide the numerical portion only.\n    - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n      if needed, to help estimate the elevation based on latitude and longitude coordinates.\n    examples:\n    - value: '100'\n    range: float\n  id:\n    name: id\n    description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_biosample_identifiers:\n    name: gold_biosample_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the GOLD biosample IDs associated with this biosample.\n    description: Unique identifier for a biosample submitted to GOLD that matches\n      the NMDC submitted biosample\n    comments:\n    - This is the ID provided by GOLD that starts with 'GB'\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a biosample submitted to additional resources.\n      Matches the entity that has been submitted to NMDC\n  lat_lon:\n    name: lat_lon\n    notes:\n    - This is currently a required field but it's not clear if this should be required\n      for human hosts\n  env_broad_scale:\n    name: env_broad_scale\n    required: true\n  env_local_scale:\n    name: env_local_scale\n    required: true\n  env_medium:\n    name: env_medium\n    required: true\n  associated_studies:\n    name: associated_studies\n    range: Study\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  fire:\n    name: fire\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    comments:\n    - Provide the date the fire occurred. If extended burning occurred provide the\n      date range.\n    examples:\n    - value: '1871-10-10'\n    - value: 1871-10-01 to 1871-10-31\n    range: string\n    pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n  flooding:\n    name: flooding\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    - What about if the \"day\" isn't known? Is this ok?\n    comments:\n    - Provide the date the flood occurred. If extended flooding occurred provide the\n      date range.\n    examples:\n    - value: '1927-04-15'\n    - value: 1927-04 to 1927-05\n    range: string\n  extreme_event:\n    name: extreme_event\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date, string\n    examples:\n    - value: 1980-05-18, volcanic eruption\n    range: string\n  slope_aspect:\n    name: slope_aspect\n    description: The direction a slope faces. While looking down a slope use a compass\n      to record the direction you are facing (direction or degrees). This measure\n      provides an indication of sun and wind exposure that will influence soil temperature\n      and evapotranspiration.\n    comments:\n    - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n      360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n      is west-facing.\n    examples:\n    - value: '35'\n  slope_gradient:\n    name: slope_gradient\n    todos:\n    - Slope is a percent. How does the validation work? Check to correct examples\n    examples:\n    - value: 10%\n    - value: 10 %\n    - value: '0.10'\n  al_sat:\n    name: al_sat\n    description: The relative abundance of aluminum in the sample\n    title: aluminum saturation/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    notes:\n    - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n      all cations, aluminum held by the cation exchange complex is in equilibrium\n      with aluminum in the soil solution.\n    examples:\n    - value: 27%\n  al_sat_meth:\n    name: al_sat_meth\n    description: Reference or method used in determining Aluminum saturation\n    title: aluminum saturation method/ extreme unusual properties\n    todos:\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n    comments:\n    - Required when aluminum saturation is provided.\n    examples:\n    - value: https://doi.org/10.1371/journal.pone.0176357\n  annual_precpt:\n    name: annual_precpt\n    examples:\n    - value: 8.94 inch\n  cur_vegetation:\n    name: cur_vegetation\n    description: Vegetation classification from one or more standard classification\n      systems, or agricultural crop\n    todos:\n    - Recommend changing this from text value to some king of ontology?\n    comments:\n    - Values provided here can be specific species of vegetation or vegetation regions\n    - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n    examples:\n    - value: deciduous forest\n    - value: forest\n    - value: Bauhinia variegata\n  cur_vegetation_meth:\n    name: cur_vegetation_meth\n    todos:\n    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n      out how they accomplish this if provided.\n    comments:\n    - Required when current vegetation is provided.\n    examples:\n    - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n  heavy_metals:\n    name: heavy_metals\n    description: Heavy metals present in the sample and their concentrations.\n    title: heavy metals/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    comments:\n    - For multiple heavy metals and concentrations, separate by ;\n    examples:\n    - value: mercury 0.09 micrograms per gram\n    - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n  heavy_metals_meth:\n    name: heavy_metals_meth\n    title: heavy metals method/ extreme unusual properties\n    comments:\n    - Required when heavy metals are provided\n    - If different methods are used for multiple metals, indicate the metal and method.\n      Separate metals by ;\n    examples:\n    - value: https://doi.org/10.3390/ijms9040434\n    - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n    multivalued: true\n  season_precpt:\n    name: season_precpt\n    title: average seasonal precipitation\n    todos:\n    - check validation & examples. always mm? so value only? Or value + unit\n    notes:\n    - mean and average are the same thing, but it seems like bad practice to not be\n      consistent. Changed mean to average\n    comments:\n    - Seasons are defined as spring (March, April, May), summer (June, July, August),\n      autumn (September, October, November) and winter (December, January, February).\n    examples:\n    - value: 0.4 inch\n    - value: 10.16 mm\n  water_cont_soil_meth:\n    name: water_cont_soil_meth\n    todos:\n    - Why is it soil water content method in the name but not the title? Is this slot\n      used in other samples?\n    - Soil water content can be measure MANY ways and often, multiple ways are used\n      in one experiment (gravimetric water content and water holding capacity and\n      water filled pore space, to name a few).\n    - Should this be multi valued? How to we manage and validate this?\n    comments:\n    - Required if providing water content\n    examples:\n    - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n    - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n  water_content:\n    name: water_content\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: string\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per gram or cubic centimeter per cubic centimeter\n    todos:\n    - value in preferred unit is too limiting. need to change this\n    - check and correct validation so examples are accepted\n    - how to manage multiple water content methods?\n    examples:\n    - value: 0.75 g water/g dry soil\n    - value: 75% water holding capacity\n    - value: 1.1 g fresh weight/ dry weight\n    - value: 10% water filled pore space\n    range: string\n    multivalued: true\n  ph_meth:\n    name: ph_meth\n    comments:\n    - This can include a link to the instrument used or a citation for the method.\n    examples:\n    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n    - value: https://doi.org/10.2136/sssabookser5.3.c16\n  tot_carb:\n    name: tot_carb\n    todos:\n    - is this inorganic and organic? both? could use some clarification.\n    - ug/L doesn't seem like the right units. Should check this slots usage in databases\n      and re-evaluate. I couldn't find any references that provided this data in this\n      format\n    examples:\n    - value: 1 ug/L\n  tot_nitro_cont_meth:\n    name: tot_nitro_cont_meth\n    examples:\n    - value: https://doi.org/10.2134/agronmonogr9.2.c32\n    - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n  tot_nitro_content:\n    name: tot_nitro_content\n    examples:\n    - value: 5 mg N/ L\n  tot_org_c_meth:\n    name: tot_org_c_meth\n    examples:\n    - value: https://doi.org/10.1080/07352680902776556\n  tot_org_carb:\n    name: tot_org_carb\n    todos:\n    - check description. How are they different?\n    examples:\n    - value: 5 mg N/ L\n  salinity_meth:\n    name: salinity_meth\n    examples:\n    - value: https://doi.org/10.1007/978-1-61779-986-0_28\n  sieving:\n    name: sieving\n    todos:\n    - check validation and examples\n    comments:\n    - Describe how samples were composited or sieved.\n    - Use 'sample link' to indicate which samples were combined.\n    examples:\n    - value: combined 2 cores | 4mm sieved\n    - value: 4 mm sieved and homogenized\n    - value: 50 g | 5 cores | 2 mm sieved\n  climate_environment:\n    name: climate_environment\n    todos:\n    - description says \"can include multiple climates\" but multivalued is set to false\n    - add examples, i need to see some examples to add correctly formatted example.\n  gaseous_environment:\n    name: gaseous_environment\n    todos:\n    - would like to see usage examples for this slot. Requiring micromole/L seems\n      too limiting and doesn't match expected_value value\n    - did I do this right? keep the example that's provided and add another? so as\n      to not override\n    examples:\n    - value: CO2; 500ppm above ambient; constant\n    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n  watering_regm:\n    name: watering_regm\n    examples:\n    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    - value: 75% water holding capacity; constant\n  source_mat_id:\n    name: source_mat_id\n    description: A globally unique identifier assigned to the biological sample.\n    title: source material identifier\n    todos:\n    - Currently, the comments say to use UUIDs. However, if we implement assigning\n      NMDC identifiers with the minter we dont need to require a GUID. It can be an\n      optional field to fill out only if they already have a resolvable ID.\n    comments:\n    - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n      NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n      IDs enable linking to derived analytes and subsamples. If you have not assigned\n      FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n    examples:\n    - value: IGSN:AU1243\n    - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\nclass_uri: nmdc:Biosample\nunique_keys:\n  samp_name_unique_key:\n    unique_key_name: samp_name_unique_key\n    unique_key_slots:\n    - samp_name\nrules:\n- preconditions:\n    slot_conditions:\n      dna_cont_well:\n        name: dna_cont_well\n        pattern: .+\n  postconditions:\n    slot_conditions:\n      dna_cont_type:\n        name: dna_cont_type\n        equals_string: plate\n  description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n    have any value for their plate position.\n  title: dna_well_requires_plate\n- preconditions:\n    slot_conditions:\n      dna_cont_type:\n        name: dna_cont_type\n        equals_string: plate\n  postconditions:\n    slot_conditions:\n      dna_cont_well:\n        name: dna_cont_well\n        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  description: DNA samples in plates must have a plate position that matches the regex.\n    Note the requirement for an empty string in the tube case. Waiting for value_present\n    validation to be added to runtime\n  title: dna_plate_requires_well\n- preconditions:\n    slot_conditions:\n      rna_cont_well:\n        name: rna_cont_well\n        pattern: .+\n  postconditions:\n    slot_conditions:\n      rna_cont_type:\n        name: rna_cont_type\n        equals_string: plate\n  description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n    have any value for their plate position.\n  title: rna_well_requires_plate\n- preconditions:\n    slot_conditions:\n      rna_cont_type:\n        name: rna_cont_type\n        equals_string: plate\n  postconditions:\n    slot_conditions:\n      rna_cont_well:\n        name: rna_cont_well\n        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  description: RNA samples in plates must have a plate position that matches the regex.\n    Note the requirement for an empty string in the tube case. Waiting for value_present\n    validation to be added to runtime\n  title: rna_plate_requires_well\n\n
"},{"location":"Biosample/#induced","title":"Induced","text":"
name: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: A sample contains information about the sequenced source material.\n      Samples are associated with checklists, which define the fields used to annotate\n      the samples. Samples are always associated with a taxon.\nnotes:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: MaterialEntity\nslot_usage:\n  collected_from:\n    name: collected_from\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  elev:\n    name: elev\n    title: elevation, meters\n    comments:\n    - All elevations must be reported in meters. Provide the numerical portion only.\n    - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n      if needed, to help estimate the elevation based on latitude and longitude coordinates.\n    examples:\n    - value: '100'\n    range: float\n  id:\n    name: id\n    description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_biosample_identifiers:\n    name: gold_biosample_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the GOLD biosample IDs associated with this biosample.\n    description: Unique identifier for a biosample submitted to GOLD that matches\n      the NMDC submitted biosample\n    comments:\n    - This is the ID provided by GOLD that starts with 'GB'\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a biosample submitted to additional resources.\n      Matches the entity that has been submitted to NMDC\n  lat_lon:\n    name: lat_lon\n    notes:\n    - This is currently a required field but it's not clear if this should be required\n      for human hosts\n  env_broad_scale:\n    name: env_broad_scale\n    required: true\n  env_local_scale:\n    name: env_local_scale\n    required: true\n  env_medium:\n    name: env_medium\n    required: true\n  associated_studies:\n    name: associated_studies\n    range: Study\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  fire:\n    name: fire\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    comments:\n    - Provide the date the fire occurred. If extended burning occurred provide the\n      date range.\n    examples:\n    - value: '1871-10-10'\n    - value: 1871-10-01 to 1871-10-31\n    range: string\n    pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n  flooding:\n    name: flooding\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    - What about if the \"day\" isn't known? Is this ok?\n    comments:\n    - Provide the date the flood occurred. If extended flooding occurred provide the\n      date range.\n    examples:\n    - value: '1927-04-15'\n    - value: 1927-04 to 1927-05\n    range: string\n  extreme_event:\n    name: extreme_event\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date, string\n    examples:\n    - value: 1980-05-18, volcanic eruption\n    range: string\n  slope_aspect:\n    name: slope_aspect\n    description: The direction a slope faces. While looking down a slope use a compass\n      to record the direction you are facing (direction or degrees). This measure\n      provides an indication of sun and wind exposure that will influence soil temperature\n      and evapotranspiration.\n    comments:\n    - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n      360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n      is west-facing.\n    examples:\n    - value: '35'\n  slope_gradient:\n    name: slope_gradient\n    todos:\n    - Slope is a percent. How does the validation work? Check to correct examples\n    examples:\n    - value: 10%\n    - value: 10 %\n    - value: '0.10'\n  al_sat:\n    name: al_sat\n    description: The relative abundance of aluminum in the sample\n    title: aluminum saturation/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    notes:\n    - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n      all cations, aluminum held by the cation exchange complex is in equilibrium\n      with aluminum in the soil solution.\n    examples:\n    - value: 27%\n  al_sat_meth:\n    name: al_sat_meth\n    description: Reference or method used in determining Aluminum saturation\n    title: aluminum saturation method/ extreme unusual properties\n    todos:\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n    comments:\n    - Required when aluminum saturation is provided.\n    examples:\n    - value: https://doi.org/10.1371/journal.pone.0176357\n  annual_precpt:\n    name: annual_precpt\n    examples:\n    - value: 8.94 inch\n  cur_vegetation:\n    name: cur_vegetation\n    description: Vegetation classification from one or more standard classification\n      systems, or agricultural crop\n    todos:\n    - Recommend changing this from text value to some king of ontology?\n    comments:\n    - Values provided here can be specific species of vegetation or vegetation regions\n    - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n    examples:\n    - value: deciduous forest\n    - value: forest\n    - value: Bauhinia variegata\n  cur_vegetation_meth:\n    name: cur_vegetation_meth\n    todos:\n    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n      out how they accomplish this if provided.\n    comments:\n    - Required when current vegetation is provided.\n    examples:\n    - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n  heavy_metals:\n    name: heavy_metals\n    description: Heavy metals present in the sample and their concentrations.\n    title: heavy metals/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    comments:\n    - For multiple heavy metals and concentrations, separate by ;\n    examples:\n    - value: mercury 0.09 micrograms per gram\n    - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n  heavy_metals_meth:\n    name: heavy_metals_meth\n    title: heavy metals method/ extreme unusual properties\n    comments:\n    - Required when heavy metals are provided\n    - If different methods are used for multiple metals, indicate the metal and method.\n      Separate metals by ;\n    examples:\n    - value: https://doi.org/10.3390/ijms9040434\n    - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n    multivalued: true\n  season_precpt:\n    name: season_precpt\n    title: average seasonal precipitation\n    todos:\n    - check validation & examples. always mm? so value only? Or value + unit\n    notes:\n    - mean and average are the same thing, but it seems like bad practice to not be\n      consistent. Changed mean to average\n    comments:\n    - Seasons are defined as spring (March, April, May), summer (June, July, August),\n      autumn (September, October, November) and winter (December, January, February).\n    examples:\n    - value: 0.4 inch\n    - value: 10.16 mm\n  water_cont_soil_meth:\n    name: water_cont_soil_meth\n    todos:\n    - Why is it soil water content method in the name but not the title? Is this slot\n      used in other samples?\n    - Soil water content can be measure MANY ways and often, multiple ways are used\n      in one experiment (gravimetric water content and water holding capacity and\n      water filled pore space, to name a few).\n    - Should this be multi valued? How to we manage and validate this?\n    comments:\n    - Required if providing water content\n    examples:\n    - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n    - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n  water_content:\n    name: water_content\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: string\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per gram or cubic centimeter per cubic centimeter\n    todos:\n    - value in preferred unit is too limiting. need to change this\n    - check and correct validation so examples are accepted\n    - how to manage multiple water content methods?\n    examples:\n    - value: 0.75 g water/g dry soil\n    - value: 75% water holding capacity\n    - value: 1.1 g fresh weight/ dry weight\n    - value: 10% water filled pore space\n    range: string\n    multivalued: true\n  ph_meth:\n    name: ph_meth\n    comments:\n    - This can include a link to the instrument used or a citation for the method.\n    examples:\n    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n    - value: https://doi.org/10.2136/sssabookser5.3.c16\n  tot_carb:\n    name: tot_carb\n    todos:\n    - is this inorganic and organic? both? could use some clarification.\n    - ug/L doesn't seem like the right units. Should check this slots usage in databases\n      and re-evaluate. I couldn't find any references that provided this data in this\n      format\n    examples:\n    - value: 1 ug/L\n  tot_nitro_cont_meth:\n    name: tot_nitro_cont_meth\n    examples:\n    - value: https://doi.org/10.2134/agronmonogr9.2.c32\n    - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n  tot_nitro_content:\n    name: tot_nitro_content\n    examples:\n    - value: 5 mg N/ L\n  tot_org_c_meth:\n    name: tot_org_c_meth\n    examples:\n    - value: https://doi.org/10.1080/07352680902776556\n  tot_org_carb:\n    name: tot_org_carb\n    todos:\n    - check description. How are they different?\n    examples:\n    - value: 5 mg N/ L\n  salinity_meth:\n    name: salinity_meth\n    examples:\n    - value: https://doi.org/10.1007/978-1-61779-986-0_28\n  sieving:\n    name: sieving\n    todos:\n    - check validation and examples\n    comments:\n    - Describe how samples were composited or sieved.\n    - Use 'sample link' to indicate which samples were combined.\n    examples:\n    - value: combined 2 cores | 4mm sieved\n    - value: 4 mm sieved and homogenized\n    - value: 50 g | 5 cores | 2 mm sieved\n  climate_environment:\n    name: climate_environment\n    todos:\n    - description says \"can include multiple climates\" but multivalued is set to false\n    - add examples, i need to see some examples to add correctly formatted example.\n  gaseous_environment:\n    name: gaseous_environment\n    todos:\n    - would like to see usage examples for this slot. Requiring micromole/L seems\n      too limiting and doesn't match expected_value value\n    - did I do this right? keep the example that's provided and add another? so as\n      to not override\n    examples:\n    - value: CO2; 500ppm above ambient; constant\n    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n  watering_regm:\n    name: watering_regm\n    examples:\n    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    - value: 75% water holding capacity; constant\n  source_mat_id:\n    name: source_mat_id\n    description: A globally unique identifier assigned to the biological sample.\n    title: source material identifier\n    todos:\n    - Currently, the comments say to use UUIDs. However, if we implement assigning\n      NMDC identifiers with the minter we dont need to require a GUID. It can be an\n      optional field to fill out only if they already have a resolvable ID.\n    comments:\n    - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n      NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n      IDs enable linking to derived analytes and subsamples. If you have not assigned\n      FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n    examples:\n    - value: IGSN:AU1243\n    - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\nattributes:\n  associated_studies:\n    name: associated_studies\n    description: The study associated with a resource.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: associated_studies\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: Study\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  biosample_categories:\n    name: biosample_categories\n    title: Categories the biosample belongs to\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: biosample_categories\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: BiosampleCategoryEnum\n    multivalued: true\n  collected_from:\n    name: collected_from\n    description: The Site from which a Biosample was collected\n    todos:\n    - add an OBO slot_uri ?\n    comments:\n    - this illustrates implementing a Biosample relation with a (binary) slot\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: collected_from\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: FieldResearchSite\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  embargoed:\n    name: embargoed\n    description: If true, the data are embargoed and not available for public access.\n    todos:\n    - make this required?\n    - first apply to Biosample\n    - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n    - applying to a Study may not be granular enough\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: embargoed\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: boolean\n    recommended: true\n  host_disease_stat:\n    name: host_disease_stat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: disease name or Disease Ontology term\n    description: List of diseases with which the host has been diagnosed; can include\n      multiple diagnoses. The value of the field depends on host; for humans the terms\n      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,\n      non-human host diseases are free text\n    title: host disease status\n    examples:\n    - value: rabies [DOID:11260]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host disease status\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{termLabel} {[termID]}|{text}'\n    slot_uri: MIXS:0000031\n    alias: host_disease_stat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_taxid:\n    name: host_taxid\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: NCBI taxon identifier\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: NCBI taxon id of the host, e.g. 9606\n    title: host taxid\n    comments:\n    - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host taxid\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000250\n    alias: host_taxid\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    multivalued: false\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: Biosample\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n  neon_biosample_identifiers:\n    name: neon_biosample_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - neon_identifiers\n    alias: neon_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  samp_name:\n    name: samp_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text\n    description: A local identifier or name that for the material sample used for\n      extracting nucleic acids, and subsequent sequencing. It can refer either to\n      the original material collected or to any derived sub-samples. It can have any\n      format, but we suggest that you make it concise, unique and consistent within\n      your lab, and as informative as possible. INSDC requires every sample name from\n      a single Submitter to be unique. Use of a globally unique identifier for the\n      field source_mat_id is recommended in addition to sample_name.\n    title: sample name\n    examples:\n    - value: ISDsoil1\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample name\n    rank: 1000\n    is_a: investigation field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001107\n    alias: samp_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  gold_biosample_identifiers:\n    name: gold_biosample_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the GOLD biosample IDs associated with this biosample.\n    description: Unique identifier for a biosample submitted to GOLD that matches\n      the NMDC submitted biosample\n    comments:\n    - This is the ID provided by GOLD that starts with 'GB'\n    examples:\n    - value: https://bioregistry.io/gold:Gb0312930\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: uriorcurie\n    multivalued: true\n    pattern: ^gold:Gb[0-9]+$\n  insdc_biosample_identifiers:\n    name: insdc_biosample_identifiers\n    description: identifiers for corresponding sample in INSDC\n    examples:\n    - value: https://bioregistry.io/biosample:SAMEA5989477\n    - value: https://bioregistry.io/biosample:SAMD00212331\n      description: I13_N_5-10 sample from Soil fungal diversity along elevational\n        gradients\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/bioregistry/bioregistry/issues/108\n    - https://www.ebi.ac.uk/biosamples/\n    - https://www.ncbi.nlm.nih.gov/biosample\n    - https://www.ddbj.nig.ac.jp/biosample/index-e.html\n    aliases:\n    - EBI biosample identifiers\n    - NCBI biosample identifiers\n    - DDBJ biosample identifiers\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: external_identifier\n    multivalued: true\n    pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n  emsl_biosample_identifiers:\n    name: emsl_biosample_identifiers\n    description: A list of identifiers for the biosample from the EMSL database.  This\n      is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n      EMSL NEXUS database.\n    title: EMSL Biosample Identifiers\n    todos:\n    - removed \"planned\" once NEXUS is online\n    - determine real expansion for emsl prefix\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - emsl_identifiers\n    alias: emsl_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  igsn_biosample_identifiers:\n    name: igsn_biosample_identifiers\n    description: A list of identifiers for the biosample from the IGSN database.\n    title: IGSN Biosample Identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - igsn_identifiers\n    alias: igsn_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  abs_air_humidity:\n    name: abs_air_humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per gram, kilogram per kilogram, kilogram, pound\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Actual mass of water vapor - mh20 - present in the air water vapor\n      mixture\n    title: absolute air humidity\n    examples:\n    - value: 9 gram per gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - absolute air humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000122\n    alias: abs_air_humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  add_recov_method:\n    name: add_recov_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration;timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n      for increase of hydrocarbon recovery from resource and start date for each one\n      of them. If \"other\" is specified, please propose entry in \"additional info\"\n      field\n    title: secondary and tertiary recovery methods and start date\n    examples:\n    - value: Polymer Addition;2018-06-21T14:30Z\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - secondary and tertiary recovery methods and start date\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001009\n    alias: add_recov_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  additional_info:\n    name: additional_info\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information that doesn't fit anywhere else. Can also be used to propose\n      new entries for fields with controlled vocabulary\n    title: additional info\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - additional info\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000300\n    alias: additional_info\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  address:\n    name: address\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The street name and building number where the sampling occurred.\n    title: address\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - address\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer}{text}'\n    slot_uri: MIXS:0000218\n    alias: address\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  adj_room:\n    name: adj_room\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: room name;room number\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of rooms (room number, room name) immediately adjacent to the\n      sampling room\n    title: adjacent rooms\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - adjacent rooms\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{integer}'\n    slot_uri: MIXS:0000219\n    alias: adj_room\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  aero_struc:\n    name: aero_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Aerospace structures typically consist of thin plates with stiffeners\n      for the external surfaces, bulkheads and frames to support the shape and fasteners\n      such as welds, rivets, screws and bolts to hold the components together\n    title: aerospace structure\n    examples:\n    - value: plane\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - aerospace structure\n    rank: 1000\n    is_a: core field\n    string_serialization: '[plane|glider]'\n    slot_uri: MIXS:0000773\n    alias: aero_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  agrochem_addition:\n    name: agrochem_addition\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: agrochemical name;agrochemical amount;timestamp\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Addition of fertilizers, pesticides, etc. - amount and time of applications\n    title: history/agrochemical additions\n    examples:\n    - value: roundup;5 milligram per liter;2018-06-21\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/agrochemical additions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{timestamp}'\n    slot_uri: MIXS:0000639\n    alias: agrochem_addition\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  air_PM_concen:\n    name: air_PM_concen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: particulate matter name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micrograms per cubic meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of substances that remain suspended in the air, and\n      comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can\n      report multiple PM's by entering numeric values preceded by name of PM\n    title: air particulate matter concentration\n    examples:\n    - value: PM2.5;10 microgram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - air particulate matter concentration\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000108\n    alias: air_PM_concen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  air_temp:\n    name: air_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Temperature of the air at the time of sampling\n    title: air temperature\n    examples:\n    - value: 20 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - air temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000124\n    alias: air_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  air_temp_regm:\n    name: air_temp_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: temperature value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to varying temperatures;\n      should include the temperature, treatment regimen including how many times the\n      treatment was repeated, how long each treatment lasted, and the start and end\n      time of the entire treatment; can include different temperature regimens\n    title: air temperature regimen\n    examples:\n    - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - air temperature regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000551\n    alias: air_temp_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  al_sat:\n    name: al_sat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative abundance of aluminum in the sample\n    title: aluminum saturation/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    notes:\n    - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n      all cations, aluminum held by the cation exchange complex is in equilibrium\n      with aluminum in the soil solution.\n    examples:\n    - value: 27%\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - extreme_unusual_properties/Al saturation\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000607\n    alias: al_sat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  al_sat_meth:\n    name: al_sat_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or URL\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining Aluminum saturation\n    title: aluminum saturation method/ extreme unusual properties\n    todos:\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n    comments:\n    - Required when aluminum saturation is provided.\n    examples:\n    - value: https://doi.org/10.1371/journal.pone.0176357\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - extreme_unusual_properties/Al saturation method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000324\n    alias: al_sat_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  alkalinity:\n    name: alkalinity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milliequivalent per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Alkalinity, the ability of a solution to neutralize acids to the\n      equivalence point of carbonate or bicarbonate\n    title: alkalinity\n    examples:\n    - value: 50 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - alkalinity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000421\n    alias: alkalinity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  alkalinity_method:\n    name: alkalinity_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: description of method\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Method used for alkalinity measurement\n    title: alkalinity method\n    examples:\n    - value: titration\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - alkalinity method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000298\n    alias: alkalinity_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  alkyl_diethers:\n    name: alkyl_diethers\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of alkyl diethers\n    title: alkyl diethers\n    examples:\n    - value: 0.005 mole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - alkyl diethers\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000490\n    alias: alkyl_diethers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  alt:\n    name: alt\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n    description: Altitude is a term used to identify heights of objects such as airplanes,\n      space shuttles, rockets, atmospheric balloons and heights of places such as\n      atmospheric layers and clouds. It is used to measure the height of an object\n      which is above the earth's surface. In this context, the altitude measurement\n      is the vertical distance between the earth's surface above sea level and the\n      sampled position in the air\n    title: altitude\n    examples:\n    - value: 100 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - altitude\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000094\n    alias: alt\n    owner: Biosample\n    domain_of:\n    - agriculture\n    - air\n    - built environment\n    - core\n    - food-animal and animal feed\n    - food-farm environment\n    - food-food production facility\n    - food-human foods\n    - host-associated\n    - human-associated\n    - human-gut\n    - human-oral\n    - human-skin\n    - human-vaginal\n    - hydrocarbon resources-cores\n    - hydrocarbon resources-fluids_swabs\n    - microbial mat_biofilm\n    - miscellaneous natural or artificial environment\n    - plant-associated\n    - sediment\n    - soil\n    - symbiont-associated\n    - wastewater_sludge\n    - water\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  aminopept_act:\n    name: aminopept_act\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per liter per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of aminopeptidase activity\n    title: aminopeptidase activity\n    examples:\n    - value: 0.269 mole per liter per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - aminopeptidase activity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000172\n    alias: aminopept_act\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ammonium:\n    name: ammonium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of ammonium in the sample\n    title: ammonium\n    examples:\n    - value: 1.5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ammonium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000427\n    alias: ammonium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ammonium_nitrogen:\n    name: ammonium_nitrogen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of ammonium nitrogen in the sample\n    title: ammonium nitrogen\n    examples:\n    - value: 2.3 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - ammonium_nitrogen\n    - NH4-N\n    rank: 1000\n    alias: ammonium_nitrogen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  amount_light:\n    name: amount_light\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: lux, lumens per square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The unit of illuminance and luminous emittance, measuring luminous\n      flux per unit area\n    title: amount of light\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - amount of light\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000140\n    alias: amount_light\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ances_data:\n    name: ances_data\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information about either pedigree or other ancestral information\n      description (e.g. parental variety in case of mutant or selection), e.g. A/3*B\n      (meaning [(A x B) x B] x B)\n    title: ancestral data\n    examples:\n    - value: A/3*B\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ancestral data\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000247\n    alias: ances_data\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  annual_precpt:\n    name: annual_precpt\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average of all annual precipitation values known, or an estimated\n      equivalent value derived by such methods as regional indexes or Isohyetal maps.\n    title: mean annual precipitation\n    examples:\n    - value: 8.94 inch\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean annual precipitation\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000644\n    alias: annual_precpt\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  annual_temp:\n    name: annual_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Mean annual temperature\n    title: mean annual temperature\n    examples:\n    - value: 12.5 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean annual temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000642\n    alias: annual_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  antibiotic_regm:\n    name: antibiotic_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: antibiotic name;antibiotic amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving antibiotic administration;\n      should include the name of antibiotic, amount administered, treatment regimen\n      including how many times the treatment was repeated, how long each treatment\n      lasted, and the start and end time of the entire treatment; can include multiple\n      antibiotic regimens\n    title: antibiotic regimen\n    examples:\n    - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - antibiotic regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000553\n    alias: antibiotic_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  api:\n    name: api\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degrees API\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'API gravity is a measure of how heavy or light a petroleum liquid\n      is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.\n      31.1\u00ac\u221e API)'\n    title: API gravity\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - API gravity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000157\n    alias: api\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  arch_struc:\n    name: arch_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: An architectural structure is a human-made, free-standing, immobile\n      outdoor construction\n    title: architectural structure\n    examples:\n    - value: shed\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - architectural structure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000774\n    alias: arch_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: arch_struc_enum\n    multivalued: false\n  aromatics_pc:\n    name: aromatics_pc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n      method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n      and polarity. There are three main methods to obtain SARA results. The most\n      popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n      https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n    title: aromatics wt%\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - aromatics wt%\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000133\n    alias: aromatics_pc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  asphaltenes_pc:\n    name: asphaltenes_pc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n      method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n      and polarity. There are three main methods to obtain SARA results. The most\n      popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n      https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n    title: asphaltenes wt%\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - asphaltenes wt%\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000135\n    alias: asphaltenes_pc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  atmospheric_data:\n    name: atmospheric_data\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: atmospheric data name;measurement value\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Measurement of atmospheric data; can include multiple data\n    title: atmospheric data\n    examples:\n    - value: wind speed;9 knots\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - atmospheric data\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0001097\n    alias: atmospheric_data\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  avg_dew_point:\n    name: avg_dew_point\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average of dew point measures taken at the beginning of every\n      hour over a 24 hour period on the sampling day\n    title: average dew point\n    examples:\n    - value: 25.5 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - average dew point\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000141\n    alias: avg_dew_point\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  avg_occup:\n    name: avg_occup\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Daily average occupancy of room. Indicate the number of person(s)\n      daily occupying the sampling room.\n    title: average daily occupancy\n    examples:\n    - value: '2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - average daily occupancy\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000775\n    alias: avg_occup\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  avg_temp:\n    name: avg_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average of temperatures taken at the beginning of every hour\n      over a 24 hour period on the sampling day\n    title: average temperature\n    examples:\n    - value: 12.5 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - average temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000142\n    alias: avg_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  bac_prod:\n    name: bac_prod\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter per day\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Bacterial production in the water column measured by isotope uptake\n    title: bacterial production\n    examples:\n    - value: 5 milligram per cubic meter per day\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bacterial production\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000683\n    alias: bac_prod\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  bac_resp:\n    name: bac_resp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter per day, micromole oxygen per liter per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of bacterial respiration in the water column\n    title: bacterial respiration\n    examples:\n    - value: 300 micromole oxygen per liter per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bacterial respiration\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000684\n    alias: bac_resp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  bacteria_carb_prod:\n    name: bacteria_carb_prod\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: nanogram per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of bacterial carbon production\n    title: bacterial carbon production\n    examples:\n    - value: 2.53 microgram per liter per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bacterial carbon production\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000173\n    alias: bacteria_carb_prod\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  barometric_press:\n    name: barometric_press\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millibar\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Force per unit area exerted against a surface by the weight of air\n      above that surface\n    title: barometric pressure\n    examples:\n    - value: 5 millibar\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - barometric pressure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000096\n    alias: barometric_press\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  basin:\n    name: basin\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of the basin (e.g. Campos)\n    title: basin name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - basin name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000290\n    alias: basin\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  bathroom_count:\n    name: bathroom_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of bathrooms in the building\n    title: bathroom count\n    examples:\n    - value: '1'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bathroom count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000776\n    alias: bathroom_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  bedroom_count:\n    name: bedroom_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of bedrooms in the building\n    title: bedroom count\n    examples:\n    - value: '2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bedroom count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000777\n    alias: bedroom_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  benzene:\n    name: benzene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of benzene in the sample\n    title: benzene\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - benzene\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000153\n    alias: benzene\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  biochem_oxygen_dem:\n    name: biochem_oxygen_dem\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Amount of dissolved oxygen needed by aerobic biological organisms\n      in a body of water to break down organic material present in a given water sample\n      at certain temperature over a specific time period\n    title: biochemical oxygen demand\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biochemical oxygen demand\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000653\n    alias: biochem_oxygen_dem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  biocide:\n    name: biocide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;name;timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of biocides (commercial name of product and supplier) and date\n      of administration\n    title: biocide administration\n    examples:\n    - value: ALPHA 1427;Baker Hughes;2008-01-23\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biocide administration\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{text};{timestamp}'\n    slot_uri: MIXS:0001011\n    alias: biocide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  biocide_admin_method:\n    name: biocide_admin_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;frequency;duration;duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Method of biocide administration (dose, frequency, duration, time\n      elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3\n      days)\n    title: biocide administration method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biocide administration method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\n    slot_uri: MIXS:0000456\n    alias: biocide_admin_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  biol_stat:\n    name: biol_stat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The level of genome modification.\n    title: biological status\n    examples:\n    - value: natural\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biological status\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000858\n    alias: biol_stat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: biol_stat_enum\n    multivalued: false\n  biomass:\n    name: biomass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: biomass type;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: ton, kilogram, gram\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Amount of biomass; should include the name for the part of biomass\n      measured, e.g. Microbial, total. Can include multiple measurements\n    title: biomass\n    examples:\n    - value: total;20 gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biomass\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000174\n    alias: biomass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  biotic_regm:\n    name: biotic_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information about treatment(s) involving use of biotic factors, such\n      as bacteria, viruses or fungi.\n    title: biotic regimen\n    examples:\n    - value: sample inoculated with Rhizobium spp. Culture\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biotic regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001038\n    alias: biotic_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  biotic_relationship:\n    name: biotic_relationship\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n    description: Description of relationship(s) between the subject organism and other\n      organism(s) it is associated with. E.g., parasite on species X; mutualist with\n      species Y. The target organism is the subject of the relationship, and the other\n      organism(s) is the object\n    title: observed biotic relationship\n    examples:\n    - value: free living\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - observed biotic relationship\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    slot_uri: MIXS:0000028\n    alias: biotic_relationship\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: biotic_relationship_enum\n    multivalued: false\n  bishomohopanol:\n    name: bishomohopanol\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, microgram per gram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of bishomohopanol\n    title: bishomohopanol\n    examples:\n    - value: 14 microgram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bishomohopanol\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000175\n    alias: bishomohopanol\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  blood_press_diast:\n    name: blood_press_diast\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter mercury\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Resting diastolic blood pressure, measured as mm mercury\n    title: host blood pressure diastolic\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host blood pressure diastolic\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000258\n    alias: blood_press_diast\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  blood_press_syst:\n    name: blood_press_syst\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter mercury\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Resting systolic blood pressure, measured as mm mercury\n    title: host blood pressure systolic\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host blood pressure systolic\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000259\n    alias: blood_press_syst\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  bromide:\n    name: bromide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of bromide\n    title: bromide\n    examples:\n    - value: 0.05 parts per million\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bromide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000176\n    alias: bromide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  build_docs:\n    name: build_docs\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The building design, construction and operation documents\n    title: design, construction, and operation documents\n    examples:\n    - value: maintenance plans\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - design, construction, and operation documents\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000787\n    alias: build_docs\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: build_docs_enum\n    multivalued: false\n  build_occup_type:\n    name: build_occup_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: The primary function for which a building or discrete part of a building\n      is intended to be used\n    title: building occupancy type\n    examples:\n    - value: market\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - building occupancy type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000761\n    alias: build_occup_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: build_occup_type_enum\n    multivalued: true\n  building_setting:\n    name: building_setting\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A location (geography) where a building is set\n    title: building setting\n    examples:\n    - value: rural\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - building setting\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000768\n    alias: building_setting\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: building_setting_enum\n    multivalued: false\n  built_struc_age:\n    name: built_struc_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: year\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The age of the built structure since construction\n    title: built structure age\n    examples:\n    - value: '15'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - built structure age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000145\n    alias: built_struc_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  built_struc_set:\n    name: built_struc_set\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The characterization of the location of the built structure as high\n      or low human density\n    title: built structure setting\n    examples:\n    - value: rural\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - built structure setting\n    rank: 1000\n    is_a: core field\n    string_serialization: '[urban|rural]'\n    slot_uri: MIXS:0000778\n    alias: built_struc_set\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  built_struc_type:\n    name: built_struc_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A physical structure that is a body or assemblage of bodies in space\n      to form a system capable of supporting loads\n    title: built structure type\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - built structure type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000721\n    alias: built_struc_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  calcium:\n    name: calcium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, micromole per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of calcium in the sample\n    title: calcium\n    examples:\n    - value: 0.2 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - calcium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000432\n    alias: calcium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  carb_dioxide:\n    name: carb_dioxide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Carbon dioxide (gas) amount or concentration at the time of sampling\n    title: carbon dioxide\n    examples:\n    - value: 410 parts per million\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - carbon dioxide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000097\n    alias: carb_dioxide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  carb_monoxide:\n    name: carb_monoxide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Carbon monoxide (gas) amount or concentration at the time of sampling\n    title: carbon monoxide\n    examples:\n    - value: 0.1 parts per million\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - carbon monoxide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000098\n    alias: carb_monoxide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  carb_nitro_ratio:\n    name: carb_nitro_ratio\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Ratio of amount or concentrations of carbon to nitrogen\n    title: carbon/nitrogen ratio\n    examples:\n    - value: '0.417361111'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - carbon/nitrogen ratio\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000310\n    alias: carb_nitro_ratio\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ceil_area:\n    name: ceil_area\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The area of the ceiling space within the room\n    title: ceiling area\n    examples:\n    - value: 25 square meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling area\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000148\n    alias: ceil_area\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ceil_cond:\n    name: ceil_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the ceiling at the time of sampling; photos\n      or video preferred; use drawings to indicate location of damaged areas\n    title: ceiling condition\n    examples:\n    - value: damaged\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000779\n    alias: ceil_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ceil_cond_enum\n    multivalued: false\n  ceil_finish_mat:\n    name: ceil_finish_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of material used to finish a ceiling\n    title: ceiling finish material\n    examples:\n    - value: stucco\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling finish material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000780\n    alias: ceil_finish_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ceil_finish_mat_enum\n    multivalued: false\n  ceil_struc:\n    name: ceil_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The construction format of the ceiling\n    title: ceiling structure\n    examples:\n    - value: concrete\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling structure\n    rank: 1000\n    is_a: core field\n    string_serialization: '[wood frame|concrete]'\n    slot_uri: MIXS:0000782\n    alias: ceil_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  ceil_texture:\n    name: ceil_texture\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The feel, appearance, or consistency of a ceiling surface\n    title: ceiling texture\n    examples:\n    - value: popcorn\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling texture\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000783\n    alias: ceil_texture\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ceil_texture_enum\n    multivalued: false\n  ceil_thermal_mass:\n    name: ceil_thermal_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: joule per degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The ability of the ceiling to provide inertia against temperature\n      fluctuations. Generally this means concrete that is exposed. A metal deck that\n      supports a concrete slab will act thermally as long as it is exposed to room\n      air flow\n    title: ceiling thermal mass\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling thermal mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000143\n    alias: ceil_thermal_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ceil_type:\n    name: ceil_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of ceiling according to the ceiling's appearance or construction\n    title: ceiling type\n    examples:\n    - value: coffered\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000784\n    alias: ceil_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ceil_type_enum\n    multivalued: false\n  ceil_water_mold:\n    name: ceil_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on the ceiling\n    title: ceiling signs of water/mold\n    examples:\n    - value: presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000781\n    alias: ceil_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  chem_administration:\n    name: chem_administration\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: CHEBI;timestamp\n      occurrence:\n        tag: occurrence\n        value: m\n    description: List of chemical compounds administered to the host or site where\n      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can\n      include multiple compounds. For chemical entities of biological interest ontology\n      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi\n    title: chemical administration\n    examples:\n    - value: agar [CHEBI:2509];2018-05-11T20:00Z\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical administration\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]};{timestamp}'\n    slot_uri: MIXS:0000751\n    alias: chem_administration\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  chem_mutagen:\n    name: chem_mutagen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: mutagen name;mutagen amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Treatment involving use of mutagens; should include the name of mutagen,\n      amount administered, treatment regimen including how many times the treatment\n      was repeated, how long each treatment lasted, and the start and end time of\n      the entire treatment; can include multiple mutagen regimens\n    title: chemical mutagen\n    examples:\n    - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical mutagen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000555\n    alias: chem_mutagen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  chem_oxygen_dem:\n    name: chem_oxygen_dem\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A measure of the capacity of water to consume oxygen during the decomposition\n      of organic matter and the oxidation of inorganic chemicals such as ammonia and\n      nitrite\n    title: chemical oxygen demand\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical oxygen demand\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000656\n    alias: chem_oxygen_dem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  chem_treat_method:\n    name: chem_treat_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;frequency;duration;duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Method of chemical administration(dose, frequency, duration, time\n      elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1\n      hr; 0 days)\n    title: chemical treatment method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical treatment method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\n    slot_uri: MIXS:0000457\n    alias: chem_treat_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  chem_treatment:\n    name: chem_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;name;timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of chemical compounds administered upstream the sampling location\n      where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n      demulsifiers, and other production chemicals etc.). The commercial name of the\n      product and name of the supplier should be provided. The date of administration\n      should also be included\n    title: chemical treatment\n    examples:\n    - value: ACCENT 1125;DOW;2010-11-17\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{text};{timestamp}'\n    slot_uri: MIXS:0001012\n    alias: chem_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  chloride:\n    name: chloride\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of chloride in the sample\n    title: chloride\n    examples:\n    - value: 5000 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chloride\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000429\n    alias: chloride\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  chlorophyll:\n    name: chlorophyll\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter, microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of chlorophyll\n    title: chlorophyll\n    examples:\n    - value: 5 milligram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chlorophyll\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000177\n    alias: chlorophyll\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  climate_environment:\n    name: climate_environment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: climate name;treatment interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Treatment involving an exposure to a particular climate; treatment\n      regimen including how many times the treatment was repeated, how long each treatment\n      lasted, and the start and end time of the entire treatment; can include multiple\n      climates\n    title: climate environment\n    todos:\n    - description says \"can include multiple climates\" but multivalued is set to false\n    - add examples, i need to see some examples to add correctly formatted example.\n    examples:\n    - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - climate environment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0001040\n    alias: climate_environment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  collection_date:\n    name: collection_date\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date and time\n    description: 'The time of sampling, either as an instance (single point in time)\n      or interval. In case no exact time is available, the date/time can be right\n      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\n    title: collection date\n    examples:\n    - value: 2018-05-11T10:00:00+01:00; 2018-05-11\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - collection date\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000011\n    alias: collection_date\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  conduc:\n    name: conduc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milliSiemens per centimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Electrical conductivity of water\n    title: conductivity\n    examples:\n    - value: 10 milliSiemens per centimeter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - conductivity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000692\n    alias: conduc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  cool_syst_id:\n    name: cool_syst_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: unique identifier\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The cooling system identifier\n    title: cooling system identifier\n    examples:\n    - value: '12345'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - cooling system identifier\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000785\n    alias: cool_syst_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  core field:\n    name: core field\n    description: basic fields\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: core_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  crop_rotation:\n    name: crop_rotation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: crop rotation status;schedule\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Whether or not crop is rotated, and if yes, rotation schedule\n    title: history/crop rotation\n    examples:\n    - value: yes;R2/2017-01-01/2018-12-31/P6M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/crop rotation\n    rank: 1000\n    is_a: core field\n    string_serialization: '{boolean};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000318\n    alias: crop_rotation\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  cult_root_med:\n    name: cult_root_med\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name, PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name or reference for the hydroponic or in vitro culture rooting\n      medium; can be the name of a commonly used medium or reference to a specific\n      medium, e.g. Murashige and Skoog medium. If the medium has not been formally\n      published, use the rooting medium descriptors.\n    title: culture rooting medium\n    examples:\n    - value: http://himedialabs.com/TD/PT158.pdf\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - culture rooting medium\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}|{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0001041\n    alias: cult_root_med\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  cur_land_use:\n    name: cur_land_use\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Present state of sample site\n    title: current land use\n    examples:\n    - value: conifers\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - current land use\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001080\n    alias: cur_land_use\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: cur_land_use_enum\n    multivalued: false\n  cur_vegetation:\n    name: cur_vegetation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: current vegetation type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Vegetation classification from one or more standard classification\n      systems, or agricultural crop\n    title: current vegetation\n    todos:\n    - Recommend changing this from text value to some king of ontology?\n    comments:\n    - Values provided here can be specific species of vegetation or vegetation regions\n    - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n    examples:\n    - value: deciduous forest\n    - value: forest\n    - value: Bauhinia variegata\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - current vegetation\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000312\n    alias: cur_vegetation\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  cur_vegetation_meth:\n    name: cur_vegetation_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in vegetation classification\n    title: current vegetation method\n    todos:\n    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n      out how they accomplish this if provided.\n    comments:\n    - Required when current vegetation is provided.\n    examples:\n    - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - current vegetation method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000314\n    alias: cur_vegetation_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  date_last_rain:\n    name: date_last_rain\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The date of the last time it rained\n    title: date last rain\n    examples:\n    - value: 2018-05-11:T14:30Z\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - date last rain\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000786\n    alias: date_last_rain\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  density:\n    name: density\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per cubic meter, gram per cubic centimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Density of the sample, which is its mass per unit volume (aka volumetric\n      mass density)\n    title: density\n    examples:\n    - value: 1000 kilogram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - density\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000435\n    alias: density\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  depos_env:\n    name: depos_env\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n      If \"other\" is specified, please propose entry in \"additional info\" field\n    title: depositional environment\n    examples:\n    - value: Continental - Alluvial\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - depositional environment\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000992\n    alias: depos_env\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: depos_env_enum\n    multivalued: false\n  depth:\n    name: depth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n    description: The vertical distance below local surface, e.g. for sediment or soil\n      samples depth is measured from sediment or soil surface, respectively. Depth\n      can be reported as an interval for subsurface samples.\n    title: depth\n    examples:\n    - value: 10 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - depth\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000018\n    alias: depth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  dew_point:\n    name: dew_point\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The temperature to which a given parcel of humid air must be cooled,\n      at constant barometric pressure, for water vapor to condense into water.\n    title: dew point\n    examples:\n    - value: 22 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dew point\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000129\n    alias: dew_point\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diether_lipids:\n    name: diether_lipids\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: diether lipid name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: nanogram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of diether lipids; can include multiple types of diether\n      lipids\n    title: diether lipids\n    examples:\n    - value: 0.2 nanogram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - diether lipids\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000178\n    alias: diether_lipids\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  diss_carb_dioxide:\n    name: diss_carb_dioxide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved carbon dioxide in the sample or liquid\n      portion of the sample\n    title: dissolved carbon dioxide\n    examples:\n    - value: 5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved carbon dioxide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000436\n    alias: diss_carb_dioxide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_hydrogen:\n    name: diss_hydrogen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved hydrogen\n    title: dissolved hydrogen\n    examples:\n    - value: 0.3 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved hydrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000179\n    alias: diss_hydrogen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_inorg_carb:\n    name: diss_inorg_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Dissolved inorganic carbon concentration in the sample, typically\n      measured after filtering the sample using a 0.45 micrometer filter\n    title: dissolved inorganic carbon\n    examples:\n    - value: 2059 micromole per kilogram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved inorganic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000434\n    alias: diss_inorg_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_inorg_nitro:\n    name: diss_inorg_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved inorganic nitrogen\n    title: dissolved inorganic nitrogen\n    examples:\n    - value: 761 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved inorganic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000698\n    alias: diss_inorg_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_inorg_phosp:\n    name: diss_inorg_phosp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved inorganic phosphorus in the sample\n    title: dissolved inorganic phosphorus\n    examples:\n    - value: 56.5 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved inorganic phosphorus\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000106\n    alias: diss_inorg_phosp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_iron:\n    name: diss_iron\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved iron in the sample\n    title: dissolved iron\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved iron\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000139\n    alias: diss_iron\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_org_carb:\n    name: diss_org_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved organic carbon in the sample, liquid portion\n      of the sample, or aqueous phase of the fluid\n    title: dissolved organic carbon\n    examples:\n    - value: 197 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved organic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000433\n    alias: diss_org_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_org_nitro:\n    name: diss_org_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Dissolved organic nitrogen concentration measured as; total dissolved\n      nitrogen - NH4 - NO3 - NO2\n    title: dissolved organic nitrogen\n    examples:\n    - value: 0.05 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved organic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000162\n    alias: diss_org_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_oxygen:\n    name: diss_oxygen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per kilogram, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved oxygen\n    title: dissolved oxygen\n    examples:\n    - value: 175 micromole per kilogram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved oxygen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000119\n    alias: diss_oxygen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_oxygen_fluid:\n    name: diss_oxygen_fluid\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per kilogram, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved oxygen in the oil field produced fluids\n      as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\n    title: dissolved oxygen in fluids\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved oxygen in fluids\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000438\n    alias: diss_oxygen_fluid\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  dna_cont_well:\n    name: dna_cont_well\n    title: DNA plate position\n    comments:\n    - Required when 'plate' is selected for container type.\n    - Leave blank if the sample will be shipped in a tube.\n    - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n      pass validation.\n    - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n    examples:\n    - value: B2\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 11\n    string_serialization: '{96 well plate pos}'\n    alias: dna_cont_well\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n    pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  door_comp_type:\n    name: door_comp_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The composite type of the door\n    title: door type, composite\n    examples:\n    - value: revolving\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door type, composite\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000795\n    alias: door_comp_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_comp_type_enum\n    multivalued: false\n  door_cond:\n    name: door_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The phsical condition of the door\n    title: door condition\n    examples:\n    - value: new\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000788\n    alias: door_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_cond_enum\n    multivalued: false\n  door_direct:\n    name: door_direct\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The direction the door opens\n    title: door direction of opening\n    examples:\n    - value: inward\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door direction of opening\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000789\n    alias: door_direct\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_direct_enum\n    multivalued: false\n  door_loc:\n    name: door_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative location of the door in the room\n    title: door location\n    examples:\n    - value: north\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000790\n    alias: door_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_loc_enum\n    multivalued: false\n  door_mat:\n    name: door_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The material the door is composed of\n    title: door material\n    examples:\n    - value: wood\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000791\n    alias: door_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_mat_enum\n    multivalued: false\n  door_move:\n    name: door_move\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of movement of the door\n    title: door movement\n    examples:\n    - value: swinging\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door movement\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000792\n    alias: door_move\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_move_enum\n    multivalued: false\n  door_size:\n    name: door_size\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The size of the door\n    title: door area or size\n    examples:\n    - value: 2.5 square meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door area or size\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000158\n    alias: door_size\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  door_type:\n    name: door_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of door material\n    title: door type\n    examples:\n    - value: wooden\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000794\n    alias: door_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_type_enum\n    multivalued: false\n  door_type_metal:\n    name: door_type_metal\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of metal door\n    title: door type, metal\n    examples:\n    - value: hollow\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door type, metal\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000796\n    alias: door_type_metal\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_type_metal_enum\n    multivalued: false\n  door_type_wood:\n    name: door_type_wood\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of wood door\n    title: door type, wood\n    examples:\n    - value: battened\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door type, wood\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000797\n    alias: door_type_wood\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_type_wood_enum\n    multivalued: false\n  door_water_mold:\n    name: door_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on a door\n    title: door signs of water/mold\n    examples:\n    - value: presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000793\n    alias: door_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  down_par:\n    name: down_par\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microEinstein per square meter per second, microEinstein per square\n          centimeter per second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Visible waveband radiance and irradiance measurements in the water\n      column\n    title: downward PAR\n    examples:\n    - value: 28.71 microEinstein per square meter per second\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - downward PAR\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000703\n    alias: down_par\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  drainage_class:\n    name: drainage_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Drainage classification from a standard system such as the USDA system\n    title: drainage classification\n    examples:\n    - value: well\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - drainage classification\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001085\n    alias: drainage_class\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: drainage_class_enum\n    multivalued: false\n  drawings:\n    name: drawings\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The buildings architectural drawings; if design is chosen, indicate\n      phase-conceptual, schematic, design development, and construction documents\n    title: drawings\n    examples:\n    - value: sketch\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - drawings\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000798\n    alias: drawings\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: drawings_enum\n    multivalued: false\n  ecosystem:\n    name: ecosystem\n    description: An ecosystem is a combination of a physical environment (abiotic\n      factors) and all the organisms (biotic factors) that interact with this environment.\n      Ecosystem is in position 1/5 in a GOLD path.\n    comments:\n    - The abiotic factors play a profound role on the type and composition of organisms\n      in a given environment. The GOLD Ecosystem at the top of the five-level classification\n      system is aimed at capturing the broader environment from which an organism\n      or environmental sample is collected. The three broad groups under Ecosystem\n      are Environmental, Host-associated, and Engineered. They represent samples collected\n      from a natural environment or from another organism or from engineered environments\n      like bioreactors respectively.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_category:\n    name: ecosystem_category\n    description: Ecosystem categories represent divisions within the ecosystem based\n      on specific characteristics of the environment from where an organism or sample\n      is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n    comments:\n    - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n      Ecosystem categories for Host-associated samples can be individual hosts or\n      phyla and for engineered samples it may be manipulated environments like bioreactors,\n      solid waste etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_category\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_subtype:\n    name: ecosystem_subtype\n    description: Ecosystem subtypes represent further subdivision of Ecosystem types\n      into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n      path.\n    comments:\n    - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n      (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n      the Ecosystem subtype category.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_subtype\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_type:\n    name: ecosystem_type\n    description: Ecosystem types represent things having common characteristics within\n      the Ecosystem Category. These common characteristics based grouping is still\n      broad but specific to the characteristics of a given environment. Ecosystem\n      type is in position 3/5 in a GOLD path.\n    comments:\n    - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n      or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n      air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n      type can represent Respiratory system, Digestive system, Roots etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  efficiency_percent:\n    name: efficiency_percent\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Percentage of volatile solids removed from the anaerobic digestor\n    title: efficiency percent\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - efficiency percent\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000657\n    alias: efficiency_percent\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  elev:\n    name: elev\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n    description: Elevation of the sampling site is its height above a fixed reference\n      point, most commonly the mean sea level. Elevation is mainly used when referring\n      to points on the earth's surface, while altitude is used for points above the\n      surface, such as an aircraft in flight or a spacecraft in orbit.\n    title: elevation, meters\n    comments:\n    - All elevations must be reported in meters. Provide the numerical portion only.\n    - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n      if needed, to help estimate the elevation based on latitude and longitude coordinates.\n    examples:\n    - value: '100'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - elevation\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000093\n    alias: elev\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: float\n    multivalued: false\n  elevator:\n    name: elevator\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of elevators within the built structure\n    title: elevator count\n    examples:\n    - value: '2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - elevator count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000799\n    alias: elevator\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  emulsions:\n    name: emulsions\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: emulsion name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Amount or concentration of substances such as paints, adhesives,\n      mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion\n      types\n    title: emulsions\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - emulsions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000660\n    alias: emulsions\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  env_broad_scale:\n    name: env_broad_scale\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: The major environment type(s) where the sample was collected. Recommend\n          subclasses of biome [ENVO:00000428]. Multiple terms can be separated by\n          one or more pipes.\n      tooltip:\n        tag: tooltip\n        value: The biome or major environmental system where the sample or specimen\n          originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]\n          in the Environment Ontology (ENVO). For host-associated or plant-associated\n          samples, use terms from the UBERON or Plant Ontology to describe the broad\n          anatomical or morphological context\n    description: 'Report the major environmental system the sample or specimen came\n      from. The system(s) identified should have a coarse spatial grain, to provide\n      the general environmental context of where the sampling was done (e.g. in the\n      desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.\n      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\n    title: broad-scale environmental context\n    examples:\n    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water\n        sample from the photic zone in middle of the Atlantic Ocean\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - broad-scale environmental context\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000012\n    alias: env_broad_scale\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    required: true\n    multivalued: false\n  env_local_scale:\n    name: env_local_scale\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: Environmental entities having causal influences upon the entity at\n          time of sampling.\n      tooltip:\n        tag: tooltip\n        value: The specific environmental entities or features near the sample or\n          specimen that significantly influence its characteristics or composition.\n          These entities are typically smaller in scale than the broad environmental\n          context. Values for this field should be countable, material nouns and must\n          be chosen from subclasses of BFO:0000040 (material entity) that appear in\n          the Environment Ontology (ENVO). For host-associated or plant-associated\n          samples, use terms from the UBERON or Plant Ontology to describe specific\n          anatomical structures or plant parts.\n    description: 'Report the entity or entities which are in the sample or specimen\u2019s\n      local vicinity and which you believe have significant causal influences on your\n      sample or specimen. We recommend using EnvO terms which are of smaller spatial\n      grain than your entry for env_broad_scale. Terms, such as anatomical sites,\n      from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)\n      are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\n    title: local environmental context\n    examples:\n    - value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from\n        various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb\n        and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub\n        layer [ENVO:01000336].'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - local environmental context\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000013\n    alias: env_local_scale\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    required: true\n    multivalued: false\n  env_medium:\n    name: env_medium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: The material displaced by the entity at time of sampling. Recommend\n          subclasses of environmental material [ENVO:00010483].\n      tooltip:\n        tag: tooltip\n        value: The predominant environmental material or substrate that directly surrounds\n          or hosts the sample or specimen at the time of sampling. Choose values from\n          subclasses of the 'environmental material' class [ENVO:00010483] in the\n          Environment Ontology (ENVO). Values for this field should be measurable\n          or mass material nouns, representing continuous environmental materials.\n          For host-associated or plant-associated samples, use terms from the UBERON\n          or Plant Ontology to indicate a tissue, organ, or plant structure\n    description: 'Report the environmental material(s) immediately surrounding the\n      sample or specimen at the time of sampling. We recommend using subclasses of\n      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO\n      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n      . Terms from other OBO ontologies are permissible as long as they reference\n      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities\n      (e.g. a tree, a leaf, a table top).'\n    title: environmental medium\n    examples:\n    - value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m\n        of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating\n        a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - environmental medium\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000014\n    alias: env_medium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    required: true\n    multivalued: false\n  env_package:\n    name: env_package\n    description: MIxS extension for reporting of measurements and observations obtained\n      from one or more of the environments where the sample was obtained. All environmental\n      packages listed here are further defined in separate subtables. By giving the\n      name of the environmental package, a selection of fields can be made from the\n      subtables and can be reported\n    notes:\n    - no longer in MIxS as of 6.0?\n    in_subset:\n    - mixs extension\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - environmental package\n    rank: 1000\n    alias: env_package\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n  environment field:\n    name: environment field\n    description: field describing environmental aspect of a sample\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: environment_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  escalator:\n    name: escalator\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of escalators within the built structure\n    title: escalator count\n    examples:\n    - value: '4'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - escalator count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000800\n    alias: escalator\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  ethylbenzene:\n    name: ethylbenzene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of ethylbenzene in the sample\n    title: ethylbenzene\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ethylbenzene\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000155\n    alias: ethylbenzene\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  exp_duct:\n    name: exp_duct\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The amount of exposed ductwork in the room\n    title: exposed ductwork\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - exposed ductwork\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000144\n    alias: exp_duct\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  exp_pipe:\n    name: exp_pipe\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of exposed pipes in the room\n    title: exposed pipes\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - exposed pipes\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000220\n    alias: exp_pipe\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  experimental_factor:\n    name: experimental_factor\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text or EFO and/or OBI\n    description: Experimental factors are essentially the variable aspects of an experiment\n      design which can be used to describe an experiment, or set of experiments, in\n      an increasingly detailed manner. This field accepts ontology terms from Experimental\n      Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For\n      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\n    title: experimental factor\n    examples:\n    - value: time series design [EFO:EFO_0001779]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - experimental factor\n    rank: 1000\n    is_a: investigation field\n    string_serialization: '{termLabel} {[termID]}|{text}'\n    slot_uri: MIXS:0000008\n    alias: experimental_factor\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  ext_door:\n    name: ext_door\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of exterior doors in the built structure\n    title: exterior door count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - exterior door count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000170\n    alias: ext_door\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  ext_wall_orient:\n    name: ext_wall_orient\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The orientation of the exterior wall\n    title: orientations of exterior wall\n    examples:\n    - value: northwest\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - orientations of exterior wall\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000817\n    alias: ext_wall_orient\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ext_wall_orient_enum\n    multivalued: false\n  ext_window_orient:\n    name: ext_window_orient\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The compass direction the exterior window of the room is facing\n    title: orientations of exterior window\n    examples:\n    - value: southwest\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - orientations of exterior window\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000818\n    alias: ext_window_orient\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ext_window_orient_enum\n    multivalued: false\n  extreme_event:\n    name: extreme_event\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date, string\n    description: Unusual physical events that may have affected microbial populations\n    title: history/extreme events\n    examples:\n    - value: 1980-05-18, volcanic eruption\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/extreme events\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000320\n    alias: extreme_event\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  fao_class:\n    name: fao_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Soil classification from the FAO World Reference Database for Soil\n      Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\n    title: soil_taxonomic/FAO classification\n    examples:\n    - value: Luvisols\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil_taxonomic/FAO classification\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001083\n    alias: fao_class\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: fao_class_enum\n    multivalued: false\n  fertilizer_regm:\n    name: fertilizer_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: fertilizer name;fertilizer amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving the use of fertilizers; should\n      include the name of fertilizer, amount administered, treatment regimen including\n      how many times the treatment was repeated, how long each treatment lasted, and\n      the start and end time of the entire treatment; can include multiple fertilizer\n      regimens\n    title: fertilizer regimen\n    examples:\n    - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - fertilizer regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000556\n    alias: fertilizer_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  field:\n    name: field\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of the hydrocarbon field (e.g. Albacora)\n    title: field name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - field name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000291\n    alias: field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  filter_type:\n    name: filter_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: A device which removes solid particulates or airborne molecular contaminants\n    title: filter type\n    examples:\n    - value: HEPA\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - filter type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000765\n    alias: filter_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: filter_type_enum\n    multivalued: true\n  fire:\n    name: fire\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    description: Historical and/or physical evidence of fire\n    title: history/fire\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    comments:\n    - Provide the date the fire occurred. If extended burning occurred provide the\n      date range.\n    examples:\n    - value: '1871-10-10'\n    - value: 1871-10-01 to 1871-10-31\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/fire\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001086\n    alias: fire\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n    pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n  fireplace_type:\n    name: fireplace_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A firebox with chimney\n    title: fireplace type\n    examples:\n    - value: wood burning\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - fireplace type\n    rank: 1000\n    is_a: core field\n    string_serialization: '[gas burning|wood burning]'\n    slot_uri: MIXS:0000802\n    alias: fireplace_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  flooding:\n    name: flooding\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    description: Historical and/or physical evidence of flooding\n    title: history/flooding\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    - What about if the \"day\" isn't known? Is this ok?\n    comments:\n    - Provide the date the flood occurred. If extended flooding occurred provide the\n      date range.\n    examples:\n    - value: '1927-04-15'\n    - value: 1927-04 to 1927-05\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/flooding\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000319\n    alias: flooding\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  floor_age:\n    name: floor_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: years, weeks, days\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The time period since installment of the carpet or flooring\n    title: floor age\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000164\n    alias: floor_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  floor_area:\n    name: floor_area\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The area of the floor space within the room\n    title: floor area\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor area\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000165\n    alias: floor_area\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  floor_cond:\n    name: floor_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the floor at the time of sampling; photos\n      or video preferred; use drawings to indicate location of damaged areas\n    title: floor condition\n    examples:\n    - value: new\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000803\n    alias: floor_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: floor_cond_enum\n    multivalued: false\n  floor_count:\n    name: floor_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of floors in the building, including basements and mechanical\n      penthouse\n    title: floor count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000225\n    alias: floor_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  floor_finish_mat:\n    name: floor_finish_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The floor covering type; the finished surface that is walked on\n    title: floor finish material\n    examples:\n    - value: carpet\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor finish material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000804\n    alias: floor_finish_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: floor_finish_mat_enum\n    multivalued: false\n  floor_struc:\n    name: floor_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Refers to the structural elements and subfloor upon which the finish\n      flooring is installed\n    title: floor structure\n    examples:\n    - value: concrete\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor structure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000806\n    alias: floor_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: floor_struc_enum\n    multivalued: false\n  floor_thermal_mass:\n    name: floor_thermal_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: joule per degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The ability of the floor to provide inertia against temperature fluctuations\n    title: floor thermal mass\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor thermal mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000166\n    alias: floor_thermal_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  floor_water_mold:\n    name: floor_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew in a room\n    title: floor signs of water/mold\n    examples:\n    - value: ceiling discoloration\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor signs of water/mold\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000805\n    alias: floor_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: floor_water_mold_enum\n    multivalued: false\n  fluor:\n    name: fluor\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram chlorophyll a per cubic meter, volts\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Raw or converted fluorescence of water\n    title: fluorescence\n    examples:\n    - value: 2.5 volts\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - fluorescence\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000704\n    alias: fluor\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  freq_clean:\n    name: freq_clean\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration or {text}\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of times the sample location is cleaned. Frequency of\n      cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\n    title: frequency of cleaning\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - frequency of cleaning\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000226\n    alias: freq_clean\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  freq_cook:\n    name: freq_cook\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of times a meal is cooked per week\n    title: frequency of cooking\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - frequency of cooking\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000227\n    alias: freq_cook\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  fungicide_regm:\n    name: fungicide_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: fungicide name;fungicide amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of fungicides; should include\n      the name of fungicide, amount administered, treatment regimen including how\n      many times the treatment was repeated, how long each treatment lasted, and the\n      start and end time of the entire treatment; can include multiple fungicide regimens\n    title: fungicide regimen\n    examples:\n    - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - fungicide regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000557\n    alias: fungicide_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  furniture:\n    name: furniture\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The types of furniture present in the sampled room\n    title: furniture\n    examples:\n    - value: chair\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - furniture\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000807\n    alias: furniture\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: furniture_enum\n    multivalued: false\n  gaseous_environment:\n    name: gaseous_environment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gaseous compound name;gaseous compound amount;treatment interval and\n          duration\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Use of conditions with differing gaseous environments; should include\n      the name of gaseous compound, amount administered, treatment duration, interval\n      and total experimental duration; can include multiple gaseous environment regimens\n    title: gaseous environment\n    todos:\n    - would like to see usage examples for this slot. Requiring micromole/L seems\n      too limiting and doesn't match expected_value value\n    - did I do this right? keep the example that's provided and add another? so as\n      to not override\n    examples:\n    - value: CO2; 500ppm above ambient; constant\n    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gaseous environment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000558\n    alias: gaseous_environment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  gaseous_substances:\n    name: gaseous_substances\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gaseous substance name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Amount or concentration of substances such as hydrogen sulfide, carbon\n      dioxide, methane, etc.; can include multiple substances\n    title: gaseous substances\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gaseous substances\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000661\n    alias: gaseous_substances\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  gender_restroom:\n    name: gender_restroom\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The gender type of the restroom\n    title: gender of restroom\n    examples:\n    - value: male\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gender of restroom\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000808\n    alias: gender_restroom\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: gender_restroom_enum\n    multivalued: false\n  genetic_mod:\n    name: genetic_mod\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url or free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Genetic modifications of the genome of an organism, which may occur\n      naturally by spontaneous mutation, or be introduced by some experimental means,\n      e.g. specification of a transgene or the gene knocked-out or details of transient\n      transfection\n    title: genetic modification\n    examples:\n    - value: aox1A transgenic\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - genetic modification\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0000859\n    alias: genetic_mod\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  geo_loc_name:\n    name: geo_loc_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n          name'\n    description: The geographical origin of the sample as defined by the country or\n      sea name followed by specific region name. Country or sea names should be chosen\n      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n      (http://purl.bioontology.org/ontology/GAZ)\n    title: geographic location (country and/or sea,region)\n    examples:\n    - value: 'USA: Maryland, Bethesda'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - geographic location (country and/or sea,region)\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{term}: {term}, {text}'\n    slot_uri: MIXS:0000010\n    alias: geo_loc_name\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  glucosidase_act:\n    name: glucosidase_act\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mol per liter per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of glucosidase activity\n    title: glucosidase activity\n    examples:\n    - value: 5 mol per liter per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - glucosidase activity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000137\n    alias: glucosidase_act\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  gravidity:\n    name: gravidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gravidity status;timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Whether or not subject is gravid, and if yes date due or date post-conception,\n      specifying which is used\n    title: gravidity\n    examples:\n    - value: yes;due date:2018-05-11\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gravidity\n    rank: 1000\n    is_a: core field\n    string_serialization: '{boolean};{timestamp}'\n    slot_uri: MIXS:0000875\n    alias: gravidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  gravity:\n    name: gravity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gravity factor value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: meter per square second, g\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of gravity factor to study\n      various types of responses in presence, absence or modified levels of gravity;\n      treatment regimen including how many times the treatment was repeated, how long\n      each treatment lasted, and the start and end time of the entire treatment; can\n      include multiple treatments\n    title: gravity\n    examples:\n    - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gravity\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000559\n    alias: gravity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  growth_facil:\n    name: growth_facil\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text or CO\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n      growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n      use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\n    title: growth facility\n    examples:\n    - value: Growth chamber [CO_715:0000189]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - growth facility\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}|{termLabel} {[termID]}'\n    slot_uri: MIXS:0001043\n    alias: growth_facil\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  growth_habit:\n    name: growth_habit\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Characteristic shape, appearance or growth form of a plant species\n    title: growth habit\n    examples:\n    - value: spreading\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - growth habit\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001044\n    alias: growth_habit\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: growth_habit_enum\n    multivalued: false\n  growth_hormone_regm:\n    name: growth_hormone_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: growth hormone name;growth hormone amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of growth hormones; should\n      include the name of growth hormone, amount administered, treatment regimen including\n      how many times the treatment was repeated, how long each treatment lasted, and\n      the start and end time of the entire treatment; can include multiple growth\n      hormone regimens\n    title: growth hormone regimen\n    examples:\n    - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - growth hormone regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000560\n    alias: growth_hormone_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  hall_count:\n    name: hall_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The total count of hallways and cooridors in the built structure\n    title: hallway/corridor count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hallway/corridor count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000228\n    alias: hall_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  handidness:\n    name: handidness\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The handidness of the individual sampled\n    title: handidness\n    examples:\n    - value: right handedness\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - handidness\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000809\n    alias: handidness\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: handidness_enum\n    multivalued: false\n  hc_produced:\n    name: hc_produced\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n      etc). If \"other\" is specified, please propose entry in \"additional info\" field\n    title: hydrocarbon type produced\n    examples:\n    - value: Gas\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon type produced\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000989\n    alias: hc_produced\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: hc_produced_enum\n    multivalued: false\n  hcr:\n    name: hcr\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR\n      defined as a natural environmental feature containing large amounts of hydrocarbons\n      at high concentrations potentially suitable for commercial exploitation. This\n      term should not be confused with the Hydrocarbon Occurrence term which also\n      includes hydrocarbon-rich environments with currently limited commercial interest\n      such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose\n      entry in \"additional info\" field\n    title: hydrocarbon resource type\n    examples:\n    - value: Oil Sand\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon resource type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000988\n    alias: hcr\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: hcr_enum\n    multivalued: false\n  hcr_fw_salinity:\n    name: hcr_fw_salinity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original formation water salinity (prior to secondary recovery e.g.\n      Waterflooding) expressed as TDS\n    title: formation water salinity\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - formation water salinity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000406\n    alias: hcr_fw_salinity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  hcr_geol_age:\n    name: hcr_geol_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n      If \"other\" is specified, please propose entry in \"additional info\" field'\n    title: hydrocarbon resource geological age\n    examples:\n    - value: Silurian\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon resource geological age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000993\n    alias: hcr_geol_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: hcr_geol_age_enum\n    multivalued: false\n  hcr_pressure:\n    name: hcr_pressure\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: atmosphere, kilopascal\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original pressure of the hydrocarbon resource\n    title: hydrocarbon resource original pressure\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon resource original pressure\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} - {float} {unit}'\n    slot_uri: MIXS:0000395\n    alias: hcr_pressure\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  hcr_temp:\n    name: hcr_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original temperature of the hydrocarbon resource\n    title: hydrocarbon resource original temperature\n    examples:\n    - value: 150-295 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon resource original temperature\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} - {float} {unit}'\n    slot_uri: MIXS:0000393\n    alias: hcr_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  heat_cool_type:\n    name: heat_cool_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Methods of conditioning or heating a room or building\n    title: heating and cooling system type\n    examples:\n    - value: heat pump\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - heating and cooling system type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000766\n    alias: heat_cool_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: heat_cool_type_enum\n    multivalued: true\n  heat_deliv_loc:\n    name: heat_deliv_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The location of heat delivery within the room\n    title: heating delivery locations\n    examples:\n    - value: north\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - heating delivery locations\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000810\n    alias: heat_deliv_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: heat_deliv_loc_enum\n    multivalued: false\n  heat_sys_deliv_meth:\n    name: heat_sys_deliv_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The method by which the heat is delivered through the system\n    title: heating system delivery method\n    examples:\n    - value: radiant\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - heating system delivery method\n    rank: 1000\n    is_a: core field\n    string_serialization: '[conductive|radiant]'\n    slot_uri: MIXS:0000812\n    alias: heat_sys_deliv_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  heat_system_id:\n    name: heat_system_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: unique identifier\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The heating system identifier\n    title: heating system identifier\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - heating system identifier\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000833\n    alias: heat_system_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  heavy_metals:\n    name: heavy_metals\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: heavy metal name;measurement value unit\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per gram\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Heavy metals present in the sample and their concentrations.\n    title: heavy metals/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    comments:\n    - For multiple heavy metals and concentrations, separate by ;\n    examples:\n    - value: mercury 0.09 micrograms per gram\n    - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - extreme_unusual_properties/heavy metals\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000652\n    alias: heavy_metals\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  heavy_metals_meth:\n    name: heavy_metals_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining heavy metals\n    title: heavy metals method/ extreme unusual properties\n    comments:\n    - Required when heavy metals are provided\n    - If different methods are used for multiple metals, indicate the metal and method.\n      Separate metals by ;\n    examples:\n    - value: https://doi.org/10.3390/ijms9040434\n    - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - extreme_unusual_properties/heavy metals method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000343\n    alias: heavy_metals_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  height_carper_fiber:\n    name: height_carper_fiber\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: centimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average carpet fiber height in the indoor environment\n    title: height carpet fiber mat\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - height carpet fiber mat\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000167\n    alias: height_carper_fiber\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  herbicide_regm:\n    name: herbicide_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: herbicide name;herbicide amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of herbicides; information\n      about treatment involving use of growth hormones; should include the name of\n      herbicide, amount administered, treatment regimen including how many times the\n      treatment was repeated, how long each treatment lasted, and the start and end\n      time of the entire treatment; can include multiple regimens\n    title: herbicide regimen\n    examples:\n    - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - herbicide regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000561\n    alias: herbicide_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  horizon_meth:\n    name: horizon_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining the horizon\n    title: soil horizon method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil horizon method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000321\n    alias: horizon_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_age:\n    name: host_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: year, day, hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Age of host at the time of sampling; relevant scale depends on species\n      and study, e.g. Could be seconds for amoebae or centuries for trees\n    title: host age\n    examples:\n    - value: 10 days\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000255\n    alias: host_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_body_habitat:\n    name: host_body_habitat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original body habitat where the sample was obtained from\n    title: host body habitat\n    examples:\n    - value: nasopharynx\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host body habitat\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000866\n    alias: host_body_habitat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_body_product:\n    name: host_body_product\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: FMA or UBERON\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Substance produced by the body, e.g. Stool, mucus, where the sample\n      was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n      ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma\n      or https://www.ebi.ac.uk/ols/ontologies/uberon\n    title: host body product\n    examples:\n    - value: Portion of mucus [fma66938]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host body product\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000888\n    alias: host_body_product\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  host_body_site:\n    name: host_body_site\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: FMA or UBERON\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of body site where the sample was obtained from, such as a specific\n      organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n      (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n      please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\n    title: host body site\n    examples:\n    - value: gill [UBERON:0002535]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host body site\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000867\n    alias: host_body_site\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  host_body_temp:\n    name: host_body_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Core body temperature of the host when sample was collected\n    title: host body temperature\n    examples:\n    - value: 15 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host body temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000274\n    alias: host_body_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_color:\n    name: host_color\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: color\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The color of host\n    title: host color\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host color\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000260\n    alias: host_color\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_common_name:\n    name: host_common_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: common name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Common name of the host.\n    title: host common name\n    examples:\n    - value: human\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host common name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000248\n    alias: host_common_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_diet:\n    name: host_diet\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: diet type\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Type of diet depending on the host, for animals omnivore, herbivore\n      etc., for humans high-fat, meditteranean etc.; can include multiple diet types\n    title: host diet\n    examples:\n    - value: herbivore\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host diet\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000869\n    alias: host_diet\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  host_dry_mass:\n    name: host_dry_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilogram, gram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of dry mass\n    title: host dry mass\n    examples:\n    - value: 500 gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host dry mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000257\n    alias: host_dry_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_family_relation:\n    name: host_family_relation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: relationship type;arbitrary identifier\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Familial relationships to other hosts in the same study; can include\n      multiple relationships\n    title: host family relationship\n    examples:\n    - value: offspring;Mussel25\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host family relationship\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{text}'\n    slot_uri: MIXS:0000872\n    alias: host_family_relation\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  host_genotype:\n    name: host_genotype\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: genotype\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Observed genotype\n    title: host genotype\n    examples:\n    - value: C57BL/6\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host genotype\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000365\n    alias: host_genotype\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_growth_cond:\n    name: host_growth_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url or free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Literature reference giving growth conditions of the host\n    title: host growth conditions\n    examples:\n    - value: https://academic.oup.com/icesjms/article/68/2/349/617247\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host growth conditions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0000871\n    alias: host_growth_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_height:\n    name: host_height\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: centimeter, millimeter, meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The height of subject\n    title: host height\n    examples:\n    - value: 0.1 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host height\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000264\n    alias: host_height\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_last_meal:\n    name: host_last_meal\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: content;duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Content of last meal and time since feeding; can include multiple\n      values\n    title: host last meal\n    examples:\n    - value: corn feed;P2H\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host last meal\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{duration}'\n    slot_uri: MIXS:0000870\n    alias: host_last_meal\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  host_length:\n    name: host_length\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: centimeter, millimeter, meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The length of subject\n    title: host length\n    examples:\n    - value: 1 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host length\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000256\n    alias: host_length\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_life_stage:\n    name: host_life_stage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: stage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Description of life stage of host\n    title: host life stage\n    examples:\n    - value: adult\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host life stage\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000251\n    alias: host_life_stage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_phenotype:\n    name: host_phenotype\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PATO or HP\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Phenotype of human or other host. For phenotypic quality ontology\n      (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.\n      For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\n    title: host phenotype\n    examples:\n    - value: elongated [PATO:0001154]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host phenotype\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000874\n    alias: host_phenotype\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  host_sex:\n    name: host_sex\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Gender or physical sex of the host.\n    title: host sex\n    examples:\n    - value: non-binary\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host sex\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000811\n    alias: host_sex\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: host_sex_enum\n    multivalued: false\n  host_shape:\n    name: host_shape\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: shape\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Morphological shape of host\n    title: host shape\n    examples:\n    - value: round\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host shape\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000261\n    alias: host_shape\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_subject_id:\n    name: host_subject_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: unique identifier\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A unique identifier by which each subject can be referred to, de-identified.\n    title: host subject id\n    examples:\n    - value: MPI123\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host subject id\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000861\n    alias: host_subject_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_subspecf_genlin:\n    name: host_subspecf_genlin\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n          e.g. serovar, biotype, ecotype, variety, cultivar.\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about the genetic distinctness of the host organism below\n      the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n      or any relevant genetic typing schemes like Group I plasmid. Subspecies should\n      not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage\n      name and the lineage rank separated by a colon, e.g., biovar:abc123.\n    title: host subspecific genetic lineage\n    examples:\n    - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host subspecific genetic lineage\n    rank: 1000\n    is_a: core field\n    string_serialization: '{rank name}:{text}'\n    slot_uri: MIXS:0001318\n    alias: host_subspecf_genlin\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  host_substrate:\n    name: host_substrate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: substrate name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The growth substrate of the host.\n    title: host substrate\n    examples:\n    - value: rock\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host substrate\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000252\n    alias: host_substrate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_symbiont:\n    name: host_symbiont\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: species name or common name\n      occurrence:\n        tag: occurrence\n        value: m\n    description: The taxonomic name of the organism(s) found living in mutualistic,\n      commensalistic, or parasitic symbiosis with the specific host.\n    title: observed host symbionts\n    examples:\n    - value: flukeworms\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - observed host symbionts\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001298\n    alias: host_symbiont\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  host_tot_mass:\n    name: host_tot_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilogram, gram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total mass of the host at collection, the unit depends on host\n    title: host total mass\n    examples:\n    - value: 2500 gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host total mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000263\n    alias: host_tot_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_wet_mass:\n    name: host_wet_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilogram, gram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of wet mass\n    title: host wet mass\n    examples:\n    - value: 1500 gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host wet mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000567\n    alias: host_wet_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  humidity:\n    name: humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per cubic meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Amount of water vapour in the air, at the time of sampling\n    title: humidity\n    examples:\n    - value: 25 gram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000100\n    alias: humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  humidity_regm:\n    name: humidity_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: humidity value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per cubic meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to varying degree\n      of humidity; information about treatment involving use of growth hormones; should\n      include amount of humidity administered, treatment regimen including how many\n      times the treatment was repeated, how long each treatment lasted, and the start\n      and end time of the entire treatment; can include multiple regimens\n    title: humidity regimen\n    examples:\n    - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - humidity regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000568\n    alias: humidity_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  indoor_space:\n    name: indoor_space\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A distinguishable space within a structure, the purpose for which\n      discrete areas of a building is used\n    title: indoor space\n    examples:\n    - value: foyer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - indoor space\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000763\n    alias: indoor_space\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: indoor_space_enum\n    multivalued: false\n  indoor_surf:\n    name: indoor_surf\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Type of indoor surface\n    title: indoor surface\n    examples:\n    - value: wall\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - indoor surface\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000764\n    alias: indoor_surf\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: indoor_surf_enum\n    multivalued: false\n  indust_eff_percent:\n    name: indust_eff_percent\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Percentage of industrial effluents received by wastewater treatment\n      plant\n    title: industrial effluent percent\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - industrial effluent percent\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000662\n    alias: indust_eff_percent\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  inorg_particles:\n    name: inorg_particles\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: inorganic particle name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of particles such as sand, grit, metal particles, ceramics,\n      etc.; can include multiple particles\n    title: inorganic particles\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - inorganic particles\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000664\n    alias: inorg_particles\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  inside_lux:\n    name: inside_lux\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilowatt per square metre\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The recorded value at sampling time (power density)\n    title: inside lux light\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - inside lux light\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000168\n    alias: inside_lux\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  int_wall_cond:\n    name: int_wall_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the wall at the time of sampling; photos\n      or video preferred; use drawings to indicate location of damaged areas\n    title: interior wall condition\n    examples:\n    - value: damaged\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - interior wall condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000813\n    alias: int_wall_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: int_wall_cond_enum\n    multivalued: false\n  investigation field:\n    name: investigation field\n    description: field describing aspect of the investigation/study to which the sample\n      belongs\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: investigation_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  iw_bt_date_well:\n    name: iw_bt_date_well\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Injection water breakthrough date per well following a secondary\n      and/or tertiary recovery\n    title: injection water breakthrough date of specific well\n    examples:\n    - value: '2018-05-11'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - injection water breakthrough date of specific well\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001010\n    alias: iw_bt_date_well\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  iwf:\n    name: iwf\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Proportion of the produced fluids derived from injected water at\n      the time of sampling. (e.g. 87%)\n    title: injection water fraction\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - injection water fraction\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000455\n    alias: iwf\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  last_clean:\n    name: last_clean\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The last time the floor was cleaned (swept, mopped, vacuumed)\n    title: last time swept/mopped/vacuumed\n    examples:\n    - value: 2018-05-11:T14:30Z\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - last time swept/mopped/vacuumed\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000814\n    alias: last_clean\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  lat_lon:\n    name: lat_lon\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: decimal degrees,  limit to 8 decimal points\n    description: The geographical origin of the sample as defined by latitude and\n      longitude. The values should be reported in decimal degrees and in WGS84 system\n    title: geographic location (latitude and longitude)\n    notes:\n    - This is currently a required field but it's not clear if this should be required\n      for human hosts\n    examples:\n    - value: 50.586825 6.408977\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - geographic location (latitude and longitude)\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{float} {float}'\n    slot_uri: MIXS:0000009\n    alias: lat_lon\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: GeolocationValue\n    multivalued: false\n  lbc_thirty:\n    name: lbc_thirty\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: ppm CaCO3/pH\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: lime buffer capacity, determined after 30 minute incubation\n    title: lime buffer capacity (at 30 minutes)\n    comments:\n    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n      one pH unit\n    examples:\n    - value: 543 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\n    aliases:\n    - lbc_thirty\n    - lbc30\n    - lime buffer capacity (at 30 minutes)\n    rank: 1000\n    alias: lbc_thirty\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  lbceq:\n    name: lbceq\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: ppm CaCO3/pH\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: lime buffer capacity, determined at equilibrium after 5 day incubation\n    title: lime buffer capacity (after 5 day incubation)\n    comments:\n    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n      one pH unit\n    examples:\n    - value: 1575 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - lbceq\n    - lime buffer capacity (at 5-day equilibrium)\n    rank: 1000\n    alias: lbceq\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  light_intensity:\n    name: light_intensity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: lux\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of light intensity\n    title: light intensity\n    examples:\n    - value: 0.3 lux\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - light intensity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000706\n    alias: light_intensity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  light_regm:\n    name: light_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: exposure type;light intensity;light quality\n      preferred_unit:\n        tag: preferred_unit\n        value: lux; micrometer, nanometer, angstrom\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information about treatment(s) involving exposure to light, including\n      both light intensity and quality.\n    title: light regimen\n    examples:\n    - value: incandescant light;10 lux;450 nanometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - light regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{float} {unit}'\n    slot_uri: MIXS:0000569\n    alias: light_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  light_type:\n    name: light_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Application of light to achieve some practical or aesthetic effect.\n      Lighting includes the use of both artificial light sources such as lamps and\n      light fixtures, as well as natural illumination by capturing daylight. Can also\n      include absence of light\n    title: light type\n    examples:\n    - value: desk lamp\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - light type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000769\n    alias: light_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: light_type_enum\n    multivalued: true\n  link_addit_analys:\n    name: link_addit_analys\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Link to additional analysis results performed on the sample\n    title: links to additional analysis\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - links to additional analysis\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000340\n    alias: link_addit_analys\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  link_class_info:\n    name: link_class_info\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Link to digitized soil maps or other soil classification information\n    title: link to classification information\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - link to classification information\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000329\n    alias: link_class_info\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  link_climate_info:\n    name: link_climate_info\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Link to climate resource\n    title: link to climate information\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - link to climate information\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000328\n    alias: link_climate_info\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  lithology:\n    name: lithology\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n      If \"other\" is specified, please propose entry in \"additional info\" field'\n    title: lithology\n    examples:\n    - value: Volcanic\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - lithology\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000990\n    alias: lithology\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: lithology_enum\n    multivalued: false\n  local_class:\n    name: local_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: local classification name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Soil classification based on local soil classification system\n    title: soil_taxonomic/local classification\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil_taxonomic/local classification\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000330\n    alias: local_class\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  local_class_meth:\n    name: local_class_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining the local soil classification\n    title: soil_taxonomic/local classification method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil_taxonomic/local classification method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000331\n    alias: local_class_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  magnesium:\n    name: magnesium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per liter, milligram per liter, parts per million, micromole per\n          kilogram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of magnesium in the sample\n    title: magnesium\n    examples:\n    - value: 52.8 micromole per kilogram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - magnesium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000431\n    alias: magnesium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  manganese:\n    name: manganese\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg (ppm)\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of manganese in the sample\n    title: manganese\n    examples:\n    - value: 24.7 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - manganese\n    rank: 1000\n    alias: manganese\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  max_occup:\n    name: max_occup\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The maximum amount of people allowed in the indoor environment\n    title: maximum occupancy\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - maximum occupancy\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000229\n    alias: max_occup\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  mean_frict_vel:\n    name: mean_frict_vel\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter per second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of mean friction velocity\n    title: mean friction velocity\n    examples:\n    - value: 0.5 meter per second\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean friction velocity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000498\n    alias: mean_frict_vel\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  mean_peak_frict_vel:\n    name: mean_peak_frict_vel\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter per second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of mean peak friction velocity\n    title: mean peak friction velocity\n    examples:\n    - value: 1 meter per second\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean peak friction velocity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000502\n    alias: mean_peak_frict_vel\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  mech_struc:\n    name: mech_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'mechanical structure: a moving structure'\n    title: mechanical structure\n    examples:\n    - value: elevator\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mechanical structure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000815\n    alias: mech_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: mech_struc_enum\n    multivalued: false\n  mechanical_damage:\n    name: mechanical_damage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: damage type;body site\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about any mechanical damage exerted on the plant; can\n      include multiple damages and sites\n    title: mechanical damage\n    examples:\n    - value: pruning;bark\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mechanical damage\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{text}'\n    slot_uri: MIXS:0001052\n    alias: mechanical_damage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  methane:\n    name: methane\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, parts per billion, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Methane (gas) amount or concentration at the time of sampling\n    title: methane\n    examples:\n    - value: 1800 parts per billion\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - methane\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000101\n    alias: methane\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  micro_biomass_meth:\n    name: micro_biomass_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining microbial biomass\n    title: microbial biomass method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - microbial biomass method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000339\n    alias: micro_biomass_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  microbial_biomass:\n    name: microbial_biomass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: ton, kilogram, gram per kilogram soil\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The part of the organic matter in the soil that constitutes living\n      microorganisms smaller than 5-10 micrometer. If you keep this, you would need\n      to have correction factors used for conversion to the final units\n    title: microbial biomass\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - microbial biomass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000650\n    alias: microbial_biomass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  mineral_nutr_regm:\n    name: mineral_nutr_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: mineral nutrient name;mineral nutrient amount;treatment interval and\n          duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving the use of mineral supplements;\n      should include the name of mineral nutrient, amount administered, treatment\n      regimen including how many times the treatment was repeated, how long each treatment\n      lasted, and the start and end time of the entire treatment; can include multiple\n      mineral nutrient regimens\n    title: mineral nutrient regimen\n    examples:\n    - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mineral nutrient regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000570\n    alias: mineral_nutr_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  misc_param:\n    name: misc_param\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: parameter name;measurement value\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Any other measurement performed or parameter collected, that is not\n      listed here\n    title: miscellaneous parameter\n    examples:\n    - value: Bicarbonate ion concentration;2075 micromole per kilogram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - miscellaneous parameter\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000752\n    alias: misc_param\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  n_alkanes:\n    name: n_alkanes\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: n-alkane name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of n-alkanes; can include multiple n-alkanes\n    title: n-alkanes\n    examples:\n    - value: n-hexadecane;100 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - n-alkanes\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000503\n    alias: n_alkanes\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  nitrate:\n    name: nitrate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrate in the sample\n    title: nitrate\n    examples:\n    - value: 65 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - nitrate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000425\n    alias: nitrate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  nitrate_nitrogen:\n    name: nitrate_nitrogen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrate nitrogen in the sample\n    title: nitrate_nitrogen\n    comments:\n    - often below some specified limit of detection\n    examples:\n    - value: 0.29 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - nitrate_nitrogen\n    - NO3-N\n    rank: 1000\n    alias: nitrate_nitrogen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  nitrite:\n    name: nitrite\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrite in the sample\n    title: nitrite\n    examples:\n    - value: 0.5 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - nitrite\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000426\n    alias: nitrite\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  nitrite_nitrogen:\n    name: nitrite_nitrogen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrite nitrogen in the sample\n    title: nitrite_nitrogen\n    examples:\n    - value: 1.2 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - nitrite_nitrogen\n    - NO2-N\n    rank: 1000\n    alias: nitrite_nitrogen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  nitro:\n    name: nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrogen (total)\n    title: nitrogen\n    examples:\n    - value: 4.2 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000504\n    alias: nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  non_min_nutr_regm:\n    name: non_min_nutr_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n          and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving the exposure of plant to non-mineral\n      nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n      nutrient, amount administered, treatment regimen including how many times the\n      treatment was repeated, how long each treatment lasted, and the start and end\n      time of the entire treatment; can include multiple non-mineral nutrient regimens\n    title: non-mineral nutrient regimen\n    examples:\n    - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - non-mineral nutrient regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000571\n    alias: non_min_nutr_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  nucleic acid sequence source field:\n    name: nucleic acid sequence source field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: nucleic_acid_sequence_source_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  number_pets:\n    name: number_pets\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of pets residing in the sampled space\n    title: number of pets\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - number of pets\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000231\n    alias: number_pets\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  number_plants:\n    name: number_plants\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of plant(s) in the sampling space\n    title: number of houseplants\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - number of houseplants\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000230\n    alias: number_plants\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  number_resident:\n    name: number_resident\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of individuals currently occupying in the sampling location\n    title: number of residents\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - number of residents\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000232\n    alias: number_resident\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  occup_density_samp:\n    name: occup_density_samp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Average number of occupants at time of sampling per square footage\n    title: occupant density at sampling\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - occupant density at sampling\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000217\n    alias: occup_density_samp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  occup_document:\n    name: occup_document\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of documentation of occupancy\n    title: occupancy documentation\n    examples:\n    - value: estimate\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - occupancy documentation\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000816\n    alias: occup_document\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: occup_document_enum\n    multivalued: false\n  occup_samp:\n    name: occup_samp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Number of occupants present at time of sample within the given space\n    title: occupancy at sampling\n    examples:\n    - value: '10'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - occupancy at sampling\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000772\n    alias: occup_samp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  org_carb:\n    name: org_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of organic carbon\n    title: organic carbon\n    examples:\n    - value: 1.5 microgram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000508\n    alias: org_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  org_count_qpcr_info:\n    name: org_count_qpcr_info\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n          denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n          elongation:degrees_minutes; total cycles\n      preferred_unit:\n        tag: preferred_unit\n        value: number of cells per gram (or ml or cm^2)\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'If qpcr was used for the cell count, the target gene name, the primer\n      sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n      FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n      annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n      30 cycles)'\n    title: organism count qPCR information\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organism count qPCR information\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n      elongation:degrees_minutes; total cycles'\n    slot_uri: MIXS:0000099\n    alias: org_count_qpcr_info\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  org_matter:\n    name: org_matter\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of organic matter\n    title: organic matter\n    examples:\n    - value: 1.75 milligram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organic matter\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000204\n    alias: org_matter\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  org_nitro:\n    name: org_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of organic nitrogen\n    title: organic nitrogen\n    examples:\n    - value: 4 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000205\n    alias: org_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  org_particles:\n    name: org_particles\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: particle name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of particles such as faeces, hairs, food, vomit, paper\n      fibers, plant material, humus, etc.\n    title: organic particles\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organic particles\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000665\n    alias: org_particles\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  organism_count:\n    name: organism_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: organism name;measurement value;enumeration\n      preferred_unit:\n        tag: preferred_unit\n        value: number of cells per cubic meter, number of cells per milliliter, number\n          of cells per cubic centimeter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: 'Total cell count of any organism (or group of organisms) per gram,\n      volume or area of sample, should include name of organism followed by count.\n      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should\n      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\n    title: organism count\n    examples:\n    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organism count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000103\n    alias: organism_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  owc_tvdss:\n    name: owc_tvdss\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\n    title: oil water contact depth\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - oil water contact depth\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000405\n    alias: owc_tvdss\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  oxy_stat_samp:\n    name: oxy_stat_samp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Oxygenation status of sample\n    title: oxygenation status of sample\n    examples:\n    - value: aerobic\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - oxygenation status of sample\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000753\n    alias: oxy_stat_samp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: oxy_stat_samp_enum\n    multivalued: false\n  oxygen:\n    name: oxygen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Oxygen (gas) amount or concentration at the time of sampling\n    title: oxygen\n    examples:\n    - value: 600 parts per million\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - oxygen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000104\n    alias: oxygen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  part_org_carb:\n    name: part_org_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of particulate organic carbon\n    title: particulate organic carbon\n    examples:\n    - value: 1.92 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - particulate organic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000515\n    alias: part_org_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  part_org_nitro:\n    name: part_org_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of particulate organic nitrogen\n    title: particulate organic nitrogen\n    examples:\n    - value: 0.3 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - particulate organic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000719\n    alias: part_org_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  particle_class:\n    name: particle_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: particle name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micrometer\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Particles are classified, based on their size, into six general categories:clay,\n      silt, sand, gravel, cobbles, and boulders; should include amount of particle\n      preceded by the name of the particle type; can include multiple values\n    title: particle classification\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - particle classification\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000206\n    alias: particle_class\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  permeability:\n    name: permeability\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: mD\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Measure of the ability of a hydrocarbon resource to allow fluids\n      to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\n    title: permeability\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - permeability\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} - {integer} {unit}'\n    slot_uri: MIXS:0000404\n    alias: permeability\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  perturbation:\n    name: perturbation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: perturbation type name;perturbation interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Type of perturbation, e.g. chemical administration, physical disturbance,\n      etc., coupled with perturbation regimen including how many times the perturbation\n      was repeated, how long each perturbation lasted, and the start and end time\n      of the entire perturbation period; can include multiple perturbation types\n    title: perturbation\n    examples:\n    - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - perturbation\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000754\n    alias: perturbation\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  pesticide_regm:\n    name: pesticide_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: pesticide name;pesticide amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of insecticides; should\n      include the name of pesticide, amount administered, treatment regimen including\n      how many times the treatment was repeated, how long each treatment lasted, and\n      the start and end time of the entire treatment; can include multiple pesticide\n      regimens\n    title: pesticide regimen\n    examples:\n    - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pesticide regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000573\n    alias: pesticide_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  petroleum_hydrocarb:\n    name: petroleum_hydrocarb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of petroleum hydrocarbon\n    title: petroleum hydrocarbon\n    examples:\n    - value: 0.05 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - petroleum hydrocarbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000516\n    alias: petroleum_hydrocarb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ph:\n    name: ph\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Ph measurement of the sample, or liquid portion of sample, or aqueous\n      phase of the fluid\n    title: pH\n    examples:\n    - value: '7.2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pH\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001001\n    alias: ph\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: double\n    multivalued: false\n  ph_meth:\n    name: ph_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining ph\n    title: pH method\n    comments:\n    - This can include a link to the instrument used or a citation for the method.\n    examples:\n    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n    - value: https://doi.org/10.2136/sssabookser5.3.c16\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pH method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0001106\n    alias: ph_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  ph_regm:\n    name: ph_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;treatment interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving exposure of plants to varying\n      levels of ph of the growth media, treatment regimen including how many times\n      the treatment was repeated, how long each treatment lasted, and the start and\n      end time of the entire treatment; can include multiple regimen\n    title: pH regimen\n    examples:\n    - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pH regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0001056\n    alias: ph_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  phaeopigments:\n    name: phaeopigments\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: phaeopigment name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of phaeopigments; can include multiple phaeopigments\n    title: phaeopigments\n    examples:\n    - value: 2.5 milligram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - phaeopigments\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000180\n    alias: phaeopigments\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  phosphate:\n    name: phosphate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of phosphate\n    title: phosphate\n    examples:\n    - value: 0.7 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - phosphate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000505\n    alias: phosphate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  phosplipid_fatt_acid:\n    name: phosplipid_fatt_acid\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: phospholipid fatty acid name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per gram, mole per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of phospholipid fatty acids; can include multiple values\n    title: phospholipid fatty acid\n    examples:\n    - value: 2.98 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - phospholipid fatty acid\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000181\n    alias: phosplipid_fatt_acid\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  photon_flux:\n    name: photon_flux\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: number of photons per second per unit area\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of photon flux\n    title: photon flux\n    examples:\n    - value: 3.926 micromole photons per second per square meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - photon flux\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000725\n    alias: photon_flux\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  plant_growth_med:\n    name: plant_growth_med\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: EO or enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Specification of the media for growing the plants or tissue cultured\n      samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in\n      vitro liquid culture medium. Recommended value is a specific value from EO:plant\n      growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)\n      or other controlled vocabulary\n    title: plant growth medium\n    examples:\n    - value: hydroponic plant culture media [EO:0007067]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - plant growth medium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001057\n    alias: plant_growth_med\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  plant_product:\n    name: plant_product\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: product name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Substance produced by the plant, where the sample was obtained from\n    title: plant product\n    examples:\n    - value: xylem sap [PO:0025539]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - plant product\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001058\n    alias: plant_product\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  plant_sex:\n    name: plant_sex\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sex of the reproductive parts on the whole plant, e.g. pistillate,\n      staminate, monoecieous, hermaphrodite.\n    title: plant sex\n    examples:\n    - value: Hermaphroditic\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - plant sex\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001059\n    alias: plant_sex\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: plant_sex_enum\n    multivalued: false\n  plant_struc:\n    name: plant_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PO\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of plant structure the sample was obtained from; for Plant Ontology\n      (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n      e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the\n      sex of it can be recorded here.\n    title: plant structure\n    examples:\n    - value: epidermis [PO:0005679]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - plant structure\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0001060\n    alias: plant_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  pollutants:\n    name: pollutants\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: pollutant name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter, microgram per cubic meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Pollutant types and, amount or concentrations measured at the time\n      of sampling; can report multiple pollutants by entering numeric values preceded\n      by name of pollutant\n    title: pollutants\n    examples:\n    - value: lead;0.15 microgram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pollutants\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000107\n    alias: pollutants\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  porosity:\n    name: porosity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value or range\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Porosity of deposited sediment is volume of voids divided by the\n      total volume of sample\n    title: porosity\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - porosity\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} - {float} {unit}'\n    slot_uri: MIXS:0000211\n    alias: porosity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  potassium:\n    name: potassium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of potassium in the sample\n    title: potassium\n    examples:\n    - value: 463 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - potassium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000430\n    alias: potassium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  pour_point:\n    name: pour_point\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Temperature at which a liquid becomes semi solid and loses its flow\n      characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with\n      a high paraffin content, typically found in crude deriving from a larger proportion\n      of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\n    title: pour point\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pour point\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000127\n    alias: pour_point\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  pre_treatment:\n    name: pre_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: pre-treatment type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The process of pre-treatment removes materials that can be easily\n      collected from the raw wastewater\n    title: pre-treatment\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pre-treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000348\n    alias: pre_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  pres_animal_insect:\n    name: pres_animal_insect\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration;count\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type and number of animals or insects present in the sampling\n      space.\n    title: presence of pets, animals, or insects\n    examples:\n    - value: cat;5\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - presence of pets, animals, or insects\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000819\n    alias: pres_animal_insect\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n    pattern: ^(cat|dog|rodent|snake|other);\\d+$\n  pressure:\n    name: pressure\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: atmosphere\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Pressure to which the sample is subject to, in atmospheres\n    title: pressure\n    examples:\n    - value: 50 atmosphere\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pressure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000412\n    alias: pressure\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  prev_land_use_meth:\n    name: prev_land_use_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining previous land use and dates\n    title: history/previous land use method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/previous land use method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000316\n    alias: prev_land_use_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  previous_land_use:\n    name: previous_land_use\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: land use name;date\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Previous land use and dates\n    title: history/previous land use\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/previous land use\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{timestamp}'\n    slot_uri: MIXS:0000315\n    alias: previous_land_use\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  primary_prod:\n    name: primary_prod\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter per day, gram per square meter per day\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of primary production, generally measured as isotope\n      uptake\n    title: primary production\n    examples:\n    - value: 100 milligram per cubic meter per day\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - primary production\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000728\n    alias: primary_prod\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  primary_treatment:\n    name: primary_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: primary treatment type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The process to produce both a generally homogeneous liquid capable\n      of being treated biologically and a sludge that can be separately treated or\n      processed\n    title: primary treatment\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - primary treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000349\n    alias: primary_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  prod_rate:\n    name: prod_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic meter per day\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Oil and/or gas production rates per well (e.g. 524 m3 / day)\n    title: production rate\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - production rate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000452\n    alias: prod_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  prod_start_date:\n    name: prod_start_date\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Date of field's first production\n    title: production start date\n    examples:\n    - value: '2018-05-11'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - production start date\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001008\n    alias: prod_start_date\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  profile_position:\n    name: profile_position\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Cross-sectional position in the hillslope where sample was collected.sample\n      area position in relation to surrounding areas\n    title: profile position\n    examples:\n    - value: summit\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - profile position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001084\n    alias: profile_position\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: profile_position_enum\n    multivalued: false\n  quad_pos:\n    name: quad_pos\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The quadrant position of the sampling room within the building\n    title: quadrant position\n    examples:\n    - value: West side\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - quadrant position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000820\n    alias: quad_pos\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: quad_pos_enum\n    multivalued: false\n  radiation_regm:\n    name: radiation_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: radiation type name;radiation amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: rad, gray\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving exposure of plant or a plant\n      part to a particular radiation regimen; should include the radiation type, amount\n      or intensity administered, treatment regimen including how many times the treatment\n      was repeated, how long each treatment lasted, and the start and end time of\n      the entire treatment; can include multiple radiation regimens\n    title: radiation regimen\n    examples:\n    - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - radiation regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000575\n    alias: radiation_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  rainfall_regm:\n    name: rainfall_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to a given amount\n      of rainfall, treatment regimen including how many times the treatment was repeated,\n      how long each treatment lasted, and the start and end time of the entire treatment;\n      can include multiple regimens\n    title: rainfall regimen\n    examples:\n    - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rainfall regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000576\n    alias: rainfall_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  reactor_type:\n    name: reactor_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: reactor type name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Anaerobic digesters can be designed and engineered to operate using\n      a number of different process configurations, as batch or continuous, mesophilic,\n      high solid or low solid, and single stage or multistage\n    title: reactor type\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - reactor type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000350\n    alias: reactor_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  redox_potential:\n    name: redox_potential\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millivolt\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Redox potential, measured relative to a hydrogen cell, indicating\n      oxidation or reduction potential\n    title: redox potential\n    examples:\n    - value: 300 millivolt\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - redox potential\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000182\n    alias: redox_potential\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  rel_air_humidity:\n    name: rel_air_humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Partial vapor and air pressure, density of the vapor and air, or\n      by the actual mass of the vapor and air\n    title: relative air humidity\n    examples:\n    - value: 80%\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - relative air humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000121\n    alias: rel_air_humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  rel_humidity_out:\n    name: rel_humidity_out\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram of air, kilogram of air\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The recorded outside relative humidity value at the time of sampling\n    title: outside relative humidity\n    examples:\n    - value: 12 per kilogram of air\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - outside relative humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000188\n    alias: rel_humidity_out\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  rel_samp_loc:\n    name: rel_samp_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The sampling location within the train car\n    title: relative sampling location\n    examples:\n    - value: center of car\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - relative sampling location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000821\n    alias: rel_samp_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: rel_samp_loc_enum\n    multivalued: false\n  reservoir:\n    name: reservoir\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of the reservoir (e.g. Carapebus)\n    title: reservoir name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - reservoir name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000303\n    alias: reservoir\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  resins_pc:\n    name: resins_pc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n      method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n      and polarity. There are three main methods to obtain SARA results. The most\n      popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n      https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n    title: resins wt%\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - resins wt%\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000134\n    alias: resins_pc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_air_exch_rate:\n    name: room_air_exch_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: liter per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The rate at which outside air replaces indoor air in a given space\n    title: room air exchange rate\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room air exchange rate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000169\n    alias: room_air_exch_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  room_architec_elem:\n    name: room_architec_elem\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The unique details and component parts that, together, form the architecture\n      of a distinguisahable space within a built structure\n    title: room architectural elements\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room architectural elements\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000233\n    alias: room_architec_elem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  room_condt:\n    name: room_condt\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The condition of the room at the time of sampling\n    title: room condition\n    examples:\n    - value: new\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000822\n    alias: room_condt\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_condt_enum\n    multivalued: false\n  room_connected:\n    name: room_connected\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of rooms connected to the sampling room by a doorway\n    title: rooms connected by a doorway\n    examples:\n    - value: office\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooms connected by a doorway\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000826\n    alias: room_connected\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_connected_enum\n    multivalued: false\n  room_count:\n    name: room_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The total count of rooms in the built structure including all room\n      types\n    title: room count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000234\n    alias: room_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_dim:\n    name: room_dim\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The length, width and height of sampling room\n    title: room dimensions\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room dimensions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\n    slot_uri: MIXS:0000192\n    alias: room_dim\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_door_dist:\n    name: room_door_dist\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Distance between doors (meters) in the hallway between the sampling\n      room and adjacent rooms\n    title: room door distance\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room door distance\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} {unit}'\n    slot_uri: MIXS:0000193\n    alias: room_door_dist\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_door_share:\n    name: room_door_share\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: room name;room number\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of room(s) (room number, room name) sharing a door with the\n      sampling room\n    title: rooms that share a door with sampling room\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooms that share a door with sampling room\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{integer}'\n    slot_uri: MIXS:0000242\n    alias: room_door_share\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_hallway:\n    name: room_hallway\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: room name;room number\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of room(s) (room number, room name) located in the same hallway\n      as sampling room\n    title: rooms that are on the same hallway\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooms that are on the same hallway\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{integer}'\n    slot_uri: MIXS:0000238\n    alias: room_hallway\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_loc:\n    name: room_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The position of the room within the building\n    title: room location in building\n    examples:\n    - value: interior room\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room location in building\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000823\n    alias: room_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_loc_enum\n    multivalued: false\n  room_moist_dam_hist:\n    name: room_moist_dam_hist\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The history of moisture damage or mold in the past 12 months. Number\n      of events of moisture damage or mold observed\n    title: room moisture damage or mold history\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room moisture damage or mold history\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000235\n    alias: room_moist_dam_hist\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: integer\n    multivalued: false\n  room_net_area:\n    name: room_net_area\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square feet, square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The net floor area of sampling room. Net area excludes wall thicknesses\n    title: room net area\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room net area\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} {unit}'\n    slot_uri: MIXS:0000194\n    alias: room_net_area\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_occup:\n    name: room_occup\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Count of room occupancy at time of sampling\n    title: room occupancy\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room occupancy\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000236\n    alias: room_occup\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  room_samp_pos:\n    name: room_samp_pos\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The horizontal sampling position in the room relative to architectural\n      elements\n    title: room sampling position\n    examples:\n    - value: south corner\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room sampling position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000824\n    alias: room_samp_pos\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_samp_pos_enum\n    multivalued: false\n  room_type:\n    name: room_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The main purpose or activity of the sampling room. A room is any\n      distinguishable space within a structure\n    title: room type\n    examples:\n    - value: bathroom\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000825\n    alias: room_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_type_enum\n    multivalued: false\n  room_vol:\n    name: room_vol\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic feet, cubic meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Volume of sampling room\n    title: room volume\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room volume\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} {unit}'\n    slot_uri: MIXS:0000195\n    alias: room_vol\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_wall_share:\n    name: room_wall_share\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: room name;room number\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of room(s) (room number, room name) sharing a wall with the\n      sampling room\n    title: rooms that share a wall with sampling room\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooms that share a wall with sampling room\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{integer}'\n    slot_uri: MIXS:0000243\n    alias: room_wall_share\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_window_count:\n    name: room_window_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Number of windows in the room\n    title: room window count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room window count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000237\n    alias: room_window_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: integer\n    multivalued: false\n  root_cond:\n    name: root_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url or free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Relevant rooting conditions such as field plot size, sowing density,\n      container dimensions, number of plants per container.\n    title: rooting conditions\n    examples:\n    - value: http://himedialabs.com/TD/PT158.pdf\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting conditions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0001061\n    alias: root_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_carbon:\n    name: root_med_carbon\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: carbon source name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Source of organic carbon in the culture rooting medium; e.g. sucrose.\n    title: rooting medium carbon\n    examples:\n    - value: sucrose\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium carbon\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000577\n    alias: root_med_carbon\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_macronutr:\n    name: root_med_macronutr\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: macronutrient name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of the culture rooting medium macronutrients (N,P, K,\n      Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\n    title: rooting medium macronutrients\n    examples:\n    - value: KH2PO4;170\u00ac\u2020milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium macronutrients\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000578\n    alias: root_med_macronutr\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_micronutr:\n    name: root_med_micronutr\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: micronutrient name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of the culture rooting medium micronutrients (Fe, Mn,\n      Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\n    title: rooting medium micronutrients\n    examples:\n    - value: H3BO3;6.2\u00ac\u2020milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium micronutrients\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000579\n    alias: root_med_micronutr\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_ph:\n    name: root_med_ph\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: pH measurement of the culture rooting medium; e.g. 5.5.\n    title: rooting medium pH\n    examples:\n    - value: '7.5'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium pH\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001062\n    alias: root_med_ph\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  root_med_regl:\n    name: root_med_regl\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: regulator name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Growth regulators in the culture rooting medium such as cytokinins,\n      auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\n    title: rooting medium regulators\n    examples:\n    - value: abscisic acid;0.75 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium regulators\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000581\n    alias: root_med_regl\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_solid:\n    name: root_med_solid\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Specification of the solidifying agent in the culture rooting medium;\n      e.g. agar.\n    title: rooting medium solidifier\n    examples:\n    - value: agar\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium solidifier\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001063\n    alias: root_med_solid\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_suppl:\n    name: root_med_suppl\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: supplement name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Organic supplements of the culture rooting medium, such as vitamins,\n      amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n      (0.5\u00ac\u2020mg/L).\n    title: rooting medium organic supplements\n    examples:\n    - value: nicotinic acid;0.5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium organic supplements\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000580\n    alias: root_med_suppl\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  salinity:\n    name: salinity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: practical salinity unit, percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The total concentration of all dissolved salts in a liquid or solid\n      sample. While salinity can be measured by a complete chemical analysis, this\n      method is difficult and time consuming. More often, it is instead derived from\n      the conductivity measurement. This is known as practical salinity. These derivations\n      compare the specific conductance of the sample to a salinity standard such as\n      seawater.\n    title: salinity\n    examples:\n    - value: 25 practical salinity unit\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - salinity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000183\n    alias: salinity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  salinity_meth:\n    name: salinity_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining salinity\n    title: salinity method\n    examples:\n    - value: https://doi.org/10.1007/978-1-61779-986-0_28\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - salinity method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000341\n    alias: salinity_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  salt_regm:\n    name: salt_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: salt name;salt amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, microgram, mole per liter, gram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of salts as supplement\n      to liquid and soil growth media; should include the name of salt, amount administered,\n      treatment regimen including how many times the treatment was repeated, how long\n      each treatment lasted, and the start and end time of the entire treatment; can\n      include multiple salt regimens\n    title: salt regimen\n    examples:\n    - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - salt regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000582\n    alias: salt_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  samp_capt_status:\n    name: samp_capt_status\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reason for the sample\n    title: sample capture status\n    examples:\n    - value: farm sample\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample capture status\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000860\n    alias: samp_capt_status\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_capt_status_enum\n    multivalued: false\n  samp_collec_device:\n    name: samp_collec_device\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: device name\n    description: The device used to collect an environmental sample. This field accepts\n      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\n    title: sample collection device\n    examples:\n    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample collection device\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{termLabel} {[termID]}|{text}'\n    slot_uri: MIXS:0000002\n    alias: samp_collec_device\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  samp_collec_method:\n    name: samp_collec_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url , or text\n    description: The method employed for collecting the sample.\n    title: sample collection method\n    examples:\n    - value: swabbing\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample collection method\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0001225\n    alias: samp_collec_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  samp_collect_point:\n    name: samp_collect_point\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sampling point on the asset were sample was collected (e.g. Wellhead,\n      storage tank, separator, etc). If \"other\" is specified, please propose entry\n      in \"additional info\" field\n    title: sample collection point\n    examples:\n    - value: well\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample collection point\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001015\n    alias: samp_collect_point\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_collect_point_enum\n    multivalued: false\n  samp_dis_stage:\n    name: samp_dis_stage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Stage of the disease at the time of sample collection, e.g. inoculation,\n      penetration, infection, growth and reproduction, dissemination of pathogen.\n    title: sample disease stage\n    examples:\n    - value: infection\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample disease stage\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000249\n    alias: samp_dis_stage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_dis_stage_enum\n    multivalued: false\n  samp_floor:\n    name: samp_floor\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The floor of the building, where the sampling room is located\n    title: sampling floor\n    examples:\n    - value: 4th floor\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sampling floor\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000828\n    alias: samp_floor\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_floor_enum\n    multivalued: false\n  samp_loc_corr_rate:\n    name: samp_loc_corr_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter per year\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Metal corrosion rate is the speed of metal deterioration due to environmental\n      conditions. As environmental conditions change corrosion rates change accordingly.\n      Therefore, long term corrosion rates are generally more informative than short\n      term rates and for that reason they are preferred during reporting. In the case\n      of suspected MIC, corrosion rate measurements at the time of sampling might\n      provide insights into the involvement of certain microbial community members\n      in MIC as well as potential microbial interplays\n    title: corrosion rate at sample location\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - corrosion rate at sample location\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} - {float} {unit}'\n    slot_uri: MIXS:0000136\n    alias: samp_loc_corr_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_mat_process:\n    name: samp_mat_process\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text\n    description: A brief description of any processing applied to the sample during\n      or after retrieving the sample from environment, or a link to the relevant protocol(s)\n      performed.\n    title: sample material processing\n    examples:\n    - value: filtering of seawater, storing samples in ethanol\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample material processing\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000016\n    alias: samp_mat_process\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  samp_md:\n    name: samp_md\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;enumeration\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: In non deviated well, measured depth is equal to the true vertical\n      depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated\n      wells, the MD is the length of trajectory of the borehole measured from the\n      same reference or datum. Common datums used are ground level (GL), drilling\n      rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL).\n      If \"other\" is specified, please propose entry in \"additional info\" field\n    title: sample measured depth\n    examples:\n    - value: 1534 meter;MSL\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample measured depth\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000413\n    alias: samp_md\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  samp_preserv:\n    name: samp_preserv\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milliliter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n      etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\n    title: preservative added to sample\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - preservative added to sample\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000463\n    alias: samp_preserv\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_room_id:\n    name: samp_room_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sampling room number. This ID should be consistent with the designations\n      on the building floor plans\n    title: sampling room ID or name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sampling room ID or name\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000244\n    alias: samp_room_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_size:\n    name: samp_size\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millliter, gram, milligram, liter\n    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n      sample collected.\n    title: amount or size of sample collected\n    examples:\n    - value: 5 liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - amount or size of sample collected\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    slot_uri: MIXS:0000001\n    alias: samp_size\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  samp_sort_meth:\n    name: samp_sort_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: description of method\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Method by which samples are sorted; open face filter collecting total\n      suspended particles, prefilter to remove particles larger than X micrometers\n      in diameter, where common values of X would be 10 and 2.5 full size sorting\n      in a cascade impactor.\n    title: sample size sorting method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample size sorting method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000216\n    alias: samp_sort_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  samp_store_dur:\n    name: samp_store_dur\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: duration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Duration for which the sample was stored\n    title: sample storage duration\n    examples:\n    - value: P1Y6M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample storage duration\n    rank: 1000\n    is_a: core field\n    string_serialization: '{duration}'\n    slot_uri: MIXS:0000116\n    alias: samp_store_dur\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_store_loc:\n    name: samp_store_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: location name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Location at which sample was stored, usually name of a specific freezer/room\n    title: sample storage location\n    examples:\n    - value: Freezer no:5\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample storage location\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000755\n    alias: samp_store_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_store_temp:\n    name: samp_store_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Temperature at which sample was stored, e.g. -80 degree Celsius\n    title: sample storage temperature\n    examples:\n    - value: -80 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample storage temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000110\n    alias: samp_store_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  samp_subtype:\n    name: samp_subtype\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of sample sub-type. For example if \"sample type\" is \"Produced\n      Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified,\n      please propose entry in \"additional info\" field\n    title: sample subtype\n    examples:\n    - value: biofilm\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample subtype\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000999\n    alias: samp_subtype\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_subtype_enum\n    multivalued: false\n  samp_taxon_id:\n    name: samp_taxon_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: Taxonomy ID\n    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa\n      sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or\n      'blank sample' for negative controls.\n    title: Taxonomy ID of DNA sample\n    comments:\n    - coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Taxonomy ID of DNA sample\n    rank: 1000\n    is_a: investigation field\n    slot_uri: MIXS:0001320\n    alias: samp_taxon_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    multivalued: false\n  samp_time_out:\n    name: samp_time_out\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: time\n      preferred_unit:\n        tag: preferred_unit\n        value: hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The recent and long term history of outside sampling\n    title: sampling time outside\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sampling time outside\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000196\n    alias: samp_time_out\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_transport_cond:\n    name: samp_transport_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: days;degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sample transport duration (in days or hrs) and temperature the sample\n      was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\n    title: sample transport conditions\n    examples:\n    - value: 5 days;-20 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample transport conditions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{float} {unit}'\n    slot_uri: MIXS:0000410\n    alias: samp_transport_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_tvdss:\n    name: samp_tvdss\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value or measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Depth of the sample i.e. The vertical distance between the sea level\n      and the sampled position in the subsurface. Depth can be reported as an interval\n      for subsurface samples e.g. 1325.75-1362.25 m\n    title: sample true vertical depth subsea\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample true vertical depth subsea\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float}-{float} {unit}'\n    slot_uri: MIXS:0000409\n    alias: samp_tvdss\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_type:\n    name: samp_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: GENEPIO:0001246\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of material from which the sample was obtained. For the\n      Hydrocarbon package, samples include types like core, rock trimmings, drill\n      cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,\n      produced water, injected water, swabs, etc. For the Food Package, samples are\n      usually categorized as food, body products or tissues, or environmental material.\n      This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\n    title: sample type\n    examples:\n    - value: built environment sample [GENEPIO:0001248]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000998\n    alias: samp_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_weather:\n    name: samp_weather\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The weather on the sampling day\n    title: sampling day weather\n    examples:\n    - value: foggy\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sampling day weather\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000827\n    alias: samp_weather\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_weather_enum\n    multivalued: false\n  samp_well_name:\n    name: samp_well_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of the well (e.g. BXA1123) where sample was taken\n    title: sample well name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample well name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000296\n    alias: samp_well_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  saturates_pc:\n    name: saturates_pc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n      method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n      and polarity. There are three main methods to obtain SARA results. The most\n      popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n      https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n    title: saturates wt%\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - saturates wt%\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000131\n    alias: saturates_pc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  season:\n    name: season\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: NCIT:C94729\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The season when sampling occurred. Any of the four periods into which\n      the year is divided by the equinoxes and solstices. This field accepts terms\n      listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).\n    title: season\n    examples:\n    - value: autumn [NCIT:C94733]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - season\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000829\n    alias: season\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  season_environment:\n    name: season_environment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: seasonal environment name;treatment interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Treatment involving an exposure to a particular season (e.g. Winter,\n      summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n      was repeated, how long each treatment lasted, and the start and end time of\n      the entire treatment\n    title: seasonal environment\n    examples:\n    - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - seasonal environment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0001068\n    alias: season_environment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  season_precpt:\n    name: season_precpt\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average of all seasonal precipitation values known, or an estimated\n      equivalent value derived by such methods as regional indexes or Isohyetal maps.\n    title: average seasonal precipitation\n    todos:\n    - check validation & examples. always mm? so value only? Or value + unit\n    notes:\n    - mean and average are the same thing, but it seems like bad practice to not be\n      consistent. Changed mean to average\n    comments:\n    - Seasons are defined as spring (March, April, May), summer (June, July, August),\n      autumn (September, October, November) and winter (December, January, February).\n    examples:\n    - value: 0.4 inch\n    - value: 10.16 mm\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean seasonal precipitation\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000645\n    alias: season_precpt\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  season_temp:\n    name: season_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Mean seasonal temperature\n    title: mean seasonal temperature\n    examples:\n    - value: 18 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean seasonal temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000643\n    alias: season_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  season_use:\n    name: season_use\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The seasons the space is occupied\n    title: seasonal use\n    examples:\n    - value: Winter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - seasonal use\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000830\n    alias: season_use\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: season_use_enum\n    multivalued: false\n  secondary_treatment:\n    name: secondary_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: secondary treatment type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The process for substantially degrading the biological content of\n      the sewage\n    title: secondary treatment\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - secondary treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000351\n    alias: secondary_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  sediment_type:\n    name: sediment_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information about the sediment type based on major constituents\n    title: sediment type\n    examples:\n    - value: biogenous\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sediment type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001078\n    alias: sediment_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sediment_type_enum\n    multivalued: false\n  sequencing field:\n    name: sequencing field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: sequencing_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  sewage_type:\n    name: sewage_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: sewage type name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Type of wastewater treatment plant as municipial or industrial\n    title: sewage type\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sewage type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000215\n    alias: sewage_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  shad_dev_water_mold:\n    name: shad_dev_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on the shading device\n    title: shading device signs of water/mold\n    examples:\n    - value: no presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000834\n    alias: shad_dev_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  shading_device_cond:\n    name: shading_device_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the shading device at the time of sampling\n    title: shading device condition\n    examples:\n    - value: new\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000831\n    alias: shading_device_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: shading_device_cond_enum\n    multivalued: false\n  shading_device_loc:\n    name: shading_device_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The location of the shading device in relation to the built structure\n    title: shading device location\n    examples:\n    - value: exterior\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device location\n    rank: 1000\n    is_a: core field\n    string_serialization: '[exterior|interior]'\n    slot_uri: MIXS:0000832\n    alias: shading_device_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  shading_device_mat:\n    name: shading_device_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: material name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The material the shading device is composed of\n    title: shading device material\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device material\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000245\n    alias: shading_device_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  shading_device_type:\n    name: shading_device_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of shading device\n    title: shading device type\n    examples:\n    - value: slatted aluminum awning\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000835\n    alias: shading_device_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: shading_device_type_enum\n    multivalued: false\n  sieving:\n    name: sieving\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: design name and/or size;amount\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Collection design of pooled samples and/or sieve size and amount\n      of sample sieved\n    title: composite design/sieving\n    todos:\n    - check validation and examples\n    comments:\n    - Describe how samples were composited or sieved.\n    - Use 'sample link' to indicate which samples were combined.\n    examples:\n    - value: combined 2 cores | 4mm sieved\n    - value: 4 mm sieved and homogenized\n    - value: 50 g | 5 cores | 2 mm sieved\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - composite design/sieving\n    rank: 1000\n    is_a: core field\n    string_serialization: '{{text}|{float} {unit}};{float} {unit}'\n    slot_uri: MIXS:0000322\n    alias: sieving\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  silicate:\n    name: silicate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of silicate\n    title: silicate\n    examples:\n    - value: 0.05 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - silicate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000184\n    alias: silicate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  size_frac:\n    name: size_frac\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: filter size value range\n    description: Filtering pore size used in sample preparation\n    title: size fraction selected\n    examples:\n    - value: 0-0.22 micrometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - size fraction selected\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{float}-{float} {unit}'\n    slot_uri: MIXS:0000017\n    alias: size_frac\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  size_frac_low:\n    name: size_frac_low\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: micrometer\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n      Materials larger than the size threshold are excluded from the sample\n    title: size-fraction lower threshold\n    examples:\n    - value: 0.2 micrometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - size-fraction lower threshold\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000735\n    alias: size_frac_low\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  size_frac_up:\n    name: size_frac_up\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: micrometer\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Refers to the mesh/pore size used to retain the sample. Materials\n      smaller than the size threshold are excluded from the sample\n    title: size-fraction upper threshold\n    examples:\n    - value: 20 micrometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - size-fraction upper threshold\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000736\n    alias: size_frac_up\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  slope_aspect:\n    name: slope_aspect\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The direction a slope faces. While looking down a slope use a compass\n      to record the direction you are facing (direction or degrees). This measure\n      provides an indication of sun and wind exposure that will influence soil temperature\n      and evapotranspiration.\n    title: slope aspect\n    comments:\n    - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n      360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n      is west-facing.\n    examples:\n    - value: '35'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - slope aspect\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000647\n    alias: slope_aspect\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  slope_gradient:\n    name: slope_gradient\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Commonly called 'slope'. The angle between ground surface and a horizontal\n      line (in percent). This is the direction that overland water would flow. This\n      measure is usually taken with a hand level meter or clinometer\n    title: slope gradient\n    todos:\n    - Slope is a percent. How does the validation work? Check to correct examples\n    examples:\n    - value: 10%\n    - value: 10 %\n    - value: '0.10'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - slope gradient\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000646\n    alias: slope_gradient\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sludge_retent_time:\n    name: sludge_retent_time\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: hours\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The time activated sludge remains in reactor\n    title: sludge retention time\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sludge retention time\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000669\n    alias: sludge_retent_time\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sodium:\n    name: sodium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sodium concentration in the sample\n    title: sodium\n    examples:\n    - value: 10.5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sodium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000428\n    alias: sodium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  soil_horizon:\n    name: soil_horizon\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Specific layer in the land area which measures parallel to the soil\n      surface and possesses physical characteristics which differ from the layers\n      above and beneath\n    title: soil horizon\n    examples:\n    - value: A horizon\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil horizon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001082\n    alias: soil_horizon\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: soil_horizon_enum\n    multivalued: false\n  soil_text_measure:\n    name: soil_text_measure\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative proportion of different grain sizes of mineral particles\n      in a soil, as described using a standard system; express as % sand (50 um to\n      2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty\n      clay loam) optional.\n    title: soil texture measurement\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil texture measurement\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000335\n    alias: soil_text_measure\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  soil_texture_meth:\n    name: soil_texture_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining soil texture\n    title: soil texture method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil texture method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000336\n    alias: soil_texture_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  soil_type:\n    name: soil_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: ENVO_00001998\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Description of the soil type or classification. This field accepts\n      terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms\n      can be separated by pipes.\n    title: soil type\n    examples:\n    - value: plinthosol [ENVO:00002250]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000332\n    alias: soil_type\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  soil_type_meth:\n    name: soil_type_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining soil series name or other\n      lower-level classification\n    title: soil type method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil type method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000334\n    alias: soil_type_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  solar_irradiance:\n    name: solar_irradiance\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilowatts per square meter per day, ergs per square centimeter per\n          second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The amount of solar energy that arrives at a specific area of a surface\n      during a specific time interval\n    title: solar irradiance\n    examples:\n    - value: 1.36 kilowatts per square meter per day\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - solar irradiance\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000112\n    alias: solar_irradiance\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  soluble_inorg_mat:\n    name: soluble_inorg_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: soluble inorganic material name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, microgram, mole per liter, gram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of substances such as ammonia, road-salt, sea-salt,\n      cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.\n    title: soluble inorganic material\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soluble inorganic material\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000672\n    alias: soluble_inorg_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  soluble_org_mat:\n    name: soluble_org_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: soluble organic material name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, microgram, mole per liter, gram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of substances such as urea, fruit sugars, soluble proteins,\n      drugs, pharmaceuticals, etc.\n    title: soluble organic material\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soluble organic material\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000673\n    alias: soluble_org_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  soluble_react_phosp:\n    name: soluble_react_phosp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of soluble reactive phosphorus\n    title: soluble reactive phosphorus\n    examples:\n    - value: 0.1 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soluble reactive phosphorus\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000738\n    alias: soluble_react_phosp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  source_mat_id:\n    name: source_mat_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: 'for cultures of microorganisms: identifiers for two culture collections;\n          for other material a unique arbitrary identifer'\n    description: A globally unique identifier assigned to the biological sample.\n    title: source material identifier\n    todos:\n    - Currently, the comments say to use UUIDs. However, if we implement assigning\n      NMDC identifiers with the minter we dont need to require a GUID. It can be an\n      optional field to fill out only if they already have a resolvable ID.\n    comments:\n    - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n      NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n      IDs enable linking to derived analytes and subsamples. If you have not assigned\n      FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n    examples:\n    - value: IGSN:AU1243\n    - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source material identifiers\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000026\n    alias: source_mat_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  space_typ_state:\n    name: space_typ_state\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Customary or normal state of the space\n    title: space typical state\n    examples:\n    - value: typically occupied\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - space typical state\n    rank: 1000\n    is_a: core field\n    string_serialization: '[typically occupied|typically unoccupied]'\n    slot_uri: MIXS:0000770\n    alias: space_typ_state\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  specific:\n    name: specific\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'The building specifications. If design is chosen, indicate phase:\n      conceptual, schematic, design development, construction documents'\n    title: specifications\n    examples:\n    - value: construction\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - specifications\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000836\n    alias: specific\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: specific_enum\n    multivalued: false\n  specific_ecosystem:\n    name: specific_ecosystem\n    description: Specific ecosystems represent specific features of the environment\n      like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n      Specific ecosystem is in position 5/5 in a GOLD path.\n    comments:\n    - Specific ecosystems help to define samples based on very specific characteristics\n      of an environment under the five-level classification system.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: specific_ecosystem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  specific_humidity:\n    name: specific_humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram of air, kilogram of air\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The mass of water vapour in a unit mass of moist air, usually expressed\n      as grams of vapour per kilogram of air, or, in air conditioning, as grains per\n      pound.\n    title: specific humidity\n    examples:\n    - value: 15 per kilogram of air\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - specific humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000214\n    alias: specific_humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sr_dep_env:\n    name: sr_dep_env\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n      If \"other\" is specified, please propose entry in \"additional info\" field\n    title: source rock depositional environment\n    examples:\n    - value: Marine\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source rock depositional environment\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000996\n    alias: sr_dep_env\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sr_dep_env_enum\n    multivalued: false\n  sr_geol_age:\n    name: sr_geol_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n      If \"other\" is specified, please propose entry in \"additional info\" field'\n    title: source rock geological age\n    examples:\n    - value: Silurian\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source rock geological age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000997\n    alias: sr_geol_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sr_geol_age_enum\n    multivalued: false\n  sr_kerog_type:\n    name: sr_kerog_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic\n      and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/\n      fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris\n      (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen).\n      If \"other\" is specified, please propose entry in \"additional info\" field'\n    title: source rock kerogen type\n    examples:\n    - value: Type IV\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source rock kerogen type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000994\n    alias: sr_kerog_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sr_kerog_type_enum\n    multivalued: false\n  sr_lithology:\n    name: sr_lithology\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n      If \"other\" is specified, please propose entry in \"additional info\" field\n    title: source rock lithology\n    examples:\n    - value: Coal\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source rock lithology\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000995\n    alias: sr_lithology\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sr_lithology_enum\n    multivalued: false\n  standing_water_regm:\n    name: standing_water_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: standing water type;treatment interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Treatment involving an exposure to standing water during a plant's\n      life span, types can be flood water or standing water, treatment regimen including\n      how many times the treatment was repeated, how long each treatment lasted, and\n      the start and end time of the entire treatment; can include multiple regimens\n    title: standing water regimen\n    examples:\n    - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - standing water regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0001069\n    alias: standing_water_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  store_cond:\n    name: store_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: storage condition type;duration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Explain how and for how long the soil sample was stored before DNA\n      extraction (fresh/frozen/other).\n    title: storage conditions\n    examples:\n    - value: -20 degree Celsius freezer;P2Y10D\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - storage conditions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{duration}'\n    slot_uri: MIXS:0000327\n    alias: store_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  substructure_type:\n    name: substructure_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: The substructure or under building is that largely hidden section\n      of the building which is built off the foundations to the ground floor level\n    title: substructure type\n    examples:\n    - value: basement\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - substructure type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000767\n    alias: substructure_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: substructure_type_enum\n    multivalued: true\n  sulfate:\n    name: sulfate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of sulfate in the sample\n    title: sulfate\n    examples:\n    - value: 5 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sulfate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000423\n    alias: sulfate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sulfate_fw:\n    name: sulfate_fw\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original sulfate concentration in the hydrocarbon resource\n    title: sulfate in formation water\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sulfate in formation water\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000407\n    alias: sulfate_fw\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sulfide:\n    name: sulfide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of sulfide in the sample\n    title: sulfide\n    examples:\n    - value: 2 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sulfide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000424\n    alias: sulfide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  surf_air_cont:\n    name: surf_air_cont\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Contaminant identified on surface\n    title: surface-air contaminant\n    examples:\n    - value: radon\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface-air contaminant\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000759\n    alias: surf_air_cont\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: surf_air_cont_enum\n    multivalued: true\n  surf_humidity:\n    name: surf_humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Surfaces: water activity as a function of air and material moisture'\n    title: surface humidity\n    examples:\n    - value: 10%\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000123\n    alias: surf_humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  surf_material:\n    name: surf_material\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Surface materials at the point of sampling\n    title: surface material\n    examples:\n    - value: wood\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000758\n    alias: surf_material\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: surf_material_enum\n    multivalued: false\n  surf_moisture:\n    name: surf_moisture\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: parts per million, gram per cubic meter, gram per square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Water held on a surface\n    title: surface moisture\n    examples:\n    - value: 0.01 gram per square meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface moisture\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000128\n    alias: surf_moisture\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  surf_moisture_ph:\n    name: surf_moisture_ph\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: ph measurement of surface\n    title: surface moisture pH\n    examples:\n    - value: '7'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface moisture pH\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000760\n    alias: surf_moisture_ph\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: double\n    multivalued: false\n  surf_temp:\n    name: surf_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Temperature of the surface at the time of sampling\n    title: surface temperature\n    examples:\n    - value: 15 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000125\n    alias: surf_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  suspend_part_matter:\n    name: suspend_part_matter\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of suspended particulate matter\n    title: suspended particulate matter\n    examples:\n    - value: 0.5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - suspended particulate matter\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000741\n    alias: suspend_part_matter\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  suspend_solids:\n    name: suspend_solids\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: suspended solid name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, microgram, milligram per liter, mole per liter, gram per liter,\n          part per million\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of substances including a wide variety of material,\n      such as silt, decaying plant and animal matter; can include multiple substances\n    title: suspended solids\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - suspended solids\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000150\n    alias: suspend_solids\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  tan:\n    name: tan\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n      by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n      the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n      oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\n    title: total acid number\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total acid number\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000120\n    alias: tan\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  temp:\n    name: temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n    description: Temperature of the sample at the time of sampling.\n    title: temperature\n    examples:\n    - value: 25 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - temperature\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000113\n    alias: temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  temp_out:\n    name: temp_out\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The recorded temperature value at sampling time outside\n    title: temperature outside house\n    examples:\n    - value: 5 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - temperature outside house\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000197\n    alias: temp_out\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tertiary_treatment:\n    name: tertiary_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: tertiary treatment type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The process providing a final treatment stage to raise the effluent\n      quality before it is discharged to the receiving environment\n    title: tertiary treatment\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - tertiary treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000352\n    alias: tertiary_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  tidal_stage:\n    name: tidal_stage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Stage of tide\n    title: tidal stage\n    examples:\n    - value: high tide\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - tidal stage\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000750\n    alias: tidal_stage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: tidal_stage_enum\n    multivalued: false\n  tillage:\n    name: tillage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Note method(s) used for tilling\n    title: history/tillage\n    examples:\n    - value: chisel\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/tillage\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001081\n    alias: tillage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: tillage_enum\n    multivalued: true\n  tiss_cult_growth_med:\n    name: tiss_cult_growth_med\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url or free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Description of plant tissue culture growth media used\n    title: tissue culture growth media\n    examples:\n    - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - tissue culture growth media\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0001070\n    alias: tiss_cult_growth_med\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  toluene:\n    name: toluene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of toluene in the sample\n    title: toluene\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - toluene\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000154\n    alias: toluene\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_carb:\n    name: tot_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total carbon content\n    title: total carbon\n    todos:\n    - is this inorganic and organic? both? could use some clarification.\n    - ug/L doesn't seem like the right units. Should check this slots usage in databases\n      and re-evaluate. I couldn't find any references that provided this data in this\n      format\n    examples:\n    - value: 1 ug/L\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000525\n    alias: tot_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_depth_water_col:\n    name: tot_depth_water_col\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of total depth of water column\n    title: total depth of water column\n    examples:\n    - value: 500 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total depth of water column\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000634\n    alias: tot_depth_water_col\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_diss_nitro:\n    name: tot_diss_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n      by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\n    title: total dissolved nitrogen\n    examples:\n    - value: 40 microgram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total dissolved nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000744\n    alias: tot_diss_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_inorg_nitro:\n    name: tot_inorg_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total inorganic nitrogen content\n    title: total inorganic nitrogen\n    examples:\n    - value: 40 microgram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total inorganic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000745\n    alias: tot_inorg_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_iron:\n    name: tot_iron\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, milligram per kilogram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of total iron in the sample\n    title: total iron\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total iron\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000105\n    alias: tot_iron\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_nitro:\n    name: tot_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Total nitrogen concentration of water samples, calculated by: total\n      nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n      without filtering, reported as nitrogen'\n    title: total nitrogen concentration\n    examples:\n    - value: 50 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total nitrogen concentration\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000102\n    alias: tot_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_nitro_cont_meth:\n    name: tot_nitro_cont_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining the total nitrogen\n    title: total nitrogen content method\n    examples:\n    - value: https://doi.org/10.2134/agronmonogr9.2.c32\n    - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total nitrogen content method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000338\n    alias: tot_nitro_cont_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  tot_nitro_content:\n    name: tot_nitro_content\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total nitrogen content of the sample\n    title: total nitrogen content\n    examples:\n    - value: 5 mg N/ L\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total nitrogen content\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000530\n    alias: tot_nitro_content\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_org_c_meth:\n    name: tot_org_c_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining total organic carbon\n    title: total organic carbon method\n    examples:\n    - value: https://doi.org/10.1080/07352680902776556\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total organic carbon method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000337\n    alias: tot_org_c_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  tot_org_carb:\n    name: tot_org_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram Carbon per kilogram sample material\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Definition for soil: total organic carbon content of the soil, definition\n      otherwise: total organic carbon content'\n    title: total organic carbon\n    todos:\n    - check description. How are they different?\n    examples:\n    - value: 5 mg N/ L\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total organic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000533\n    alias: tot_org_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_part_carb:\n    name: tot_part_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total particulate carbon content\n    title: total particulate carbon\n    examples:\n    - value: 35 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total particulate carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000747\n    alias: tot_part_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_phosp:\n    name: tot_phosp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Total phosphorus concentration in the sample, calculated by: total\n      phosphorus = total dissolved phosphorus + particulate phosphorus'\n    title: total phosphorus\n    examples:\n    - value: 0.03 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total phosphorus\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000117\n    alias: tot_phosp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_phosphate:\n    name: tot_phosphate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total amount or concentration of phosphate\n    title: total phosphate\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total phosphate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000689\n    alias: tot_phosphate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_sulfur:\n    name: tot_sulfur\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of total sulfur in the sample\n    title: total sulfur\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total sulfur\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000419\n    alias: tot_sulfur\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  train_line:\n    name: train_line\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The subway line name\n    title: train line\n    examples:\n    - value: red\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - train line\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000837\n    alias: train_line\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: train_line_enum\n    multivalued: false\n  train_stat_loc:\n    name: train_stat_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The train station collection location\n    title: train station collection location\n    examples:\n    - value: forest hills\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - train station collection location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000838\n    alias: train_stat_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: train_stat_loc_enum\n    multivalued: false\n  train_stop_loc:\n    name: train_stop_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The train stop collection location\n    title: train stop collection location\n    examples:\n    - value: end\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - train stop collection location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000839\n    alias: train_stop_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: train_stop_loc_enum\n    multivalued: false\n  turbidity:\n    name: turbidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: formazin turbidity unit, formazin nephelometric units\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measure of the amount of cloudiness or haziness in water caused by\n      individual particles\n    title: turbidity\n    examples:\n    - value: 0.3 nephelometric turbidity units\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - turbidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000191\n    alias: turbidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tvdss_of_hcr_press:\n    name: tvdss_of_hcr_press\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n      the original pressure was measured (e.g. 1578 m).\n    title: depth (TVDSS) of hydrocarbon resource pressure\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - depth (TVDSS) of hydrocarbon resource pressure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000397\n    alias: tvdss_of_hcr_press\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tvdss_of_hcr_temp:\n    name: tvdss_of_hcr_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n      the original temperature was measured (e.g. 1345 m).\n    title: depth (TVDSS) of hydrocarbon resource temperature\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - depth (TVDSS) of hydrocarbon resource temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000394\n    alias: tvdss_of_hcr_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  typ_occup_density:\n    name: typ_occup_density\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Customary or normal density of occupants\n    title: typical occupant density\n    examples:\n    - value: '25'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - typical occupant density\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000771\n    alias: typ_occup_density\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: double\n    multivalued: false\n  ventilation_rate:\n    name: ventilation_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic meter per minute, liters per second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Ventilation rate of the system in the sampled premises\n    title: ventilation rate\n    examples:\n    - value: 750 cubic meter per minute\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ventilation rate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000114\n    alias: ventilation_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ventilation_type:\n    name: ventilation_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: ventilation type name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Ventilation system used in the sampled premises\n    title: ventilation type\n    examples:\n    - value: Operable windows\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ventilation type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000756\n    alias: ventilation_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  vfa:\n    name: vfa\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of Volatile Fatty Acids in the sample\n    title: volatile fatty acids\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - volatile fatty acids\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000152\n    alias: vfa\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  vfa_fw:\n    name: vfa_fw\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original volatile fatty acid concentration in the hydrocarbon resource\n    title: vfa in formation water\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - vfa in formation water\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000408\n    alias: vfa_fw\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  vis_media:\n    name: vis_media\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The building visual media\n    title: visual media\n    examples:\n    - value: 3D scans\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - visual media\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000840\n    alias: vis_media\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: vis_media_enum\n    multivalued: false\n  viscosity:\n    name: viscosity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cP at degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n      stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\n    title: viscosity\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - viscosity\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{float} {unit}'\n    slot_uri: MIXS:0000126\n    alias: viscosity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  volatile_org_comp:\n    name: volatile_org_comp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: volatile organic compound name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per cubic meter, parts per million, nanogram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of carbon-based chemicals that easily evaporate at\n      room temperature; can report multiple volatile organic compounds by entering\n      numeric values preceded by name of compound\n    title: volatile organic compounds\n    examples:\n    - value: formaldehyde;500 nanogram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - volatile organic compounds\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000115\n    alias: volatile_org_comp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  wall_area:\n    name: wall_area\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The total area of the sampled room's walls\n    title: wall area\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall area\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000198\n    alias: wall_area\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  wall_const_type:\n    name: wall_const_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The building class of the wall defined by the composition of the\n      building elements and fire-resistance rating.\n    title: wall construction type\n    examples:\n    - value: fire resistive\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall construction type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000841\n    alias: wall_const_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_const_type_enum\n    multivalued: false\n  wall_finish_mat:\n    name: wall_finish_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The material utilized to finish the outer most layer of the wall\n    title: wall finish material\n    examples:\n    - value: wood\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall finish material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000842\n    alias: wall_finish_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_finish_mat_enum\n    multivalued: false\n  wall_height:\n    name: wall_height\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: centimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average height of the walls in the sampled room\n    title: wall height\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall height\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000221\n    alias: wall_height\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  wall_loc:\n    name: wall_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative location of the wall within the room\n    title: wall location\n    examples:\n    - value: north\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000843\n    alias: wall_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_loc_enum\n    multivalued: false\n  wall_surf_treatment:\n    name: wall_surf_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The surface treatment of interior wall\n    title: wall surface treatment\n    examples:\n    - value: paneling\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall surface treatment\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000845\n    alias: wall_surf_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_surf_treatment_enum\n    multivalued: false\n  wall_texture:\n    name: wall_texture\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The feel, appearance, or consistency of a wall surface\n    title: wall texture\n    examples:\n    - value: popcorn\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall texture\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000846\n    alias: wall_texture\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_texture_enum\n    multivalued: false\n  wall_thermal_mass:\n    name: wall_thermal_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: joule per degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The ability of the wall to provide inertia against temperature fluctuations.\n      Generally this means concrete or concrete block that is either exposed or covered\n      only with paint\n    title: wall thermal mass\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall thermal mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000222\n    alias: wall_thermal_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  wall_water_mold:\n    name: wall_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on a wall\n    title: wall signs of water/mold\n    examples:\n    - value: no presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000844\n    alias: wall_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  wastewater_type:\n    name: wastewater_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: wastewater type name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The origin of wastewater such as human waste, rainfall, storm drains,\n      etc.\n    title: wastewater type\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wastewater type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000353\n    alias: wastewater_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  water_cont_soil_meth:\n    name: water_cont_soil_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining the water content of soil\n    title: water content method\n    todos:\n    - Why is it soil water content method in the name but not the title? Is this slot\n      used in other samples?\n    - Soil water content can be measure MANY ways and often, multiple ways are used\n      in one experiment (gravimetric water content and water holding capacity and\n      water filled pore space, to name a few).\n    - Should this be multi valued? How to we manage and validate this?\n    comments:\n    - Required if providing water content\n    examples:\n    - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n    - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water content method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000323\n    alias: water_cont_soil_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  water_content:\n    name: water_content\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: string\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per gram or cubic centimeter per cubic centimeter\n    description: Water content measurement\n    title: water content\n    todos:\n    - value in preferred unit is too limiting. need to change this\n    - check and correct validation so examples are accepted\n    - how to manage multiple water content methods?\n    examples:\n    - value: 0.75 g water/g dry soil\n    - value: 75% water holding capacity\n    - value: 1.1 g fresh weight/ dry weight\n    - value: 10% water filled pore space\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water content\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000185\n    alias: water_content\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  water_current:\n    name: water_current\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic meter per second, knots\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of magnitude and direction of flow within a fluid\n    title: water current\n    examples:\n    - value: 10 cubic meter per second\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water current\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000203\n    alias: water_current\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  water_cut:\n    name: water_cut\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Current amount of water (%) in a produced fluid stream; or the average\n      of the combined streams\n    title: water cut\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water cut\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000454\n    alias: water_cut\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  water_feat_size:\n    name: water_feat_size\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The size of the water feature\n    title: water feature size\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water feature size\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000223\n    alias: water_feat_size\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  water_feat_type:\n    name: water_feat_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of water feature present within the building being sampled\n    title: water feature type\n    examples:\n    - value: stream\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water feature type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000847\n    alias: water_feat_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: water_feat_type_enum\n    multivalued: false\n  water_prod_rate:\n    name: water_prod_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic meter per day\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Water production rates per well (e.g. 987 m3 / day)\n    title: water production rate\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water production rate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000453\n    alias: water_prod_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  water_temp_regm:\n    name: water_temp_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to water with varying\n      degree of temperature, treatment regimen including how many times the treatment\n      was repeated, how long each treatment lasted, and the start and end time of\n      the entire treatment; can include multiple regimens\n    title: water temperature regimen\n    examples:\n    - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water temperature regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000590\n    alias: water_temp_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  watering_regm:\n    name: watering_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milliliter, liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to watering frequencies,\n      treatment regimen including how many times the treatment was repeated, how long\n      each treatment lasted, and the start and end time of the entire treatment; can\n      include multiple regimens\n    title: watering regimen\n    examples:\n    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    - value: 75% water holding capacity; constant\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - watering regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000591\n    alias: watering_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  weekday:\n    name: weekday\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The day of the week when sampling occurred\n    title: weekday\n    examples:\n    - value: Sunday\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - weekday\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000848\n    alias: weekday\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: weekday_enum\n    multivalued: false\n  win:\n    name: win\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'A unique identifier of a well or wellbore. This is part of the Global\n      Framework for Well Identification initiative which is compiled by the Professional\n      Petroleum Data Management Association (PPDM) in an effort to improve well identification\n      systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\n    title: well identification number\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - well identification number\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000297\n    alias: win\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  wind_direction:\n    name: wind_direction\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: wind direction name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Wind direction is the direction from which a wind originates\n    title: wind direction\n    examples:\n    - value: Northwest\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wind direction\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000757\n    alias: wind_direction\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  wind_speed:\n    name: wind_speed\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter per second, kilometer per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Speed of wind measured at the time of sampling\n    title: wind speed\n    examples:\n    - value: 21 kilometer per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wind speed\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000118\n    alias: wind_speed\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  window_cond:\n    name: window_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the window at the time of sampling\n    title: window condition\n    examples:\n    - value: rupture\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000849\n    alias: window_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_cond_enum\n    multivalued: false\n  window_cover:\n    name: window_cover\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of window covering\n    title: window covering\n    examples:\n    - value: curtains\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window covering\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000850\n    alias: window_cover\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_cover_enum\n    multivalued: false\n  window_horiz_pos:\n    name: window_horiz_pos\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The horizontal position of the window on the wall\n    title: window horizontal position\n    examples:\n    - value: middle\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window horizontal position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000851\n    alias: window_horiz_pos\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_horiz_pos_enum\n    multivalued: false\n  window_loc:\n    name: window_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative location of the window within the room\n    title: window location\n    examples:\n    - value: west\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000852\n    alias: window_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_loc_enum\n    multivalued: false\n  window_mat:\n    name: window_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of material used to finish a window\n    title: window material\n    examples:\n    - value: wood\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000853\n    alias: window_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_mat_enum\n    multivalued: false\n  window_open_freq:\n    name: window_open_freq\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of times windows are opened per week\n    title: window open frequency\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window open frequency\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000246\n    alias: window_open_freq\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  window_size:\n    name: window_size\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: inch, meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The window's length and width\n    title: window area/size\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window area/size\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit} x {float} {unit}'\n    slot_uri: MIXS:0000224\n    alias: window_size\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  window_status:\n    name: window_status\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Defines whether the windows were open or closed during environmental\n      testing\n    title: window status\n    examples:\n    - value: open\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window status\n    rank: 1000\n    is_a: core field\n    string_serialization: '[closed|open]'\n    slot_uri: MIXS:0000855\n    alias: window_status\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  window_type:\n    name: window_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of windows\n    title: window type\n    examples:\n    - value: fixed window\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000856\n    alias: window_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_type_enum\n    multivalued: false\n  window_vert_pos:\n    name: window_vert_pos\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The vertical position of the window on the wall\n    title: window vertical position\n    examples:\n    - value: middle\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window vertical position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000857\n    alias: window_vert_pos\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_vert_pos_enum\n    multivalued: false\n  window_water_mold:\n    name: window_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on the window.\n    title: window signs of water/mold\n    examples:\n    - value: no presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000854\n    alias: window_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  xylene:\n    name: xylene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of xylene in the sample\n    title: xylene\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - xylene\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000156\n    alias: xylene\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  zinc:\n    name: zinc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg (ppm)\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of zinc in the sample\n    title: zinc\n    examples:\n    - value: 2.5 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - zinc\n    rank: 1000\n    alias: zinc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  add_date:\n    name: add_date\n    description: The date on which the information was added to the database.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: add_date\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  community:\n    name: community\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: community\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  habitat:\n    name: habitat\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: habitat\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: string\n  host_name:\n    name: host_name\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: host_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  location:\n    name: location\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: location\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  mod_date:\n    name: mod_date\n    description: The last date on which the database information was modified.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mod_date\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  ncbi_taxonomy_name:\n    name: ncbi_taxonomy_name\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: ncbi_taxonomy_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  proport_woa_temperature:\n    name: proport_woa_temperature\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: proport_woa_temperature\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  salinity_category:\n    name: salinity_category\n    description: 'Categorical description of the sample''s salinity. Examples: halophile,\n      halotolerant, hypersaline, huryhaline'\n    notes:\n    - maps to gold:salinity\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-metadata/pull/297\n    rank: 1000\n    alias: salinity_category\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  sample_collection_site:\n    name: sample_collection_site\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: sample_collection_site\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  soluble_iron_micromol:\n    name: soluble_iron_micromol\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: soluble_iron_micromol\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  subsurface_depth:\n    name: subsurface_depth\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: subsurface_depth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  dna_absorb1:\n    name: dna_absorb1\n    description: 260/280 measurement of DNA sample purity\n    title: DNA absorbance 260/280\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 7\n    is_a: biomaterial_purity\n    alias: dna_absorb1\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - ProcessedSample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n  dna_absorb2:\n    name: dna_absorb2\n    description: 260/230 measurement of DNA sample purity\n    title: DNA absorbance 260/230\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 8\n    is_a: biomaterial_purity\n    alias: dna_absorb2\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n  dna_collect_site:\n    name: dna_collect_site\n    description: Provide information on the site your DNA sample was collected from\n    title: DNA collection site\n    examples:\n    - value: untreated pond water\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 15\n    string_serialization: '{text}'\n    alias: dna_collect_site\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_concentration:\n    name: dna_concentration\n    title: DNA concentration in ng/ul\n    comments:\n    - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n      a fluorometric method. Acceptable values are 0-2000.\n    examples:\n    - value: '100'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:nucleic_acid_concentration\n    rank: 5\n    alias: dna_concentration\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - ProcessedSample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 2000\n  dna_cont_type:\n    name: dna_cont_type\n    description: Tube or plate (96-well)\n    title: DNA container type\n    examples:\n    - value: plate\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 10\n    alias: dna_cont_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: JgiContTypeEnum\n    recommended: true\n  dna_container_id:\n    name: dna_container_id\n    title: DNA container label\n    comments:\n    - Must be unique across all tubes and plates, and <20 characters. All samples\n      in a plate should have the same plate label.\n    examples:\n    - value: Pond_MT_041618\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 9\n    string_serialization: '{text < 20 characters}'\n    alias: dna_container_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_dnase:\n    name: dna_dnase\n    title: DNase treatment DNA\n    comments:\n    - Note DNase treatment is required for all RNA samples.\n    examples:\n    - value: 'no'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 13\n    alias: dna_dnase\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: YesNoEnum\n    recommended: true\n  dna_isolate_meth:\n    name: dna_isolate_meth\n    description: Describe the method/protocol/kit used to extract DNA/RNA.\n    title: DNA isolation method\n    examples:\n    - value: phenol/chloroform extraction\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Sample Isolation Method\n    rank: 16\n    string_serialization: '{text}'\n    alias: dna_isolate_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_organisms:\n    name: dna_organisms\n    description: List any organisms known or suspected to grow in co-culture, as well\n      as estimated % of the organism in that culture.\n    title: DNA expected organisms\n    examples:\n    - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n        (1%)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 14\n    string_serialization: '{text}'\n    alias: dna_organisms\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_project_contact:\n    name: dna_project_contact\n    title: DNA seq project contact\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: John Jones\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 18\n    string_serialization: '{text}'\n    alias: dna_project_contact\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_samp_id:\n    name: dna_samp_id\n    title: DNA sample ID\n    todos:\n    - Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n      have two identifiers. How to force uniqueness? Moot because that column will\n      be prefilled?\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '187654'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 3\n    string_serialization: '{text}'\n    alias: dna_samp_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_sample_format:\n    name: dna_sample_format\n    description: Solution in which the DNA sample has been suspended\n    title: DNA sample format\n    examples:\n    - value: Water\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 12\n    alias: dna_sample_format\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: DNASampleFormatEnum\n    recommended: true\n  dna_sample_name:\n    name: dna_sample_name\n    description: Give the DNA sample a name that is meaningful to you. Sample names\n      must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n    title: DNA sample name\n    examples:\n    - value: JGI_pond_041618\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 4\n    string_serialization: '{text}'\n    alias: dna_sample_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_seq_project:\n    name: dna_seq_project\n    title: DNA seq project ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '1191234'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Seq Project ID\n    rank: 1\n    string_serialization: '{text}'\n    alias: dna_seq_project\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_seq_project_pi:\n    name: dna_seq_project_pi\n    title: DNA seq project PI\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: Jane Johnson\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 17\n    string_serialization: '{text}'\n    alias: dna_seq_project_pi\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_seq_project_name:\n    name: dna_seq_project_name\n    title: DNA seq project name\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: JGI Pond metagenomics\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 2\n    string_serialization: '{text}'\n    alias: dna_seq_project_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_volume:\n    name: dna_volume\n    title: DNA volume in ul\n    comments:\n    - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n      form accepts values < 25, but JGI may refuse to process them unless permission\n      has been granted by a project manager\n    examples:\n    - value: '25'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 6\n    string_serialization: '{float}'\n    alias: dna_volume\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 1000\n  proposal_dna:\n    name: proposal_dna\n    title: DNA proposal ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '504000'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 19\n    string_serialization: '{text}'\n    alias: proposal_dna\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dnase_rna:\n    name: dnase_rna\n    title: DNase treated\n    comments:\n    - Note DNase treatment is required for all RNA samples.\n    examples:\n    - value: 'no'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Was Sample DNAse treated?\n    rank: 13\n    alias: dnase_rna\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: YesNoEnum\n    recommended: true\n  proposal_rna:\n    name: proposal_rna\n    title: RNA proposal ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '504000'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 19\n    string_serialization: '{text}'\n    alias: proposal_rna\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_absorb1:\n    name: rna_absorb1\n    description: 260/280 measurement of RNA sample purity\n    title: RNA absorbance 260/280\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 7\n    string_serialization: '{float}'\n    alias: rna_absorb1\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: float\n    recommended: true\n  rna_absorb2:\n    name: rna_absorb2\n    description: 260/230 measurement of RNA sample purity\n    title: RNA absorbance 260/230\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 8\n    string_serialization: '{float}'\n    alias: rna_absorb2\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: float\n    recommended: true\n  rna_collect_site:\n    name: rna_collect_site\n    description: Provide information on the site your RNA sample was collected from\n    title: RNA collection site\n    examples:\n    - value: untreated pond water\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 15\n    string_serialization: '{text}'\n    alias: rna_collect_site\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_concentration:\n    name: rna_concentration\n    title: RNA concentration in ng/ul\n    comments:\n    - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n      a fluorometric method. Acceptable values are 0-2000.\n    examples:\n    - value: '100'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:nucleic_acid_concentration\n    rank: 5\n    string_serialization: '{float}'\n    alias: rna_concentration\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 1000\n  rna_cont_type:\n    name: rna_cont_type\n    description: Tube or plate (96-well)\n    title: RNA container type\n    examples:\n    - value: plate\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 10\n    alias: rna_cont_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: JgiContTypeEnum\n    recommended: true\n  rna_cont_well:\n    name: rna_cont_well\n    title: RNA plate position\n    comments:\n    - Required when 'plate' is selected for container type.\n    - Leave blank if the sample will be shipped in a tube.\n    - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n      pass validation.\n    - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n    examples:\n    - value: B2\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 11\n    string_serialization: '{96 well plate pos}'\n    alias: rna_cont_well\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n    pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  rna_container_id:\n    name: rna_container_id\n    title: RNA container label\n    comments:\n    - Must be unique across all tubes and plates, and <20 characters. All samples\n      in a plate should have the same plate label.\n    examples:\n    - value: Pond_MT_041618\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 9\n    string_serialization: '{text < 20 characters}'\n    alias: rna_container_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_isolate_meth:\n    name: rna_isolate_meth\n    description: Describe the method/protocol/kit used to extract DNA/RNA.\n    title: RNA isolation method\n    examples:\n    - value: phenol/chloroform extraction\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Sample Isolation Method\n    rank: 16\n    string_serialization: '{text}'\n    alias: rna_isolate_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_organisms:\n    name: rna_organisms\n    description: List any organisms known or suspected to grow in co-culture, as well\n      as estimated % of the organism in that culture.\n    title: RNA expected organisms\n    examples:\n    - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n        (1%)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 14\n    string_serialization: '{text}'\n    alias: rna_organisms\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_project_contact:\n    name: rna_project_contact\n    title: RNA seq project contact\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: John Jones\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 18\n    string_serialization: '{text}'\n    alias: rna_project_contact\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_samp_id:\n    name: rna_samp_id\n    title: RNA sample ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '187654'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 3\n    string_serialization: '{text}'\n    alias: rna_samp_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_sample_format:\n    name: rna_sample_format\n    description: Solution in which the RNA sample has been suspended\n    title: RNA sample format\n    examples:\n    - value: Water\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 12\n    alias: rna_sample_format\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: RNASampleFormatEnum\n    recommended: true\n  rna_sample_name:\n    name: rna_sample_name\n    description: Give the RNA sample a name that is meaningful to you. Sample names\n      must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n    title: RNA sample name\n    examples:\n    - value: JGI_pond_041618\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 4\n    string_serialization: '{text}'\n    alias: rna_sample_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n    minimum_value: 0\n    maximum_value: 2000\n  rna_seq_project:\n    name: rna_seq_project\n    title: RNA seq project ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '1191234'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Seq Project ID\n    rank: 1\n    string_serialization: '{text}'\n    alias: rna_seq_project\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_seq_project_pi:\n    name: rna_seq_project_pi\n    title: RNA seq project PI\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: Jane Johnson\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 17\n    string_serialization: '{text}'\n    alias: rna_seq_project_pi\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_seq_project_name:\n    name: rna_seq_project_name\n    title: RNA seq project name\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: JGI Pond metatranscriptomics\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 2\n    string_serialization: '{text}'\n    alias: rna_seq_project_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_volume:\n    name: rna_volume\n    title: RNA volume in ul\n    comments:\n    - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n      form accepts values < 25, but JGI may refuse to process them unless permission\n      has been granted by a project manager\n    examples:\n    - value: '25'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 6\n    string_serialization: '{float}'\n    alias: rna_volume\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 1000\n  collection_date_inc:\n    name: collection_date_inc\n    description: Date the incubation was harvested/collected/ended. Only relevant\n      for incubation samples.\n    title: incubation collection date\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n      date only\n    comments:\n    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n      are all acceptable.\n    examples:\n    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 2\n    string_serialization: '{date, arbitrary precision}'\n    alias: collection_date_inc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  collection_time:\n    name: collection_time\n    description: The time of sampling, either as an instance (single point) or interval.\n    title: collection time, GMT\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n      time only\n    comments:\n    - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n    examples:\n    - value: 13:33 or 13:33:55\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 1\n    string_serialization: '{time, seconds optional}'\n    alias: collection_time\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  collection_time_inc:\n    name: collection_time_inc\n    description: Time the incubation was harvested/collected/ended. Only relevant\n      for incubation samples.\n    title: incubation collection time, GMT\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n      time only\n    comments:\n    - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n    examples:\n    - value: 13:33 or 13:33:55\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 3\n    string_serialization: '{time, seconds optional}'\n    alias: collection_time_inc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  experimental_factor_other:\n    name: experimental_factor_other\n    description: Other details about your sample that you feel can't be accurately\n      represented in the available columns.\n    title: experimental factor- other\n    comments:\n    - This slot accepts open-ended text about your sample.\n    - We recommend using key:value pairs.\n    - Provided pairs will be considered for inclusion as future slots/terms in this\n      data collection template.\n    examples:\n    - value: 'experimental treatment: value'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000008\n    - MIXS:0000300\n    rank: 7\n    string_serialization: '{text}'\n    alias: experimental_factor_other\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  filter_method:\n    name: filter_method\n    description: Type of filter used or how the sample was filtered\n    title: filter method\n    comments:\n    - describe the filter or provide a catalog number and manufacturer\n    examples:\n    - value: C18\n    - value: Basix PES, 13-100-106 FisherSci\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000765\n    rank: 6\n    string_serialization: '{text}'\n    alias: filter_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  isotope_exposure:\n    name: isotope_exposure\n    description: List isotope exposure or addition applied to your sample.\n    title: isotope exposure/addition\n    todos:\n    - Can we make the H218O correctly super and subscripted?\n    comments:\n    - This is required when your experimental design includes the use of isotopically\n      labeled compounds\n    examples:\n    - value: 13C glucose\n    - value: H218O\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000751\n    rank: 16\n    string_serialization: '{termLabel} {[termID]}; {timestamp}'\n    alias: isotope_exposure\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  micro_biomass_c_meth:\n    name: micro_biomass_c_meth\n    description: Reference or method used in determining microbial biomass carbon\n    title: microbial biomass carbon method\n    todos:\n    - How should we separate values? | or ;? lets be consistent\n    comments:\n    - required if \"microbial_biomass_c\" is provided\n    examples:\n    - value: https://doi.org/10.1016/0038-0717(87)90052-6\n    - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000339\n    rank: 11\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    alias: micro_biomass_c_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  micro_biomass_n_meth:\n    name: micro_biomass_n_meth\n    description: Reference or method used in determining microbial biomass nitrogen\n    title: microbial biomass nitrogen method\n    comments:\n    - required if \"microbial_biomass_n\" is provided\n    examples:\n    - value: https://doi.org/10.1016/0038-0717(87)90052-6\n    - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000339\n    rank: 13\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    alias: micro_biomass_n_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  microbial_biomass_c:\n    name: microbial_biomass_c\n    description: The part of the organic matter in the soil that constitutes living\n      microorganisms smaller than 5-10 micrometer.\n    title: microbial biomass carbon\n    comments:\n    - If you provide this, correction factors used for conversion to the final units\n      and method are required\n    examples:\n    - value: 0.05 ug C/g dry soil\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000650\n    rank: 10\n    string_serialization: '{float} {unit}'\n    alias: microbial_biomass_c\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  microbial_biomass_n:\n    name: microbial_biomass_n\n    description: The part of the organic matter in the soil that constitutes living\n      microorganisms smaller than 5-10 micrometer.\n    title: microbial biomass nitrogen\n    comments:\n    - If you provide this, correction factors used for conversion to the final units\n      and method are required\n    examples:\n    - value: 0.05 ug N/g dry soil\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000650\n    rank: 12\n    string_serialization: '{float} {unit}'\n    alias: microbial_biomass_n\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  non_microb_biomass:\n    name: non_microb_biomass\n    description: Amount of biomass; should include the name for the part of biomass\n      measured, e.g.insect, plant, total. Can include multiple measurements separated\n      by ;\n    title: non-microbial biomass\n    examples:\n    - value: insect 0.23 ug; plant 1g\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000174\n    - MIXS:0000650\n    rank: 8\n    string_serialization: '{text};{float} {unit}'\n    alias: non_microb_biomass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  non_microb_biomass_method:\n    name: non_microb_biomass_method\n    description: Reference or method used in determining biomass\n    title: non-microbial biomass method\n    comments:\n    - required if \"non-microbial biomass\" is provided\n    examples:\n    - value: https://doi.org/10.1038/s41467-021-26181-3\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000650\n    rank: 9\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    alias: non_microb_biomass_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  org_nitro_method:\n    name: org_nitro_method\n    description: Method used for obtaining organic nitrogen\n    title: organic nitrogen method\n    comments:\n    - required if \"org_nitro\" is provided\n    examples:\n    - value: https://doi.org/10.1016/0038-0717(85)90144-0\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000338\n    - MIXS:0000205\n    rank: 14\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    alias: org_nitro_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  other_treatment:\n    name: other_treatment\n    description: Other treatments applied to your samples that are not applicable\n      to the provided fields\n    title: other treatments\n    notes:\n    - Values entered here will be used to determine potential new slots.\n    comments:\n    - This is an open text field to provide any treatments that cannot be captured\n      in the provided slots.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000300\n    rank: 15\n    string_serialization: '{text}'\n    alias: other_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  start_date_inc:\n    name: start_date_inc\n    description: Date the incubation was started. Only relevant for incubation samples.\n    title: incubation start date\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n      date only\n    comments:\n    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n      are all acceptable.\n    examples:\n    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 4\n    string_serialization: '{date, arbitrary precision}'\n    alias: start_date_inc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  start_time_inc:\n    name: start_time_inc\n    description: Time the incubation was started. Only relevant for incubation samples.\n    title: incubation start time, GMT\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n      time only\n    comments:\n    - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n    examples:\n    - value: 13:33 or 13:33:55\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 5\n    string_serialization: '{time, seconds optional}'\n    alias: start_time_inc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  project_id:\n    name: project_id\n    description: Proposal IDs or names associated with dataset\n    title: project ID\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1\n    string_serialization: '{text}'\n    alias: project_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: string\n    recommended: true\n  replicate_number:\n    name: replicate_number\n    description: If sending biological replicates, indicate the rep number here.\n    title: replicate number\n    comments:\n    - This will guide staff in ensuring your samples are blocked & randomized correctly\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 6\n    string_serialization: '{integer}'\n    alias: replicate_number\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: string\n    recommended: true\n  sample_shipped:\n    name: sample_shipped\n    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n      sample sent to EMSL.\n    title: sample shipped amount\n    comments:\n    - This field is only required when completing metadata for samples being submitted\n      to EMSL for analyses.\n    examples:\n    - value: 15 g\n    - value: 100 uL\n    - value: 5 mL\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 3\n    string_serialization: '{float} {unit}'\n    alias: sample_shipped\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: string\n    recommended: true\n  sample_type:\n    name: sample_type\n    description: Type of sample being submitted\n    title: sample type\n    comments:\n    - This can vary from 'environmental package' if the sample is an extraction.\n    examples:\n    - value: water extracted soil\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 2\n    alias: sample_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: SampleTypeEnum\n    recommended: true\n  technical_reps:\n    name: technical_reps\n    description: If sending technical replicates of the same sample, indicate the\n      replicate count.\n    title: number technical replicate\n    comments:\n    - This field is only required when completing metadata for samples being submitted\n      to EMSL for analyses.\n    examples:\n    - value: '2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 5\n    string_serialization: '{integer}'\n    alias: technical_reps\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: string\n    recommended: true\n  analysis_type:\n    name: analysis_type\n    description: Select all the data types associated or available for this biosample\n    title: analysis/data type\n    examples:\n    - value: metagenomics; metabolomics; proteomics\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIxS:investigation_type\n    rank: 3\n    alias: analysis_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: Sample ID\n    range: AnalysisTypeEnum\n    recommended: true\n    multivalued: true\n  sample_link:\n    name: sample_link\n    description: A unique identifier to assign parent-child, subsample, or sibling\n      samples. This is relevant when a sample or other material was used to generate\n      the new sample.\n    title: sample linkage\n    comments:\n    - 'This field allows multiple entries separated by ; (Examples: Soil collected\n      from the field will link with the soil used in an incubation. The soil a plant\n      was grown in links to the plant sample. An original culture sample was transferred\n      to a new vial and generated a new sample)'\n    examples:\n    - value: IGSN:DSJ0284\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 5\n    string_serialization: '{text}:{text}'\n    alias: sample_link\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: Sample ID\n    range: string\n    recommended: true\n    multivalued: true\n  bulk_elect_conductivity:\n    name: bulk_elect_conductivity\n    description: Electrical conductivity is a measure of the ability to carry electric\n      current, which is mostly dictated by the chemistry of and amount of water.\n    title: bulk electrical conductivity\n    comments:\n    - Provide the value output of the field instrument.\n    examples:\n    - value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')\n      description: The conductivity measurement was 0.017 millisiemens per centimeter.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: bulk_elect_conductivity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  infiltrations:\n    name: infiltrations\n    description: The amount of time it takes to complete each infiltration activity\n    examples:\n    - value: '[''00:01:32'', ''00:00:53'']'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1\n    aliases:\n    - infiltration_1\n    - infiltration_2\n    rank: 1000\n    list_elements_ordered: true\n    alias: infiltrations\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n    pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$\n  id:\n    name: id\n    description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Biosample\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Biosample\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Biosample\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a biosample submitted to additional resources.\n      Matches the entity that has been submitted to NMDC\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Biosample\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Biosample\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Biosample\nunique_keys:\n  samp_name_unique_key:\n    unique_key_name: samp_name_unique_key\n    unique_key_slots:\n    - samp_name\nrules:\n- preconditions:\n    slot_conditions:\n      dna_cont_well:\n        name: dna_cont_well\n        pattern: .+\n  postconditions:\n    slot_conditions:\n      dna_cont_type:\n        name: dna_cont_type\n        equals_string: plate\n  description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n    have any value for their plate position.\n  title: dna_well_requires_plate\n- preconditions:\n    slot_conditions:\n      dna_cont_type:\n        name: dna_cont_type\n        equals_string: plate\n  postconditions:\n    slot_conditions:\n      dna_cont_well:\n        name: dna_cont_well\n        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  description: DNA samples in plates must have a plate position that matches the regex.\n    Note the requirement for an empty string in the tube case. Waiting for value_present\n    validation to be added to runtime\n  title: dna_plate_requires_well\n- preconditions:\n    slot_conditions:\n      rna_cont_well:\n        name: rna_cont_well\n        pattern: .+\n  postconditions:\n    slot_conditions:\n      rna_cont_type:\n        name: rna_cont_type\n        equals_string: plate\n  description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n    have any value for their plate position.\n  title: rna_well_requires_plate\n- preconditions:\n    slot_conditions:\n      rna_cont_type:\n        name: rna_cont_type\n        equals_string: plate\n  postconditions:\n    slot_conditions:\n      rna_cont_well:\n        name: rna_cont_well\n        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  description: RNA samples in plates must have a plate position that matches the regex.\n    Note the requirement for an empty string in the tube case. Waiting for value_present\n    validation to be added to runtime\n  title: rna_plate_requires_well\n\n
"},{"location":"BiosampleCategoryEnum/","title":"Enum: BiosampleCategoryEnum","text":"

Funding-based, sample location-based, or experimental method-based defined categories

URI: BiosampleCategoryEnum

"},{"location":"BiosampleCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description LTER https://lternet.edu/ SIP None SFA https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance Science Focus Area projects funded through the Department of Energy Office of... FICUS https://jgi.doe.gov/user-programs/program-info/ficus-overview NEON https://www.neonscience.org"},{"location":"BiosampleCategoryEnum/#slots","title":"Slots","text":"Name Description biosample_categories"},{"location":"BiosampleCategoryEnum/#aliases","title":"Aliases","text":""},{"location":"BiosampleCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BiosampleCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"BiosampleCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: BiosampleCategoryEnum\ndescription: Funding-based, sample location-based, or experimental method-based defined\n  categories\nnotes:\n- Currently, these values can associated with biosamples via the biosample_categories\n  slot\n- They might also be applicable to other classes\n- They are intended to enable metadata search and or filtering, for example in the\n  NMDC data portal, https://data.microbiomedata.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- category tag\nrank: 1000\npermissible_values:\n  LTER:\n    text: LTER\n    meaning: https://lternet.edu/\n    title: National Science Foundation's Long Term Ecological Research Network\n  SIP:\n    text: SIP\n  SFA:\n    text: SFA\n    description: Science Focus Area projects funded through the Department of Energy\n      Office of Science Biological and Environmental Research Program\n    meaning: https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance\n    title: Department of Energy Office of Science Biological and Environmental Research\n      Program Laboratory Science Focus Areas\n  FICUS:\n    text: FICUS\n    meaning: https://jgi.doe.gov/user-programs/program-info/ficus-overview\n    title: Facilities Integrating Collaborations for User Science\n  NEON:\n    text: NEON\n    meaning: https://www.neonscience.org\n    title: National Science Foundation's National Ecological Observatory Network\n\n
"},{"location":"BioticRelationshipEnum/","title":"Enum: BioticRelationshipEnum","text":"

URI: BioticRelationshipEnum

"},{"location":"BioticRelationshipEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description free living None parasite None commensal None symbiont None"},{"location":"BioticRelationshipEnum/#slots","title":"Slots","text":"Name Description biotic_relationship Description of relationship(s) between the subject organism and other organis..."},{"location":"BioticRelationshipEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BioticRelationshipEnum/#schema-source","title":"Schema Source","text":""},{"location":"BioticRelationshipEnum/#linkml-source","title":"LinkML Source","text":"
name: biotic_relationship_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  free living:\n    text: free living\n  parasite:\n    text: parasite\n  commensal:\n    text: commensal\n  symbiont:\n    text: symbiont\n\n
"},{"location":"Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Boolean/#schema-source","title":"Schema Source","text":""},{"location":"Boolean/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:boolean native nmdc:boolean exact schema:Boolean"},{"location":"BuildDocsEnum/","title":"Enum: BuildDocsEnum","text":"

URI: BuildDocsEnum

"},{"location":"BuildDocsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building information model None commissioning report None complaint logs None contract administration None cost estimate None janitorial schedules or logs None maintenance plans None schedule None sections None shop drawings None submittals None ventilation system None windows None"},{"location":"BuildDocsEnum/#slots","title":"Slots","text":"Name Description build_docs The building design, construction and operation documents"},{"location":"BuildDocsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildDocsEnum/#schema-source","title":"Schema Source","text":""},{"location":"BuildDocsEnum/#linkml-source","title":"LinkML Source","text":"
name: build_docs_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  building information model:\n    text: building information model\n  commissioning report:\n    text: commissioning report\n  complaint logs:\n    text: complaint logs\n  contract administration:\n    text: contract administration\n  cost estimate:\n    text: cost estimate\n  janitorial schedules or logs:\n    text: janitorial schedules or logs\n  maintenance plans:\n    text: maintenance plans\n  schedule:\n    text: schedule\n  sections:\n    text: sections\n  shop drawings:\n    text: shop drawings\n  submittals:\n    text: submittals\n  ventilation system:\n    text: ventilation system\n  windows:\n    text: windows\n\n
"},{"location":"BuildOccupTypeEnum/","title":"Enum: BuildOccupTypeEnum","text":"

URI: BuildOccupTypeEnum

"},{"location":"BuildOccupTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description office None market None restaurant None residence None school None residential None commercial None low rise None high rise None wood framed None health care None airport None sports complex None"},{"location":"BuildOccupTypeEnum/#slots","title":"Slots","text":"Name Description build_occup_type The primary function for which a building or discrete part of a building is i..."},{"location":"BuildOccupTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildOccupTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"BuildOccupTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: build_occup_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  office:\n    text: office\n  market:\n    text: market\n  restaurant:\n    text: restaurant\n  residence:\n    text: residence\n  school:\n    text: school\n  residential:\n    text: residential\n  commercial:\n    text: commercial\n  low rise:\n    text: low rise\n  high rise:\n    text: high rise\n  wood framed:\n    text: wood framed\n  health care:\n    text: health care\n  airport:\n    text: airport\n  sports complex:\n    text: sports complex\n\n
"},{"location":"BuildingSettingEnum/","title":"Enum: BuildingSettingEnum","text":"

URI: BuildingSettingEnum

"},{"location":"BuildingSettingEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description urban None suburban None exurban None rural None"},{"location":"BuildingSettingEnum/#slots","title":"Slots","text":"Name Description building_setting A location (geography) where a building is set"},{"location":"BuildingSettingEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildingSettingEnum/#schema-source","title":"Schema Source","text":""},{"location":"BuildingSettingEnum/#linkml-source","title":"LinkML Source","text":"
name: building_setting_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  urban:\n    text: urban\n  suburban:\n    text: suburban\n  exurban:\n    text: exurban\n  rural:\n    text: rural\n\n
"},{"location":"Bytes/","title":"Type: Bytes","text":"

An integer value that corresponds to a size in bytes

URI: xsd:long

"},{"location":"Bytes/#see-also","title":"See Also","text":""},{"location":"Bytes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Bytes/#schema-source","title":"Schema Source","text":""},{"location":"Bytes/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:long native nmdc:bytes"},{"location":"CalibrationInformation/","title":"Class: CalibrationInformation","text":"

A calibration object that is associated with a process.

URI: nmdc:CalibrationInformation

classDiagram\n  class CalibrationInformation\n  click CalibrationInformation href \"../CalibrationInformation\"\n    InformationObject <|-- CalibrationInformation\n      click InformationObject href \"../InformationObject\"\n\n\n\n  CalibrationInformation : alternative_identifiers\n\n  CalibrationInformation : calibration_object\n\n      CalibrationInformation --> \"0..1\" DataObject : calibration_object\n    click DataObject href \"../DataObject\"\n\n  CalibrationInformation : calibration_standard\n\n      CalibrationInformation --> \"0..1\" CalibrationStandardEnum : calibration_standard\n    click CalibrationStandardEnum href \"../CalibrationStandardEnum\"\n\n  CalibrationInformation : calibration_target\n\n      CalibrationInformation --> \"1\" CalibrationTargetEnum : calibration_target\n    click CalibrationTargetEnum href \"../CalibrationTargetEnum\"\n\n  CalibrationInformation : description\n\n  CalibrationInformation : id\n\n  CalibrationInformation : internal_calibration\n\n  CalibrationInformation : name\n\n  CalibrationInformation : type\n\n\n\n
"},{"location":"CalibrationInformation/#inheritance","title":"Inheritance","text":""},{"location":"CalibrationInformation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance calibration_object 0..1 DataObject the file containing calibration data object direct internal_calibration 1 Boolean whether internal calibration was used, if false, external calibration was use... direct calibration_target 1 CalibrationTargetEnum the target measurement of the calibration direct calibration_standard 0..1 CalibrationStandardEnum the reference standard(s) used for calibration direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"CalibrationInformation/#usages","title":"Usages","text":"used by used in type used MassSpectrometry has_calibration any_of[range] CalibrationInformation Database calibration_set range CalibrationInformation MetabolomicsAnalysis has_calibration any_of[range] CalibrationInformation NomAnalysis has_calibration any_of[range] CalibrationInformation"},{"location":"CalibrationInformation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationInformation/#schema-source","title":"Schema Source","text":""},{"location":"CalibrationInformation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:CalibrationInformation native nmdc:CalibrationInformation"},{"location":"CalibrationInformation/#linkml-source","title":"LinkML Source","text":""},{"location":"CalibrationInformation/#direct","title":"Direct","text":"
name: CalibrationInformation\ndescription: A calibration object that is associated with a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- calibration_object\n- internal_calibration\n- calibration_target\n- calibration_standard\nslot_usage:\n  internal_calibration:\n    name: internal_calibration\n    required: true\n  calibration_target:\n    name: calibration_target\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:CalibrationInformation\nrules:\n- preconditions:\n    slot_conditions:\n      calibration_target:\n        name: calibration_target\n        equals_string: retention_index\n  postconditions:\n    slot_conditions:\n      calibration_standard:\n        name: calibration_standard\n        required: true\n  description: If the calibration_target is retention_index, a calibration_standard\n    is required.\n  title: calibration_standard_if_rt\n- preconditions:\n    slot_conditions:\n      internal_calibration:\n        name: internal_calibration\n        id_prefixes:\n        - 'False'\n  postconditions:\n    slot_conditions:\n      calibration_object:\n        name: calibration_object\n        required: true\n  description: If internal_calibration is false, a calibration_object is required.\n  title: calibration_object_if_not_internal_calibration\n\n
"},{"location":"CalibrationInformation/#induced","title":"Induced","text":"
name: CalibrationInformation\ndescription: A calibration object that is associated with a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n  internal_calibration:\n    name: internal_calibration\n    required: true\n  calibration_target:\n    name: calibration_target\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  calibration_object:\n    name: calibration_object\n    description: the file containing calibration data object\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: calibration_object\n    owner: CalibrationInformation\n    domain_of:\n    - CalibrationInformation\n    range: DataObject\n  internal_calibration:\n    name: internal_calibration\n    description: whether internal calibration was used, if false, external calibration\n      was used\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: internal_calibration\n    owner: CalibrationInformation\n    domain_of:\n    - CalibrationInformation\n    range: boolean\n    required: true\n  calibration_target:\n    name: calibration_target\n    description: the target measurement of the calibration\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: calibration_target\n    owner: CalibrationInformation\n    domain_of:\n    - CalibrationInformation\n    range: CalibrationTargetEnum\n    required: true\n  calibration_standard:\n    name: calibration_standard\n    description: the reference standard(s) used for calibration\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: calibration_standard\n    owner: CalibrationInformation\n    domain_of:\n    - CalibrationInformation\n    range: CalibrationStandardEnum\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CalibrationInformation\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: CalibrationInformation\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: CalibrationInformation\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: CalibrationInformation\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: CalibrationInformation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:CalibrationInformation\nrules:\n- preconditions:\n    slot_conditions:\n      calibration_target:\n        name: calibration_target\n        equals_string: retention_index\n  postconditions:\n    slot_conditions:\n      calibration_standard:\n        name: calibration_standard\n        required: true\n  description: If the calibration_target is retention_index, a calibration_standard\n    is required.\n  title: calibration_standard_if_rt\n- preconditions:\n    slot_conditions:\n      internal_calibration:\n        name: internal_calibration\n        id_prefixes:\n        - 'False'\n  postconditions:\n    slot_conditions:\n      calibration_object:\n        name: calibration_object\n        required: true\n  description: If internal_calibration is false, a calibration_object is required.\n  title: calibration_object_if_not_internal_calibration\n\n
"},{"location":"CalibrationStandardEnum/","title":"Enum: CalibrationStandardEnum","text":"

URI: CalibrationStandardEnum

"},{"location":"CalibrationStandardEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fames None alkanes None"},{"location":"CalibrationStandardEnum/#slots","title":"Slots","text":"Name Description calibration_standard the reference standard(s) used for calibration"},{"location":"CalibrationStandardEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationStandardEnum/#schema-source","title":"Schema Source","text":""},{"location":"CalibrationStandardEnum/#linkml-source","title":"LinkML Source","text":"
name: CalibrationStandardEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  fames:\n    text: fames\n    aliases:\n    - FAMES\n  alkanes:\n    text: alkanes\n    aliases:\n    - Alkanes\n\n
"},{"location":"CalibrationTargetEnum/","title":"Enum: CalibrationTargetEnum","text":"

URI: CalibrationTargetEnum

"},{"location":"CalibrationTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mass_charge_ratio None retention_time None retention_index None"},{"location":"CalibrationTargetEnum/#slots","title":"Slots","text":"Name Description calibration_target the target measurement of the calibration"},{"location":"CalibrationTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationTargetEnum/#schema-source","title":"Schema Source","text":""},{"location":"CalibrationTargetEnum/#linkml-source","title":"LinkML Source","text":"
name: CalibrationTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  mass_charge_ratio:\n    text: mass_charge_ratio\n    title: m/z\n    aliases:\n    - Mass\n    - m/z\n  retention_time:\n    text: retention_time\n    aliases:\n    - RT\n  retention_index:\n    text: retention_index\n    aliases:\n    - RI\n\n
"},{"location":"CeilCondEnum/","title":"Enum: CeilCondEnum","text":"

URI: CeilCondEnum

"},{"location":"CeilCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"CeilCondEnum/#slots","title":"Slots","text":"Name Description ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide..."},{"location":"CeilCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"CeilCondEnum/#linkml-source","title":"LinkML Source","text":"
name: ceil_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  new:\n    text: new\n  visible wear:\n    text: visible wear\n  needs repair:\n    text: needs repair\n  damaged:\n    text: damaged\n  rupture:\n    text: rupture\n\n
"},{"location":"CeilFinishMatEnum/","title":"Enum: CeilFinishMatEnum","text":"

URI: CeilFinishMatEnum

"},{"location":"CeilFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drywall None mineral fibre None tiles None PVC None plasterboard None metal None fiberglass None stucco None mineral wool/calcium silicate None wood None"},{"location":"CeilFinishMatEnum/#slots","title":"Slots","text":"Name Description ceil_finish_mat The type of material used to finish a ceiling"},{"location":"CeilFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilFinishMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"CeilFinishMatEnum/#linkml-source","title":"LinkML Source","text":"
name: ceil_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  drywall:\n    text: drywall\n  mineral fibre:\n    text: mineral fibre\n  tiles:\n    text: tiles\n  PVC:\n    text: PVC\n  plasterboard:\n    text: plasterboard\n  metal:\n    text: metal\n  fiberglass:\n    text: fiberglass\n  stucco:\n    text: stucco\n  mineral wool/calcium silicate:\n    text: mineral wool/calcium silicate\n  wood:\n    text: wood\n\n
"},{"location":"CeilTextureEnum/","title":"Enum: CeilTextureEnum","text":"

URI: CeilTextureEnum

"},{"location":"CeilTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"CeilTextureEnum/#slots","title":"Slots","text":"Name Description ceil_texture The feel, appearance, or consistency of a ceiling surface"},{"location":"CeilTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTextureEnum/#schema-source","title":"Schema Source","text":""},{"location":"CeilTextureEnum/#linkml-source","title":"LinkML Source","text":"
name: ceil_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  crows feet:\n    text: crows feet\n  crows-foot stomp:\n    text: crows-foot stomp\n  double skip:\n    text: double skip\n  hawk and trowel:\n    text: hawk and trowel\n  knockdown:\n    text: knockdown\n  popcorn:\n    text: popcorn\n  orange peel:\n    text: orange peel\n  rosebud stomp:\n    text: rosebud stomp\n  Santa-Fe texture:\n    text: Santa-Fe texture\n  skip trowel:\n    text: skip trowel\n  smooth:\n    text: smooth\n  stomp knockdown:\n    text: stomp knockdown\n  swirl:\n    text: swirl\n\n
"},{"location":"CeilTypeEnum/","title":"Enum: CeilTypeEnum","text":"

URI: CeilTypeEnum

"},{"location":"CeilTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cathedral None dropped None concave None barrel-shaped None coffered None cove None stretched None"},{"location":"CeilTypeEnum/#slots","title":"Slots","text":"Name Description ceil_type The type of ceiling according to the ceiling's appearance or construction"},{"location":"CeilTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"CeilTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: ceil_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  cathedral:\n    text: cathedral\n  dropped:\n    text: dropped\n  concave:\n    text: concave\n  barrel-shaped:\n    text: barrel-shaped\n  coffered:\n    text: coffered\n  cove:\n    text: cove\n  stretched:\n    text: stretched\n\n
"},{"location":"Checklist/","title":"Subset: Checklist","text":"

A MIxS checklist. These can be combined with packages

URI: Checklist

"},{"location":"Checklist/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Checklist/#schema-source","title":"Schema Source","text":""},{"location":"ChecklistPackageCombination/","title":"Subset: ChecklistPackageCombination","text":"

A combination of a checklist and a package

URI: ChecklistPackageCombination

"},{"location":"ChecklistPackageCombination/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChecklistPackageCombination/#schema-source","title":"Schema Source","text":""},{"location":"ChemicalConversionCategoryEnum/","title":"Enum: ChemicalConversionCategoryEnum","text":"

URI: ChemicalConversionCategoryEnum

"},{"location":"ChemicalConversionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description addition None substitution None acid_base None reduction_oxidation None combustion None decomposition None protease_cleavage OBI:0600056 an enzymatic cleavage which relies on an enzyme with protease activity to act..."},{"location":"ChemicalConversionCategoryEnum/#slots","title":"Slots","text":"Name Description chemical_conversion_category The type of chemical conversion process"},{"location":"ChemicalConversionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalConversionCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ChemicalConversionCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ChemicalConversionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  addition:\n    text: addition\n  substitution:\n    text: substitution\n  acid_base:\n    text: acid_base\n  reduction_oxidation:\n    text: reduction_oxidation\n  combustion:\n    text: combustion\n  decomposition:\n    text: decomposition\n  protease_cleavage:\n    text: protease_cleavage\n    description: an enzymatic cleavage which relies on an enzyme with protease activity\n      to act on proteins and to produce polypeptides (protein fragments).\n    meaning: OBI:0600056\n\n
"},{"location":"ChemicalConversionProcess/","title":"Class: ChemicalConversionProcess","text":"

A process that results in the interconversion of chemical species by a reaction to transform the reagents into products.

__

URI: nmdc:ChemicalConversionProcess

classDiagram\n  class ChemicalConversionProcess\n  click ChemicalConversionProcess href \"../ChemicalConversionProcess\"\n    MaterialProcessing <|-- ChemicalConversionProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  ChemicalConversionProcess : alternative_identifiers\n\n  ChemicalConversionProcess : chemical_conversion_category\n\n      ChemicalConversionProcess --> \"0..1\" ChemicalConversionCategoryEnum : chemical_conversion_category\n    click ChemicalConversionCategoryEnum href \"../ChemicalConversionCategoryEnum\"\n\n  ChemicalConversionProcess : description\n\n  ChemicalConversionProcess : duration\n\n      ChemicalConversionProcess --> \"0..1\" QuantityValue : duration\n    click QuantityValue href \"../QuantityValue\"\n\n  ChemicalConversionProcess : end_date\n\n  ChemicalConversionProcess : has_failure_categorization\n\n      ChemicalConversionProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ChemicalConversionProcess : has_input\n\n      ChemicalConversionProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ChemicalConversionProcess : has_output\n\n      ChemicalConversionProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  ChemicalConversionProcess : id\n\n  ChemicalConversionProcess : instrument_used\n\n      ChemicalConversionProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  ChemicalConversionProcess : name\n\n  ChemicalConversionProcess : processing_institution\n\n      ChemicalConversionProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ChemicalConversionProcess : protocol_link\n\n      ChemicalConversionProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ChemicalConversionProcess : qc_comment\n\n  ChemicalConversionProcess : qc_status\n\n      ChemicalConversionProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ChemicalConversionProcess : start_date\n\n  ChemicalConversionProcess : substances_used\n\n      ChemicalConversionProcess --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  ChemicalConversionProcess : substances_volume\n\n      ChemicalConversionProcess --> \"0..1\" QuantityValue : substances_volume\n    click QuantityValue href \"../QuantityValue\"\n\n  ChemicalConversionProcess : temperature\n\n      ChemicalConversionProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  ChemicalConversionProcess : type\n\n\n\n
"},{"location":"ChemicalConversionProcess/#inheritance","title":"Inheritance","text":""},{"location":"ChemicalConversionProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance chemical_conversion_category 0..1 ChemicalConversionCategoryEnum The type of chemical conversion process direct duration 0..1 QuantityValue The elapsed time of an activity direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct substances_used * PortionOfSubstance The substances that are combined to enable a ChemicalConversionProcess direct substances_volume 0..1 QuantityValue The volume of the combined substances that was included in a ChemicalConversi... direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ChemicalConversionProcess/#aliases","title":"Aliases","text":""},{"location":"ChemicalConversionProcess/#comments","title":"Comments","text":""},{"location":"ChemicalConversionProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalConversionProcess/#schema-source","title":"Schema Source","text":""},{"location":"ChemicalConversionProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ChemicalConversionProcess native nmdc:ChemicalConversionProcess exact MISO:0000001"},{"location":"ChemicalConversionProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"ChemicalConversionProcess/#direct","title":"Direct","text":"
name: ChemicalConversionProcess\ndescription: 'A process that results in the interconversion of chemical species by\n  a reaction to transform the reagents into products.\n\n  '\ncomments:\n- The values of both has_reagents slot and has_input slot are considered the reagents\n  of a chemical process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical reaction\nexact_mappings:\n- MISO:0000001\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- chemical_conversion_category\n- duration\n- temperature\n- substances_used\n- substances_volume\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ChemicalConversionProcess\n\n
"},{"location":"ChemicalConversionProcess/#induced","title":"Induced","text":"
name: ChemicalConversionProcess\ndescription: 'A process that results in the interconversion of chemical species by\n  a reaction to transform the reagents into products.\n\n  '\ncomments:\n- The values of both has_reagents slot and has_input slot are considered the reagents\n  of a chemical process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical reaction\nexact_mappings:\n- MISO:0000001\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  chemical_conversion_category:\n    name: chemical_conversion_category\n    description: The type of chemical conversion process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: chemical_conversion_category\n    owner: ChemicalConversionProcess\n    domain_of:\n    - ChemicalConversionProcess\n    range: ChemicalConversionCategoryEnum\n  duration:\n    name: duration\n    description: The elapsed time of an activity.\n    examples:\n    - value: JsonObj(has_numeric_value=2, has_unit='hours')\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: duration\n    owner: ChemicalConversionProcess\n    domain_of:\n    - MixingProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: QuantityValue\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: ChemicalConversionProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  substances_used:\n    name: substances_used\n    description: The substances that are combined to enable a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: ChemicalConversionProcess\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  substances_volume:\n    name: substances_volume\n    description: The volume of the combined substances that was included in a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_volume\n    owner: ChemicalConversionProcess\n    domain_of:\n    - ChemicalConversionProcess\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: ChemicalConversionProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalConversionProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ChemicalConversionProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ChemicalConversionProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ChemicalConversionProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ChemicalConversionProcess\n\n
"},{"location":"ChemicalEntity/","title":"Class: ChemicalEntity","text":"

An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states

URI: nmdc:ChemicalEntity

classDiagram\n  class ChemicalEntity\n  click ChemicalEntity href \"../ChemicalEntity\"\n    OntologyClass <|-- ChemicalEntity\n      click OntologyClass href \"../OntologyClass\"\n\n\n\n  ChemicalEntity : alternative_identifiers\n\n  ChemicalEntity : alternative_names\n\n  ChemicalEntity : chemical_formula\n\n  ChemicalEntity : description\n\n  ChemicalEntity : id\n\n  ChemicalEntity : inchi\n\n  ChemicalEntity : inchi_key\n\n  ChemicalEntity : name\n\n  ChemicalEntity : smiles\n\n  ChemicalEntity : type\n\n\n\n
"},{"location":"ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance alternative_names * String A list of alternative names used to refer to the entity direct chemical_formula 0..1 String A generic grouping for molecular formulae and empirical formulae direct inchi 0..1 String direct inchi_key 0..1 String direct smiles * String A string encoding of a molecular graph, no chiral or isotopic information direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ChemicalEntity/#usages","title":"Usages","text":"used by used in type used Database chemical_entity_set range ChemicalEntity PortionOfSubstance known_as range ChemicalEntity MetaboliteIdentification metabolite_identified range ChemicalEntity"},{"location":"ChemicalEntity/#aliases","title":"Aliases","text":""},{"location":"ChemicalEntity/#comments","title":"Comments","text":""},{"location":"ChemicalEntity/#see-also","title":"See Also","text":""},{"location":"ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ChemicalEntity native nmdc:ChemicalEntity exact biolink:ChemicalSubstance"},{"location":"ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- cas\n- CHEBI\n- CHEMBL.COMPOUND\n- DRUGBANK\n- HMDB\n- KEGG.COMPOUND\n- MESH\n- PUBCHEM.COMPOUND\ndescription: An atom or molecule that can be represented with a chemical formula.\n  Include lipids, glycans, natural products, drugs. There may be different terms for\n  distinct acid-base forms, protonation states\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n  to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nslots:\n- alternative_names\n- chemical_formula\n- inchi\n- inchi_key\n- smiles\nclass_uri: nmdc:ChemicalEntity\n\n
"},{"location":"ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- cas\n- CHEBI\n- CHEMBL.COMPOUND\n- DRUGBANK\n- HMDB\n- KEGG.COMPOUND\n- MESH\n- PUBCHEM.COMPOUND\ndescription: An atom or molecule that can be represented with a chemical formula.\n  Include lipids, glycans, natural products, drugs. There may be different terms for\n  distinct acid-base forms, protonation states\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n  to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nattributes:\n  alternative_names:\n    name: alternative_names\n    description: A list of alternative names used to refer to the entity. The distinction\n      between name and alternative names is application-specific.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - dcterms:alternative\n    - skos:altLabel\n    rank: 1000\n    alias: alternative_names\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    - Study\n    range: string\n    multivalued: true\n  chemical_formula:\n    name: chemical_formula\n    description: A generic grouping for molecular formulae and empirical formulae\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: chemical_formula\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    range: string\n  inchi:\n    name: inchi\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: inchi\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    range: string\n  inchi_key:\n    name: inchi_key\n    notes:\n    - 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n      K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n      testing. J Cheminform. 4:12'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: inchi_key\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    range: string\n  smiles:\n    name: smiles\n    description: A string encoding of a molecular graph, no chiral or isotopic information.\n      There are usually a large number of valid SMILES which represent a given structure.\n      For example, CCO, OCC and C(O)C all specify the structure of ethanol.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: smiles\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    range: string\n    multivalued: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ChemicalEntity\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ChemicalEntity\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ChemicalEntity\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ChemicalEntity\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ChemicalEntity\n\n
"},{"location":"ChromatographicCategoryEnum/","title":"Enum: ChromatographicCategoryEnum","text":"

URI: ChromatographicCategoryEnum

"},{"location":"ChromatographicCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description liquid_chromatography None gas_chromatography None solid_phase_extraction None"},{"location":"ChromatographicCategoryEnum/#slots","title":"Slots","text":"Name Description chromatographic_category The type of chromatography used in a process"},{"location":"ChromatographicCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChromatographicCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ChromatographicCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ChromatographicCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  liquid_chromatography:\n    text: liquid_chromatography\n    aliases:\n    - LC\n  gas_chromatography:\n    text: gas_chromatography\n    aliases:\n    - GC\n  solid_phase_extraction:\n    text: solid_phase_extraction\n    aliases:\n    - SPE\n\n
"},{"location":"ChromatographicSeparationProcess/","title":"Class: ChromatographicSeparationProcess","text":"

The process of using a selective partitioning of the analyte or interferent between two immiscible phases.

URI: nmdc:ChromatographicSeparationProcess

classDiagram\n  class ChromatographicSeparationProcess\n  click ChromatographicSeparationProcess href \"../ChromatographicSeparationProcess\"\n    MaterialProcessing <|-- ChromatographicSeparationProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  ChromatographicSeparationProcess : alternative_identifiers\n\n  ChromatographicSeparationProcess : chromatographic_category\n\n      ChromatographicSeparationProcess --> \"0..1\" ChromatographicCategoryEnum : chromatographic_category\n    click ChromatographicCategoryEnum href \"../ChromatographicCategoryEnum\"\n\n  ChromatographicSeparationProcess : description\n\n  ChromatographicSeparationProcess : end_date\n\n  ChromatographicSeparationProcess : has_failure_categorization\n\n      ChromatographicSeparationProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ChromatographicSeparationProcess : has_input\n\n      ChromatographicSeparationProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ChromatographicSeparationProcess : has_output\n\n      ChromatographicSeparationProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  ChromatographicSeparationProcess : id\n\n  ChromatographicSeparationProcess : instrument_used\n\n      ChromatographicSeparationProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  ChromatographicSeparationProcess : name\n\n  ChromatographicSeparationProcess : ordered_mobile_phases\n\n      ChromatographicSeparationProcess --> \"*\" MobilePhaseSegment : ordered_mobile_phases\n    click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n  ChromatographicSeparationProcess : processing_institution\n\n      ChromatographicSeparationProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ChromatographicSeparationProcess : protocol_link\n\n      ChromatographicSeparationProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ChromatographicSeparationProcess : qc_comment\n\n  ChromatographicSeparationProcess : qc_status\n\n      ChromatographicSeparationProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ChromatographicSeparationProcess : start_date\n\n  ChromatographicSeparationProcess : stationary_phase\n\n      ChromatographicSeparationProcess --> \"0..1\" StationaryPhaseEnum : stationary_phase\n    click StationaryPhaseEnum href \"../StationaryPhaseEnum\"\n\n  ChromatographicSeparationProcess : temperature\n\n      ChromatographicSeparationProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  ChromatographicSeparationProcess : type\n\n\n\n
"},{"location":"ChromatographicSeparationProcess/#inheritance","title":"Inheritance","text":""},{"location":"ChromatographicSeparationProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance chromatographic_category 0..1 ChromatographicCategoryEnum The type of chromatography used in a process direct ordered_mobile_phases * MobilePhaseSegment The solution(s) that moves through a chromatography column direct stationary_phase 0..1 StationaryPhaseEnum The material the stationary phase is comprised of used in chromatography direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ChromatographicSeparationProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChromatographicSeparationProcess/#schema-source","title":"Schema Source","text":""},{"location":"ChromatographicSeparationProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ChromatographicSeparationProcess native nmdc:ChromatographicSeparationProcess"},{"location":"ChromatographicSeparationProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"ChromatographicSeparationProcess/#direct","title":"Direct","text":"
name: ChromatographicSeparationProcess\ndescription: The process of using a selective partitioning of the analyte or interferent\n  between two immiscible phases.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- chromatographic_category\n- ordered_mobile_phases\n- stationary_phase\n- temperature\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ChromatographicSeparationProcess\n\n
"},{"location":"ChromatographicSeparationProcess/#induced","title":"Induced","text":"
name: ChromatographicSeparationProcess\ndescription: The process of using a selective partitioning of the analyte or interferent\n  between two immiscible phases.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  chromatographic_category:\n    name: chromatographic_category\n    description: The type of chromatography used in a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: chromatographic_category\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: ChromatographicCategoryEnum\n  ordered_mobile_phases:\n    name: ordered_mobile_phases\n    description: The solution(s) that moves through a chromatography column.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    list_elements_ordered: true\n    alias: ordered_mobile_phases\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: MobilePhaseSegment\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  stationary_phase:\n    name: stationary_phase\n    description: The material the stationary phase is comprised of used in chromatography.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: stationary_phase\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: StationaryPhaseEnum\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ChromatographicSeparationProcess\n\n
"},{"location":"ChromatographyConfiguration/","title":"Class: ChromatographyConfiguration","text":"

A set of parameters that define and control the actions of a chromatography process.

URI: nmdc:ChromatographyConfiguration

classDiagram\n  class ChromatographyConfiguration\n  click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n    Configuration <|-- ChromatographyConfiguration\n      click Configuration href \"../Configuration\"\n\n\n\n  ChromatographyConfiguration : alternative_identifiers\n\n  ChromatographyConfiguration : chromatographic_category\n\n      ChromatographyConfiguration --> \"0..1\" ChromatographicCategoryEnum : chromatographic_category\n    click ChromatographicCategoryEnum href \"../ChromatographicCategoryEnum\"\n\n  ChromatographyConfiguration : description\n\n  ChromatographyConfiguration : id\n\n  ChromatographyConfiguration : name\n\n  ChromatographyConfiguration : ordered_mobile_phases\n\n      ChromatographyConfiguration --> \"*\" MobilePhaseSegment : ordered_mobile_phases\n    click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n  ChromatographyConfiguration : stationary_phase\n\n      ChromatographyConfiguration --> \"0..1\" StationaryPhaseEnum : stationary_phase\n    click StationaryPhaseEnum href \"../StationaryPhaseEnum\"\n\n  ChromatographyConfiguration : temperature\n\n      ChromatographyConfiguration --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  ChromatographyConfiguration : type\n\n\n\n
"},{"location":"ChromatographyConfiguration/#inheritance","title":"Inheritance","text":""},{"location":"ChromatographyConfiguration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance chromatographic_category 0..1 ChromatographicCategoryEnum The type of chromatography used in a process direct ordered_mobile_phases * MobilePhaseSegment The solution(s) that moves through a chromatography column direct stationary_phase 0..1 StationaryPhaseEnum The material the stationary phase is comprised of used in chromatography direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 1 String A human readable label for an entity NamedThing description 1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ChromatographyConfiguration/#usages","title":"Usages","text":"used by used in type used MassSpectrometry has_chromatography_configuration range ChromatographyConfiguration"},{"location":"ChromatographyConfiguration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChromatographyConfiguration/#schema-source","title":"Schema Source","text":""},{"location":"ChromatographyConfiguration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ChromatographyConfiguration native nmdc:ChromatographyConfiguration"},{"location":"ChromatographyConfiguration/#linkml-source","title":"LinkML Source","text":""},{"location":"ChromatographyConfiguration/#direct","title":"Direct","text":"
name: ChromatographyConfiguration\ndescription: A set of parameters that define and control the actions of a chromatography\n  process.\nnotes:\n- This class is intended to represent a chromatography method file associated with\n  a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslots:\n- chromatographic_category\n- ordered_mobile_phases\n- stationary_phase\n- temperature\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ChromatographyConfiguration\n\n
"},{"location":"ChromatographyConfiguration/#induced","title":"Induced","text":"
name: ChromatographyConfiguration\ndescription: A set of parameters that define and control the actions of a chromatography\n  process.\nnotes:\n- This class is intended to represent a chromatography method file associated with\n  a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  chromatographic_category:\n    name: chromatographic_category\n    description: The type of chromatography used in a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: chromatographic_category\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: ChromatographicCategoryEnum\n  ordered_mobile_phases:\n    name: ordered_mobile_phases\n    description: The solution(s) that moves through a chromatography column.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    list_elements_ordered: true\n    alias: ordered_mobile_phases\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: MobilePhaseSegment\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  stationary_phase:\n    name: stationary_phase\n    description: The material the stationary phase is comprised of used in chromatography.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: stationary_phase\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: StationaryPhaseEnum\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChromatographyConfiguration\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ChromatographyConfiguration\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n    required: true\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n    required: true\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ChromatographyConfiguration\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ChromatographyConfiguration\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ChromatographyConfiguration\n\n
"},{"location":"CollectingBiosamplesFromSite/","title":"Class: Collecting Biosamples From Site (CollectingBiosamplesFromSite)","text":"

URI: nmdc:CollectingBiosamplesFromSite

classDiagram\n  class CollectingBiosamplesFromSite\n  click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n    PlannedProcess <|-- CollectingBiosamplesFromSite\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n\n  CollectingBiosamplesFromSite : alternative_identifiers\n\n  CollectingBiosamplesFromSite : description\n\n  CollectingBiosamplesFromSite : end_date\n\n  CollectingBiosamplesFromSite : has_failure_categorization\n\n      CollectingBiosamplesFromSite --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  CollectingBiosamplesFromSite : has_input\n\n      CollectingBiosamplesFromSite --> \"1..*\" Site : has_input\n    click Site href \"../Site\"\n\n  CollectingBiosamplesFromSite : has_output\n\n      CollectingBiosamplesFromSite --> \"1..*\" Biosample : has_output\n    click Biosample href \"../Biosample\"\n\n  CollectingBiosamplesFromSite : id\n\n  CollectingBiosamplesFromSite : name\n\n  CollectingBiosamplesFromSite : processing_institution\n\n      CollectingBiosamplesFromSite --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  CollectingBiosamplesFromSite : protocol_link\n\n      CollectingBiosamplesFromSite --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  CollectingBiosamplesFromSite : qc_comment\n\n  CollectingBiosamplesFromSite : qc_status\n\n      CollectingBiosamplesFromSite --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  CollectingBiosamplesFromSite : start_date\n\n  CollectingBiosamplesFromSite : type\n\n\n\n
"},{"location":"CollectingBiosamplesFromSite/#inheritance","title":"Inheritance","text":""},{"location":"CollectingBiosamplesFromSite/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_input 1..* Site An input to a process PlannedProcess has_output 1..* Biosample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"CollectingBiosamplesFromSite/#usages","title":"Usages","text":"used by used in type used Database collecting_biosamples_from_site_set range CollectingBiosamplesFromSite"},{"location":"CollectingBiosamplesFromSite/#comments","title":"Comments","text":""},{"location":"CollectingBiosamplesFromSite/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CollectingBiosamplesFromSite/#schema-source","title":"Schema Source","text":""},{"location":"CollectingBiosamplesFromSite/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:CollectingBiosamplesFromSite native nmdc:CollectingBiosamplesFromSite close OBI:0000744"},{"location":"CollectingBiosamplesFromSite/#linkml-source","title":"LinkML Source","text":""},{"location":"CollectingBiosamplesFromSite/#direct","title":"Direct","text":"
name: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n  has_input:\n    name: has_input\n    range: Site\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    range: Biosample\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:CollectingBiosamplesFromSite\n\n
"},{"location":"CollectingBiosamplesFromSite/#induced","title":"Induced","text":"
name: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n  has_input:\n    name: has_input\n    range: Site\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    range: Biosample\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: Site\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: Biosample\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:CollectingBiosamplesFromSite\n\n
"},{"location":"Configuration/","title":"Class: Configuration","text":"

A set of parameters that define the actions of a process and is shared among multiple instances of the process.

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:Configuration

classDiagram\n  class Configuration\n  click Configuration href \"../Configuration\"\n    InformationObject <|-- Configuration\n      click InformationObject href \"../InformationObject\"\n\n\n    Configuration <|-- MassSpectrometryConfiguration\n      click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n    Configuration <|-- ChromatographyConfiguration\n      click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n\n\n\n  Configuration : alternative_identifiers\n\n  Configuration : description\n\n  Configuration : id\n\n  Configuration : name\n\n  Configuration : type\n\n\n\n
"},{"location":"Configuration/#inheritance","title":"Inheritance","text":""},{"location":"Configuration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Configuration/#usages","title":"Usages","text":"used by used in type used Database configuration_set range Configuration"},{"location":"Configuration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Configuration/#schema-source","title":"Schema Source","text":""},{"location":"Configuration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Configuration native nmdc:Configuration"},{"location":"Configuration/#linkml-source","title":"LinkML Source","text":""},{"location":"Configuration/#direct","title":"Direct","text":"
name: Configuration\ndescription: A set of parameters that define the actions of a process and is shared\n  among multiple instances of the process.\nnotes:\n- This class is intended to represent the parameters within a method file (or similar)\n  that control a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nabstract: true\nclass_uri: nmdc:Configuration\n\n
"},{"location":"Configuration/#induced","title":"Induced","text":"
name: Configuration\ndescription: A set of parameters that define the actions of a process and is shared\n  among multiple instances of the process.\nnotes:\n- This class is intended to represent the parameters within a method file (or similar)\n  that control a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Configuration\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Configuration\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Configuration\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Configuration\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Configuration\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Configuration\n\n
"},{"location":"ContainerCategoryEnum/","title":"Enum: ContainerCategoryEnum","text":"

The permitted types of containers used in processing metabolomic samples.

URI: ContainerCategoryEnum

"},{"location":"ContainerCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description v-bottom_conical_tube None falcon_tube None"},{"location":"ContainerCategoryEnum/#slots","title":"Slots","text":"Name Description contained_in A type of container"},{"location":"ContainerCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ContainerCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ContainerCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ContainerCategoryEnum\ndescription: The permitted types of containers used in processing metabolomic samples.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\npermissible_values:\n  v-bottom_conical_tube:\n    text: v-bottom_conical_tube\n  falcon_tube:\n    text: falcon_tube\n\n
"},{"location":"ControlledIdentifiedTermValue/","title":"Class: ControlledIdentifiedTermValue","text":"

A controlled term or class from an ontology, requiring the presence of term with an id

URI: nmdc:ControlledIdentifiedTermValue

classDiagram\n  class ControlledIdentifiedTermValue\n  click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n    ControlledTermValue <|-- ControlledIdentifiedTermValue\n      click ControlledTermValue href \"../ControlledTermValue\"\n\n\n\n  ControlledIdentifiedTermValue : has_raw_value\n\n  ControlledIdentifiedTermValue : term\n\n      ControlledIdentifiedTermValue --> \"1\" OntologyClass : term\n    click OntologyClass href \"../OntologyClass\"\n\n  ControlledIdentifiedTermValue : type\n\n\n\n
"},{"location":"ControlledIdentifiedTermValue/#inheritance","title":"Inheritance","text":""},{"location":"ControlledIdentifiedTermValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance term 1 OntologyClass pointer to an ontology class ControlledTermValue has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"ControlledIdentifiedTermValue/#usages","title":"Usages","text":"used by used in type used Biosample host_taxid range ControlledIdentifiedTermValue Biosample env_broad_scale range ControlledIdentifiedTermValue Biosample env_local_scale range ControlledIdentifiedTermValue Biosample env_medium range ControlledIdentifiedTermValue Biosample samp_taxon_id range ControlledIdentifiedTermValue GenomeFeature feature_category range ControlledIdentifiedTermValue FunctionalAnnotation feature_category range ControlledIdentifiedTermValue"},{"location":"ControlledIdentifiedTermValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ControlledIdentifiedTermValue/#schema-source","title":"Schema Source","text":""},{"location":"ControlledIdentifiedTermValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ControlledIdentifiedTermValue native nmdc:ControlledIdentifiedTermValue"},{"location":"ControlledIdentifiedTermValue/#linkml-source","title":"LinkML Source","text":""},{"location":"ControlledIdentifiedTermValue/#direct","title":"Direct","text":"
name: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n  term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n  term:\n    name: term\n    required: true\nclass_uri: nmdc:ControlledIdentifiedTermValue\n\n
"},{"location":"ControlledIdentifiedTermValue/#induced","title":"Induced","text":"
name: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n  term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n  term:\n    name: term\n    required: true\nattributes:\n  term:\n    name: term\n    description: pointer to an ontology class\n    notes:\n    - 'removed ''slot_uri: rdf:type'''\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: term\n    owner: ControlledIdentifiedTermValue\n    domain_of:\n    - ControlledTermValue\n    range: OntologyClass\n    required: true\n    inlined: true\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: ControlledIdentifiedTermValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ControlledIdentifiedTermValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ControlledIdentifiedTermValue\n\n
"},{"location":"ControlledTermValue/","title":"Class: ControlledTermValue","text":"

A controlled term or class from an ontology

URI: nmdc:ControlledTermValue

classDiagram\n  class ControlledTermValue\n  click ControlledTermValue href \"../ControlledTermValue\"\n    AttributeValue <|-- ControlledTermValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n    ControlledTermValue <|-- ControlledIdentifiedTermValue\n      click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n\n\n  ControlledTermValue : has_raw_value\n\n  ControlledTermValue : term\n\n      ControlledTermValue --> \"0..1\" OntologyClass : term\n    click OntologyClass href \"../OntologyClass\"\n\n  ControlledTermValue : type\n\n\n\n
"},{"location":"ControlledTermValue/#inheritance","title":"Inheritance","text":""},{"location":"ControlledTermValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance term 0..1 OntologyClass pointer to an ontology class direct has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"ControlledTermValue/#usages","title":"Usages","text":"used by used in type used Biosample chem_administration range ControlledTermValue Biosample experimental_factor range ControlledTermValue Biosample growth_facil range ControlledTermValue Biosample host_body_product range ControlledTermValue Biosample host_body_site range ControlledTermValue Biosample host_phenotype range ControlledTermValue Biosample plant_growth_med range ControlledTermValue Biosample plant_struc range ControlledTermValue Biosample samp_mat_process range ControlledTermValue"},{"location":"ControlledTermValue/#todos","title":"TODOs","text":""},{"location":"ControlledTermValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ControlledTermValue/#schema-source","title":"Schema Source","text":""},{"location":"ControlledTermValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ControlledTermValue native nmdc:ControlledTermValue"},{"location":"ControlledTermValue/#linkml-source","title":"LinkML Source","text":""},{"location":"ControlledTermValue/#direct","title":"Direct","text":"
name: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- term\nclass_uri: nmdc:ControlledTermValue\n\n
"},{"location":"ControlledTermValue/#induced","title":"Induced","text":"
name: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n  term:\n    name: term\n    description: pointer to an ontology class\n    notes:\n    - 'removed ''slot_uri: rdf:type'''\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: term\n    owner: ControlledTermValue\n    domain_of:\n    - ControlledTermValue\n    range: OntologyClass\n    inlined: true\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: ControlledTermValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ControlledTermValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ControlledTermValue\n\n
"},{"location":"CreditAssociation/","title":"Class: CreditAssociation","text":"

This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role and for a person value. Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0

URI: prov:Association

classDiagram\n  class CreditAssociation\n  click CreditAssociation href \"../CreditAssociation\"\n\n  CreditAssociation : applied_roles\n\n      CreditAssociation --> \"1..*\" CreditEnum : applied_roles\n    click CreditEnum href \"../CreditEnum\"\n\n  CreditAssociation : applies_to_person\n\n      CreditAssociation --> \"1\" PersonValue : applies_to_person\n    click PersonValue href \"../PersonValue\"\n\n  CreditAssociation : type\n\n\n\n
"},{"location":"CreditAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance applies_to_person 1 PersonValue direct applied_roles 1..* CreditEnum direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"CreditAssociation/#usages","title":"Usages","text":"used by used in type used Study has_credit_associations range CreditAssociation"},{"location":"CreditAssociation/#aliases","title":"Aliases","text":""},{"location":"CreditAssociation/#see-also","title":"See Also","text":""},{"location":"CreditAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CreditAssociation/#schema-source","title":"Schema Source","text":""},{"location":"CreditAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self prov:Association native nmdc:CreditAssociation"},{"location":"CreditAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"CreditAssociation/#direct","title":"Direct","text":"
name: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n  will be at least a slot for a CRediT Contributor Role and for a person value. Specifically\n  see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n  at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://casrai.org/credit/\naliases:\n- study role\n- credit table\n- associated researchers\nslots:\n- applies_to_person\n- applied_roles\n- type\nclass_uri: prov:Association\n\n
"},{"location":"CreditAssociation/#induced","title":"Induced","text":"
name: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n  will be at least a slot for a CRediT Contributor Role and for a person value. Specifically\n  see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n  at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://casrai.org/credit/\naliases:\n- study role\n- credit table\n- associated researchers\nattributes:\n  applies_to_person:\n    name: applies_to_person\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: applies_to_person\n    owner: CreditAssociation\n    domain_of:\n    - CreditAssociation\n    range: PersonValue\n    required: true\n  applied_roles:\n    name: applied_roles\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: 'Identify all CRediT roles associated with this contributor. CRediT\n          Information: https://info.orcid.org/credit-for-research-contribution ; CRediT:\n          https://credit.niso.org/'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: applied_roles\n    owner: CreditAssociation\n    domain_of:\n    - CreditAssociation\n    range: CreditEnum\n    required: true\n    multivalued: true\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: CreditAssociation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: prov:Association\n\n
"},{"location":"CreditEnum/","title":"Enum: CreditEnum","text":"

URI: CreditEnum

"},{"location":"CreditEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Conceptualization None Conceptualization Data curation None Data curation Formal Analysis None Formal Analysis Funding acquisition None Funding acquisition Investigation None Investigation Methodology None Methodology Project administration None Project administration Resources None Resources Software None Software Supervision None Supervision Validation None Validation Visualization None Visualization Writing original draft None Writing \u2013 original draft Writing review and editing None Writing \u2013 review & editing Principal Investigator OBI:0000103 principal investigator role Submitter EFO:0001741 the person(s) who enter study and biosample metadata into the NMDC submission..."},{"location":"CreditEnum/#slots","title":"Slots","text":"Name Description applied_roles"},{"location":"CreditEnum/#comments","title":"Comments","text":""},{"location":"CreditEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CreditEnum/#schema-source","title":"Schema Source","text":""},{"location":"CreditEnum/#linkml-source","title":"LinkML Source","text":"
name: CreditEnum\ncomments:\n- CreditEnums come from https://casrai.org/credit/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Conceptualization:\n    text: Conceptualization\n    description: Conceptualization\n  Data curation:\n    text: Data curation\n    description: Data curation\n  Formal Analysis:\n    text: Formal Analysis\n    description: Formal Analysis\n  Funding acquisition:\n    text: Funding acquisition\n    description: Funding acquisition\n  Investigation:\n    text: Investigation\n    description: Investigation\n  Methodology:\n    text: Methodology\n    description: Methodology\n  Project administration:\n    text: Project administration\n    description: Project administration\n  Resources:\n    text: Resources\n    description: Resources\n  Software:\n    text: Software\n    description: Software\n  Supervision:\n    text: Supervision\n    description: Supervision\n  Validation:\n    text: Validation\n    description: Validation\n  Visualization:\n    text: Visualization\n    description: Visualization\n  Writing original draft:\n    text: Writing original draft\n    description: Writing \u2013 original draft\n  Writing review and editing:\n    text: Writing review and editing\n    description: Writing \u2013 review & editing\n  Principal Investigator:\n    text: Principal Investigator\n    description: principal investigator role\n    meaning: OBI:0000103\n  Submitter:\n    text: Submitter\n    description: the person(s) who enter study and biosample metadata into the NMDC\n      submission portal\n    meaning: EFO:0001741\n\n
"},{"location":"CurLandUseEnum/","title":"Enum: CurLandUseEnum","text":"

URI: CurLandUseEnum

"},{"location":"CurLandUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description badlands None cities None conifers None crop trees None farmstead None gravel None hardwoods None hayland None horticultural plants None industrial areas None intermixed hardwood and conifers None marshlands None meadows None mines/quarries None mudflats None oil waste areas None pastureland None permanent snow or ice None rainforest None rangeland None roads/railroads None rock None row crops None saline seeps None salt flats None sand None shrub crops None shrub land None small grains None successional shrub land None swamp None tropical None tundra None vegetable crops None vine crops None"},{"location":"CurLandUseEnum/#slots","title":"Slots","text":"Name Description cur_land_use Present state of sample site"},{"location":"CurLandUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CurLandUseEnum/#schema-source","title":"Schema Source","text":""},{"location":"CurLandUseEnum/#linkml-source","title":"LinkML Source","text":"
name: cur_land_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  badlands:\n    text: badlands\n  cities:\n    text: cities\n  conifers:\n    text: conifers\n    annotations:\n      originally:\n        tag: originally\n        value: conifers (e.g. pine,spruce,fir,cypress)\n    examples:\n    - value: cypress\n    - value: fir\n    - value: pine\n    - value: spruce\n  crop trees:\n    text: crop trees\n    annotations:\n      originally:\n        tag: originally\n        value: crop trees (nuts,fruit,christmas trees,nursery trees)\n    examples:\n    - value: christmas trees\n    - value: fruit\n    - value: nursery trees\n    - value: nuts\n  farmstead:\n    text: farmstead\n  gravel:\n    text: gravel\n  hardwoods:\n    text: hardwoods\n    annotations:\n      originally:\n        tag: originally\n        value: hardwoods (e.g. oak,hickory,elm,aspen)\n    examples:\n    - value: aspen\n    - value: elm\n    - value: hickory\n    - value: oak\n  hayland:\n    text: hayland\n  horticultural plants:\n    text: horticultural plants\n    annotations:\n      originally:\n        tag: originally\n        value: horticultural plants (e.g. tulips)\n    examples:\n    - value: tulips\n  industrial areas:\n    text: industrial areas\n  intermixed hardwood and conifers:\n    text: intermixed hardwood and conifers\n  marshlands:\n    text: marshlands\n    annotations:\n      originally:\n        tag: originally\n        value: marshlands (grass,sedges,rushes)\n    examples:\n    - value: grass\n    - value: rushes\n    - value: sedgees\n  meadows:\n    text: meadows\n    annotations:\n      originally:\n        tag: originally\n        value: meadows (grasses,alfalfa,fescue,bromegrass,timothy)\n    examples:\n    - value: alfalfa\n    - value: bromegrass\n    - value: fescue\n    - value: grasses\n    - value: timothy\n  mines/quarries:\n    text: mines/quarries\n  mudflats:\n    text: mudflats\n  oil waste areas:\n    text: oil waste areas\n  pastureland:\n    text: pastureland\n    annotations:\n      originally:\n        tag: originally\n        value: pastureland (grasslands used for livestock grazing)\n    comments:\n    - grasslands used for livestock grazing\n  permanent snow or ice:\n    text: permanent snow or ice\n  rainforest:\n    text: rainforest\n    annotations:\n      originally:\n        tag: originally\n        value: rainforest (evergreen forest receiving greater than 406 cm annual rainfall)\n    comments:\n    - evergreen forest receiving greater than 406 cm annual rainfall\n  rangeland:\n    text: rangeland\n  roads/railroads:\n    text: roads/railroads\n  rock:\n    text: rock\n  row crops:\n    text: row crops\n  saline seeps:\n    text: saline seeps\n  salt flats:\n    text: salt flats\n  sand:\n    text: sand\n  shrub crops:\n    text: shrub crops\n    annotations:\n      originally:\n        tag: originally\n        value: shrub crops (blueberries,nursery ornamentals,filberts)\n    examples:\n    - value: blueberries\n    - value: filberts\n    - value: nursery ornamentals\n  shrub land:\n    text: shrub land\n    annotations:\n      originally:\n        tag: originally\n        value: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)\n    examples:\n    - value: creosote bush\n    - value: eucalyptus\n    - value: mesquite\n    - value: sage-brush\n    - value: shrub oak\n  small grains:\n    text: small grains\n  successional shrub land:\n    text: successional shrub land\n    annotations:\n      originally:\n        tag: originally\n        value: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub\n          dogwoods,blackberries)\n    examples:\n    - value: blackberries\n    - value: chokecherry\n    - value: hazels\n    - value: shrub dogwoods\n    - value: sumacs\n    - value: tree saplings\n  swamp:\n    text: swamp\n    annotations:\n      originally:\n        tag: originally\n        value: swamp (permanent or semi-permanent water body dominated by woody plants)\n    comments:\n    - permanent or semi-permanent water body dominated by woody plants\n  tropical:\n    text: tropical\n    annotations:\n      originally:\n        tag: originally\n        value: tropical (e.g. mangrove,palms)\n    examples:\n    - value: mangrove\n    - value: palms\n  tundra:\n    text: tundra\n    annotations:\n      originally:\n        tag: originally\n        value: tundra (mosses,lichens)\n    examples:\n    - value: lichens\n    - value: mosses\n  vegetable crops:\n    text: vegetable crops\n  vine crops:\n    text: vine crops\n    annotations:\n      originally:\n        tag: originally\n        value: vine crops (grapes)\n    examples:\n    - value: grapes\n\n
"},{"location":"Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"Curie/#comments","title":"Comments","text":""},{"location":"Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Curie/#schema-source","title":"Schema Source","text":""},{"location":"Curie/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:curie"},{"location":"DNASampleFormatEnum/","title":"Enum: DNASampleFormatEnum","text":"

URI: DNASampleFormatEnum

"},{"location":"DNASampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"DNASampleFormatEnum/#slots","title":"Slots","text":"Name Description dna_sample_format Solution in which the DNA sample has been suspended"},{"location":"DNASampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DNASampleFormatEnum/#schema-source","title":"Schema Source","text":""},{"location":"DNASampleFormatEnum/#linkml-source","title":"LinkML Source","text":"
name: DNASampleFormatEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  10 mM Tris-HCl:\n    text: 10 mM Tris-HCl\n  DNAStable:\n    text: DNAStable\n  Ethanol:\n    text: Ethanol\n  Low EDTA TE:\n    text: Low EDTA TE\n  MDA reaction buffer:\n    text: MDA reaction buffer\n  PBS:\n    text: PBS\n  Pellet:\n    text: Pellet\n  RNAStable:\n    text: RNAStable\n  TE:\n    text: TE\n  Water:\n    text: Water\n  Gentegra-DNA:\n    text: Gentegra-DNA\n  Gentegra-RNA:\n    text: Gentegra-RNA\n\n
"},{"location":"DataCategoryEnum/","title":"Enum: DataCategoryEnum","text":"

URI: DataCategoryEnum

"},{"location":"DataCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description instrument_data None Data generated by a DataGeneration PlannedProcess processed_data None Data generated by a WorkflowExecution PlannedProcess workflow_parameter_data None Data used as input into a workflow providing workflow specification"},{"location":"DataCategoryEnum/#slots","title":"Slots","text":"Name Description data_category The category of the file, such as instrument data from data generation or pro..."},{"location":"DataCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"DataCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: DataCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  instrument_data:\n    text: instrument_data\n    description: Data generated by a DataGeneration PlannedProcess\n  processed_data:\n    text: processed_data\n    description: Data generated by a WorkflowExecution PlannedProcess\n  workflow_parameter_data:\n    text: workflow_parameter_data\n    description: Data used as input into a workflow providing workflow specification.\n    related_mappings:\n    - edam.data:0949\n\n
"},{"location":"DataGeneration/","title":"Class: DataGeneration","text":"

The methods and processes used to generate omics data from a biosample or organism.

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:DataGeneration

classDiagram\n  class DataGeneration\n  click DataGeneration href \"../DataGeneration\"\n    PlannedProcess <|-- DataGeneration\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n    DataGeneration <|-- NucleotideSequencing\n      click NucleotideSequencing href \"../NucleotideSequencing\"\n    DataGeneration <|-- MassSpectrometry\n      click MassSpectrometry href \"../MassSpectrometry\"\n\n\n\n  DataGeneration : add_date\n\n  DataGeneration : alternative_identifiers\n\n  DataGeneration : analyte_category\n\n      DataGeneration --> \"1\" AnalyteCategoryEnum : analyte_category\n    click AnalyteCategoryEnum href \"../AnalyteCategoryEnum\"\n\n  DataGeneration : associated_studies\n\n      DataGeneration --> \"1..*\" Study : associated_studies\n    click Study href \"../Study\"\n\n  DataGeneration : description\n\n  DataGeneration : end_date\n\n  DataGeneration : has_failure_categorization\n\n      DataGeneration --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  DataGeneration : has_input\n\n      DataGeneration --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  DataGeneration : has_output\n\n      DataGeneration --> \"*\" DataObject : has_output\n    click DataObject href \"../DataObject\"\n\n  DataGeneration : id\n\n  DataGeneration : instrument_used\n\n      DataGeneration --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  DataGeneration : mod_date\n\n  DataGeneration : name\n\n  DataGeneration : principal_investigator\n\n      DataGeneration --> \"0..1\" PersonValue : principal_investigator\n    click PersonValue href \"../PersonValue\"\n\n  DataGeneration : processing_institution\n\n      DataGeneration --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  DataGeneration : protocol_link\n\n      DataGeneration --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  DataGeneration : qc_comment\n\n  DataGeneration : qc_status\n\n      DataGeneration --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  DataGeneration : start_date\n\n  DataGeneration : type\n\n\n\n
"},{"location":"DataGeneration/#inheritance","title":"Inheritance","text":""},{"location":"DataGeneration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance add_date 0..1 String The date on which the information was added to the database direct analyte_category 1 AnalyteCategoryEnum The type of analyte(s) that were measured in the data generation process and ... direct associated_studies 1..* Study The study associated with a resource direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing direct mod_date 0..1 String The last date on which the database information was modified direct principal_investigator 0..1 PersonValue Principal Investigator who led the study and/or generated the dataset direct has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * DataObject An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"DataGeneration/#usages","title":"Usages","text":"used by used in type used Database data_generation_set range DataGeneration MetagenomeAnnotation was_informed_by range DataGeneration FunctionalAnnotation was_generated_by any_of[range] DataGeneration DataObject was_generated_by any_of[range] DataGeneration WorkflowExecution was_informed_by range DataGeneration MetagenomeAssembly was_informed_by range DataGeneration MetatranscriptomeAssembly was_informed_by range DataGeneration MetatranscriptomeAnnotation was_informed_by range DataGeneration MetatranscriptomeExpressionAnalysis was_informed_by range DataGeneration MagsAnalysis was_informed_by range DataGeneration MetagenomeSequencing was_informed_by range DataGeneration ReadQcAnalysis was_informed_by range DataGeneration ReadBasedTaxonomyAnalysis was_informed_by range DataGeneration MetabolomicsAnalysis was_informed_by range DataGeneration MetaproteomicsAnalysis was_informed_by range DataGeneration NomAnalysis was_informed_by range DataGeneration"},{"location":"DataGeneration/#aliases","title":"Aliases","text":""},{"location":"DataGeneration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataGeneration/#schema-source","title":"Schema Source","text":""},{"location":"DataGeneration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:DataGeneration native nmdc:DataGeneration broad OBI:0000070, ISA:Assay"},{"location":"DataGeneration/#linkml-source","title":"LinkML Source","text":""},{"location":"DataGeneration/#direct","title":"Direct","text":"
name: DataGeneration\ndescription: The methods and processes used to generate omics data from a biosample\n  or organism.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: An experiment contains information about a sequencing experiment\n      including library and instrument details.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OmicsProcessing\n- assay\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nabstract: true\nslots:\n- add_date\n- analyte_category\n- associated_studies\n- instrument_used\n- mod_date\n- principal_investigator\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  associated_studies:\n    name: associated_studies\n    range: Study\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    range: DataObject\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:DataGeneration\n\n
"},{"location":"DataGeneration/#induced","title":"Induced","text":"
name: DataGeneration\ndescription: The methods and processes used to generate omics data from a biosample\n  or organism.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: An experiment contains information about a sequencing experiment\n      including library and instrument details.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OmicsProcessing\n- assay\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  associated_studies:\n    name: associated_studies\n    range: Study\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    range: DataObject\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  add_date:\n    name: add_date\n    description: The date on which the information was added to the database.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: add_date\n    owner: DataGeneration\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  analyte_category:\n    name: analyte_category\n    description: \"The type of analyte(s) that were measured in the data generation\\\n      \\ process and analyzed\\n  in the Workflow Chain\\n\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: analyte_category\n    owner: DataGeneration\n    domain_of:\n    - DataGeneration\n    range: AnalyteCategoryEnum\n    required: true\n  associated_studies:\n    name: associated_studies\n    description: The study associated with a resource.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: associated_studies\n    owner: DataGeneration\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: Study\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: DataGeneration\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  mod_date:\n    name: mod_date\n    description: The last date on which the database information was modified.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mod_date\n    owner: DataGeneration\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  principal_investigator:\n    name: principal_investigator\n    description: Principal Investigator who led the study and/or generated the dataset.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - PI\n    rank: 1000\n    alias: principal_investigator\n    owner: DataGeneration\n    domain_of:\n    - Study\n    - DataGeneration\n    range: PersonValue\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: DataObject\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DataGeneration\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: DataGeneration\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: DataGeneration\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: DataGeneration\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: DataGeneration\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:DataGeneration\n\n
"},{"location":"DataObject/","title":"Class: DataObject","text":"

An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.

URI: nmdc:DataObject

classDiagram\n  class DataObject\n  click DataObject href \"../DataObject\"\n    InformationObject <|-- DataObject\n      click InformationObject href \"../InformationObject\"\n\n\n\n  DataObject : alternative_identifiers\n\n  DataObject : compression_type\n\n  DataObject : data_category\n\n      DataObject --> \"0..1\" DataCategoryEnum : data_category\n    click DataCategoryEnum href \"../DataCategoryEnum\"\n\n  DataObject : data_object_type\n\n      DataObject --> \"0..1\" FileTypeEnum : data_object_type\n    click FileTypeEnum href \"../FileTypeEnum\"\n\n  DataObject : description\n\n  DataObject : file_size_bytes\n\n  DataObject : id\n\n  DataObject : in_manifest\n\n      DataObject --> \"*\" Manifest : in_manifest\n    click Manifest href \"../Manifest\"\n\n  DataObject : insdc_experiment_identifiers\n\n  DataObject : md5_checksum\n\n  DataObject : name\n\n  DataObject : type\n\n  DataObject : url\n\n  DataObject : was_generated_by\n\n      DataObject --> \"0..1\" WorkflowExecution : was_generated_by\n    click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n
"},{"location":"DataObject/#inheritance","title":"Inheritance","text":""},{"location":"DataObject/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance compression_type 0..1 String If provided, specifies the compression type direct data_category 0..1 DataCategoryEnum The category of the file, such as instrument data from data generation or pro... direct data_object_type 0..1 FileTypeEnum The type of file represented by the data object direct file_size_bytes 0..1 Bytes Size of the file in bytes direct insdc_experiment_identifiers * ExternalIdentifier direct md5_checksum 0..1 String MD5 checksum of file (pre-compressed) direct url 0..1 String direct was_generated_by 0..1 WorkflowExecution\u00a0or\u00a0WorkflowExecution\u00a0or\u00a0DataGeneration direct in_manifest * Manifest direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 1 String A human readable label for an entity NamedThing description 1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"DataObject/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_output range DataObject MassSpectrometry has_output range DataObject Database data_object_set range DataObject DataGeneration has_output range DataObject CalibrationInformation calibration_object range DataObject"},{"location":"DataObject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataObject/#schema-source","title":"Schema Source","text":""},{"location":"DataObject/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:DataObject native nmdc:DataObject"},{"location":"DataObject/#linkml-source","title":"LinkML Source","text":""},{"location":"DataObject/#direct","title":"Direct","text":"
name: DataObject\ndescription: An object that primarily consists of symbols that represent information.   Files,\n  records, and omics data are examples of data objects.\nin_subset:\n- data object subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- compression_type\n- data_category\n- data_object_type\n- file_size_bytes\n- insdc_experiment_identifiers\n- md5_checksum\n- url\n- was_generated_by\n- in_manifest\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_generated_by:\n    name: was_generated_by\n    structured_pattern:\n      syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n      interpolated: true\nclass_uri: nmdc:DataObject\n\n
"},{"location":"DataObject/#induced","title":"Induced","text":"
name: DataObject\ndescription: An object that primarily consists of symbols that represent information.   Files,\n  records, and omics data are examples of data objects.\nin_subset:\n- data object subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_generated_by:\n    name: was_generated_by\n    structured_pattern:\n      syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n      interpolated: true\nattributes:\n  compression_type:\n    name: compression_type\n    description: If provided, specifies the compression type\n    todos:\n    - consider setting the range to an enum\n    examples:\n    - value: gzip\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: compression_type\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: string\n  data_category:\n    name: data_category\n    description: The category of the file, such as instrument data from data generation\n      or processed data from a workflow execution.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: data_category\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: DataCategoryEnum\n  data_object_type:\n    name: data_object_type\n    description: The type of file represented by the data object.\n    examples:\n    - value: FT ICR-MS Analysis Results\n    - value: GC-MS Metabolomics Results\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: data_object_type\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: FileTypeEnum\n  file_size_bytes:\n    name: file_size_bytes\n    description: Size of the file in bytes\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: file_size_bytes\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: bytes\n  insdc_experiment_identifiers:\n    name: insdc_experiment_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_experiment_identifiers\n    owner: DataObject\n    domain_of:\n    - NucleotideSequencing\n    - DataObject\n    range: external_identifier\n    multivalued: true\n    pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n  md5_checksum:\n    name: md5_checksum\n    description: MD5 checksum of file (pre-compressed)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: md5_checksum\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: string\n  url:\n    name: url\n    notes:\n    - See issue 207 - this clashes with the mixs field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: url\n    owner: DataObject\n    domain_of:\n    - ImageValue\n    - Protocol\n    - DataObject\n    range: string\n  was_generated_by:\n    name: was_generated_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasGeneratedBy\n    rank: 1000\n    alias: was_generated_by\n    owner: DataObject\n    domain_of:\n    - FunctionalAnnotation\n    - DataObject\n    range: WorkflowExecution\n    structured_pattern:\n      syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n      interpolated: true\n    any_of:\n    - range: WorkflowExecution\n    - range: DataGeneration\n  in_manifest:\n    name: in_manifest\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: in_manifest\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: Manifest\n    multivalued: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DataObject\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: DataObject\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n    required: true\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: DataObject\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n    required: true\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: DataObject\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: DataObject\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:DataObject\n\n
"},{"location":"DataObjectSubset/","title":"Subset: DataObjectSubset","text":"

Subset consisting of the data objects that either inputs or outputs of processes or workflows.

URI: DataObjectSubset

"},{"location":"DataObjectSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataObjectSubset/#schema-source","title":"Schema Source","text":""},{"location":"DataObjectSubset/#classes-in-subset","title":"Classes in subset","text":"Class Description DataObject An object that primarily consists of symbols that represent information"},{"location":"DataPortalSubset/","title":"Subset: DataPortalSubset","text":"

Subset consisting of entities that Kitware/nmdc-server use to populate the data portal.

URI: DataPortalSubset

"},{"location":"DataPortalSubset/#comments","title":"Comments","text":""},{"location":"DataPortalSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataPortalSubset/#schema-source","title":"Schema Source","text":""},{"location":"DataPortalSubset/#slots-in-subset","title":"Slots in subset","text":"Slot Description associated_dois A list of DOIs associated with a resource, such as a list of DOIS associated ... doi_category The resource type the corresponding doi resolves to doi_provider The authority, or organization, the DOI is associated with doi_value A digital object identifier, which is intended to persistantly identify some ..."},{"location":"Database/","title":"Class: Database","text":"

An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to collections.

URI: nmdc:Database

classDiagram\n  class Database\n  click Database href \"../Database\"\n\n  Database : biosample_set\n\n      Database --> \"*\" Biosample : biosample_set\n    click Biosample href \"../Biosample\"\n\n  Database : calibration_set\n\n      Database --> \"*\" CalibrationInformation : calibration_set\n    click CalibrationInformation href \"../CalibrationInformation\"\n\n  Database : chemical_entity_set\n\n      Database --> \"*\" ChemicalEntity : chemical_entity_set\n    click ChemicalEntity href \"../ChemicalEntity\"\n\n  Database : collecting_biosamples_from_site_set\n\n      Database --> \"*\" CollectingBiosamplesFromSite : collecting_biosamples_from_site_set\n    click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n\n  Database : configuration_set\n\n      Database --> \"*\" Configuration : configuration_set\n    click Configuration href \"../Configuration\"\n\n  Database : data_generation_set\n\n      Database --> \"*\" DataGeneration : data_generation_set\n    click DataGeneration href \"../DataGeneration\"\n\n  Database : data_object_set\n\n      Database --> \"*\" DataObject : data_object_set\n    click DataObject href \"../DataObject\"\n\n  Database : field_research_site_set\n\n      Database --> \"*\" FieldResearchSite : field_research_site_set\n    click FieldResearchSite href \"../FieldResearchSite\"\n\n  Database : functional_annotation_agg\n\n      Database --> \"*\" FunctionalAnnotationAggMember : functional_annotation_agg\n    click FunctionalAnnotationAggMember href \"../FunctionalAnnotationAggMember\"\n\n  Database : functional_annotation_set\n\n      Database --> \"*\" FunctionalAnnotation : functional_annotation_set\n    click FunctionalAnnotation href \"../FunctionalAnnotation\"\n\n  Database : genome_feature_set\n\n      Database --> \"*\" GenomeFeature : genome_feature_set\n    click GenomeFeature href \"../GenomeFeature\"\n\n  Database : instrument_set\n\n      Database --> \"*\" Instrument : instrument_set\n    click Instrument href \"../Instrument\"\n\n  Database : manifest_set\n\n      Database --> \"*\" Manifest : manifest_set\n    click Manifest href \"../Manifest\"\n\n  Database : material_processing_set\n\n      Database --> \"*\" MaterialProcessing : material_processing_set\n    click MaterialProcessing href \"../MaterialProcessing\"\n\n  Database : processed_sample_set\n\n      Database --> \"*\" ProcessedSample : processed_sample_set\n    click ProcessedSample href \"../ProcessedSample\"\n\n  Database : protocol_execution_set\n\n      Database --> \"*\" ProtocolExecution : protocol_execution_set\n    click ProtocolExecution href \"../ProtocolExecution\"\n\n  Database : storage_process_set\n\n      Database --> \"*\" StorageProcess : storage_process_set\n    click StorageProcess href \"../StorageProcess\"\n\n  Database : study_set\n\n      Database --> \"*\" Study : study_set\n    click Study href \"../Study\"\n\n  Database : workflow_execution_set\n\n      Database --> \"*\" WorkflowExecution : workflow_execution_set\n    click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n
"},{"location":"Database/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance biosample_set * Biosample This property links a database object to the set of samples within it direct calibration_set * CalibrationInformation This property links a database object to the set of calibrations within it direct chemical_entity_set * ChemicalEntity This property links a database object to the set of chemical entities within ... direct collecting_biosamples_from_site_set * CollectingBiosamplesFromSite direct configuration_set * Configuration This property links a database object to the set of configurations within it direct data_generation_set * DataGeneration This property links a database object to the set of data generations within i... direct data_object_set * DataObject This property links a database object to the set of data objects within it direct field_research_site_set * FieldResearchSite direct functional_annotation_agg * FunctionalAnnotationAggMember direct functional_annotation_set * FunctionalAnnotation This property links a database object to the set of all functional annotation... direct genome_feature_set * GenomeFeature This property links a database object to the set of all features direct instrument_set * Instrument This property links a database object to the set of instruments within it direct manifest_set * Manifest This property links a database object to the set of manifests within it direct material_processing_set * MaterialProcessing This property links a database object to the set of material processing withi... direct processed_sample_set * ProcessedSample This property links a database object to the set of processed samples within ... direct protocol_execution_set * ProtocolExecution This property links a database object to the set of protocol executions withi... direct storage_process_set * StorageProcess This property links a database object to the set of storage processes within ... direct study_set * Study This property links a database object to the set of studies within it direct workflow_execution_set * WorkflowExecution This property links a database object to the set of workflow executions direct"},{"location":"Database/#aliases","title":"Aliases","text":""},{"location":"Database/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Database/#schema-source","title":"Schema Source","text":""},{"location":"Database/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Database native nmdc:Database"},{"location":"Database/#linkml-source","title":"LinkML Source","text":""},{"location":"Database/#direct","title":"Direct","text":"
name: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n  to correspond to an actual managed database top level holder class. When translated\n  to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n  of interest. For MongoDB, the lists of objects that Database slots point to correspond\n  to **collections**.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nslots:\n- biosample_set\n- calibration_set\n- chemical_entity_set\n- collecting_biosamples_from_site_set\n- configuration_set\n- data_generation_set\n- data_object_set\n- field_research_site_set\n- functional_annotation_agg\n- functional_annotation_set\n- genome_feature_set\n- instrument_set\n- manifest_set\n- material_processing_set\n- processed_sample_set\n- protocol_execution_set\n- storage_process_set\n- study_set\n- workflow_execution_set\nclass_uri: nmdc:Database\ntree_root: true\n\n
"},{"location":"Database/#induced","title":"Induced","text":"
name: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n  to correspond to an actual managed database top level holder class. When translated\n  to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n  of interest. For MongoDB, the lists of objects that Database slots point to correspond\n  to **collections**.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nattributes:\n  biosample_set:\n    name: biosample_set\n    description: This property links a database object to the set of samples within\n      it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: biosample_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Biosample\n    multivalued: true\n    inlined_as_list: true\n  calibration_set:\n    name: calibration_set\n    description: This property links a database object to the set of calibrations\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: calibration_set\n    owner: Database\n    domain_of:\n    - Database\n    range: CalibrationInformation\n    multivalued: true\n    inlined_as_list: true\n  chemical_entity_set:\n    name: chemical_entity_set\n    description: This property links a database object to the set of chemical entities\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: chemical_entity_set\n    owner: Database\n    domain_of:\n    - Database\n    range: ChemicalEntity\n    multivalued: true\n    inlined_as_list: true\n  collecting_biosamples_from_site_set:\n    name: collecting_biosamples_from_site_set\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: collecting_biosamples_from_site_set\n    owner: Database\n    domain_of:\n    - Database\n    range: CollectingBiosamplesFromSite\n    multivalued: true\n    inlined_as_list: true\n  configuration_set:\n    name: configuration_set\n    description: This property links a database object to the set of configurations\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: configuration_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Configuration\n    multivalued: true\n    inlined_as_list: true\n  data_generation_set:\n    name: data_generation_set\n    description: This property links a database object to the set of data generations\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: data_generation_set\n    owner: Database\n    domain_of:\n    - Database\n    range: DataGeneration\n    multivalued: true\n    inlined_as_list: true\n  data_object_set:\n    name: data_object_set\n    description: This property links a database object to the set of data objects\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: data_object_set\n    owner: Database\n    domain_of:\n    - Database\n    range: DataObject\n    multivalued: true\n    inlined_as_list: true\n  field_research_site_set:\n    name: field_research_site_set\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: field_research_site_set\n    owner: Database\n    domain_of:\n    - Database\n    range: FieldResearchSite\n    multivalued: true\n    inlined_as_list: true\n  functional_annotation_agg:\n    name: functional_annotation_agg\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: functional_annotation_agg\n    owner: Database\n    domain_of:\n    - Database\n    range: FunctionalAnnotationAggMember\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  functional_annotation_set:\n    name: functional_annotation_set\n    description: This property links a database object to the set of all functional\n      annotations\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: functional_annotation_set\n    owner: Database\n    domain_of:\n    - Database\n    range: FunctionalAnnotation\n    multivalued: true\n    inlined_as_list: true\n  genome_feature_set:\n    name: genome_feature_set\n    description: This property links a database object to the set of all features\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: genome_feature_set\n    owner: Database\n    domain_of:\n    - Database\n    range: GenomeFeature\n    multivalued: true\n    inlined_as_list: true\n  instrument_set:\n    name: instrument_set\n    description: This property links a database object to the set of instruments within\n      it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: instrument_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Instrument\n    multivalued: true\n    inlined_as_list: true\n  manifest_set:\n    name: manifest_set\n    description: This property links a database object to the set of manifests within\n      it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: manifest_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Manifest\n    multivalued: true\n    inlined_as_list: true\n  material_processing_set:\n    name: material_processing_set\n    description: This property links a database object to the set of material processing\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: material_processing_set\n    owner: Database\n    domain_of:\n    - Database\n    range: MaterialProcessing\n    multivalued: true\n    inlined_as_list: true\n  processed_sample_set:\n    name: processed_sample_set\n    description: This property links a database object to the set of processed samples\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: processed_sample_set\n    owner: Database\n    domain_of:\n    - Database\n    range: ProcessedSample\n    multivalued: true\n    inlined_as_list: true\n  protocol_execution_set:\n    name: protocol_execution_set\n    description: This property links a database object to the set of protocol executions\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: protocol_execution_set\n    owner: Database\n    domain_of:\n    - Database\n    range: ProtocolExecution\n    multivalued: true\n    inlined_as_list: true\n  storage_process_set:\n    name: storage_process_set\n    description: This property links a database object to the set of storage processes\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: storage_process_set\n    owner: Database\n    domain_of:\n    - Database\n    range: StorageProcess\n    multivalued: true\n    inlined_as_list: true\n  study_set:\n    name: study_set\n    description: This property links a database object to the set of studies within\n      it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: study_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Study\n    multivalued: true\n    inlined_as_list: true\n  workflow_execution_set:\n    name: workflow_execution_set\n    description: This property links a database object to the set of workflow executions.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: workflow_execution_set\n    owner: Database\n    domain_of:\n    - Database\n    range: WorkflowExecution\n    multivalued: true\n    inlined_as_list: true\nclass_uri: nmdc:Database\ntree_root: true\n\n
"},{"location":"Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Date/#schema-source","title":"Schema Source","text":""},{"location":"Date/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:date native nmdc:date exact schema:Date"},{"location":"DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"DateOrDatetime/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:DateOrDatetime native nmdc:date_or_datetime"},{"location":"Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Datetime/#schema-source","title":"Schema Source","text":""},{"location":"Datetime/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:dateTime native nmdc:datetime exact schema:DateTime"},{"location":"Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Decimal/#schema-source","title":"Schema Source","text":""},{"location":"Decimal/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:decimal native nmdc:decimal broad schema:Number"},{"location":"DecimalDegree/","title":"Type: DecimalDegree","text":"

A decimal degree expresses latitude or longitude as decimal fractions.

URI: xsd:decimal

"},{"location":"DecimalDegree/#see-also","title":"See Also","text":""},{"location":"DecimalDegree/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DecimalDegree/#schema-source","title":"Schema Source","text":""},{"location":"DecimalDegree/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:decimal native nmdc:decimal_degree"},{"location":"DeposEnvEnum/","title":"Enum: DeposEnvEnum","text":"

URI: DeposEnvEnum

"},{"location":"DeposEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Continental - Alluvial None Continental - Aeolian None Continental - Fluvial None Continental - Lacustrine None Transitional - Deltaic None Transitional - Tidal None Transitional - Lagoonal None Transitional - Beach None Transitional - Lake None Marine - Shallow None Marine - Deep None Marine - Reef None Other - Evaporite None Other - Glacial None Other - Volcanic None other None"},{"location":"DeposEnvEnum/#slots","title":"Slots","text":"Name Description depos_env Main depositional environment (https://en"},{"location":"DeposEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DeposEnvEnum/#schema-source","title":"Schema Source","text":""},{"location":"DeposEnvEnum/#linkml-source","title":"LinkML Source","text":"
name: depos_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Continental - Alluvial:\n    text: Continental - Alluvial\n  Continental - Aeolian:\n    text: Continental - Aeolian\n  Continental - Fluvial:\n    text: Continental - Fluvial\n  Continental - Lacustrine:\n    text: Continental - Lacustrine\n  Transitional - Deltaic:\n    text: Transitional - Deltaic\n  Transitional - Tidal:\n    text: Transitional - Tidal\n  Transitional - Lagoonal:\n    text: Transitional - Lagoonal\n  Transitional - Beach:\n    text: Transitional - Beach\n  Transitional - Lake:\n    text: Transitional - Lake\n  Marine - Shallow:\n    text: Marine - Shallow\n  Marine - Deep:\n    text: Marine - Deep\n  Marine - Reef:\n    text: Marine - Reef\n  Other - Evaporite:\n    text: Other - Evaporite\n  Other - Glacial:\n    text: Other - Glacial\n  Other - Volcanic:\n    text: Other - Volcanic\n  other:\n    text: other\n\n
"},{"location":"DirectInfusionEnum/","title":"Enum: DirectInfusionEnum","text":"

URI: DirectInfusionEnum

"},{"location":"DirectInfusionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description direct_infusion None autosampler None"},{"location":"DirectInfusionEnum/#slots","title":"Slots","text":"Name Description direct_infusion_category used when a processed sample is introduced into a mass spectrometer without c..."},{"location":"DirectInfusionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DirectInfusionEnum/#schema-source","title":"Schema Source","text":""},{"location":"DirectInfusionEnum/#linkml-source","title":"LinkML Source","text":"
name: DirectInfusionEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  direct_infusion:\n    text: direct_infusion\n    aliases:\n    - DI\n  autosampler:\n    text: autosampler\n\n
"},{"location":"DissolvingProcess/","title":"Class: DissolvingProcess","text":"

A mixing step where a soluble component is mixed with a liquid component.

__

URI: nmdc:DissolvingProcess

classDiagram\n  class DissolvingProcess\n  click DissolvingProcess href \"../DissolvingProcess\"\n    MaterialProcessing <|-- DissolvingProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  DissolvingProcess : alternative_identifiers\n\n  DissolvingProcess : description\n\n  DissolvingProcess : duration\n\n      DissolvingProcess --> \"0..1\" QuantityValue : duration\n    click QuantityValue href \"../QuantityValue\"\n\n  DissolvingProcess : end_date\n\n  DissolvingProcess : has_failure_categorization\n\n      DissolvingProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  DissolvingProcess : has_input\n\n      DissolvingProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  DissolvingProcess : has_output\n\n      DissolvingProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  DissolvingProcess : id\n\n  DissolvingProcess : instrument_used\n\n      DissolvingProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  DissolvingProcess : name\n\n  DissolvingProcess : processing_institution\n\n      DissolvingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  DissolvingProcess : protocol_link\n\n      DissolvingProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  DissolvingProcess : qc_comment\n\n  DissolvingProcess : qc_status\n\n      DissolvingProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  DissolvingProcess : start_date\n\n  DissolvingProcess : substances_used\n\n      DissolvingProcess --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  DissolvingProcess : temperature\n\n      DissolvingProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  DissolvingProcess : type\n\n\n\n
"},{"location":"DissolvingProcess/#inheritance","title":"Inheritance","text":""},{"location":"DissolvingProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance duration 0..1 QuantityValue The elapsed time of an activity direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct substances_used * PortionOfSubstance The substances that are combined to enable a ChemicalConversionProcess direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"DissolvingProcess/#aliases","title":"Aliases","text":""},{"location":"DissolvingProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DissolvingProcess/#schema-source","title":"Schema Source","text":""},{"location":"DissolvingProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:DissolvingProcess native nmdc:DissolvingProcess exact CHMO:0002773"},{"location":"DissolvingProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"DissolvingProcess/#direct","title":"Direct","text":"
name: DissolvingProcess\ndescription: 'A mixing step where a soluble component is mixed with a liquid component.\n\n  '\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Solubilization\nexact_mappings:\n- CHMO:0002773\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- duration\n- temperature\n- substances_used\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:DissolvingProcess\n\n
"},{"location":"DissolvingProcess/#induced","title":"Induced","text":"
name: DissolvingProcess\ndescription: 'A mixing step where a soluble component is mixed with a liquid component.\n\n  '\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Solubilization\nexact_mappings:\n- CHMO:0002773\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  duration:\n    name: duration\n    description: The elapsed time of an activity.\n    examples:\n    - value: JsonObj(has_numeric_value=2, has_unit='hours')\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: duration\n    owner: DissolvingProcess\n    domain_of:\n    - MixingProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: QuantityValue\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: DissolvingProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  substances_used:\n    name: substances_used\n    description: The substances that are combined to enable a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: DissolvingProcess\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: DissolvingProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DissolvingProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: DissolvingProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: DissolvingProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: DissolvingProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: DissolvingProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:DissolvingProcess\n\n
"},{"location":"Doi/","title":"Class: Doi","text":"

A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.

URI: nmdc:Doi

classDiagram\n  class Doi\n  click Doi href \"../Doi\"\n\n  Doi : doi_category\n\n      Doi --> \"1\" DoiCategoryEnum : doi_category\n    click DoiCategoryEnum href \"../DoiCategoryEnum\"\n\n  Doi : doi_provider\n\n      Doi --> \"0..1\" DoiProviderEnum : doi_provider\n    click DoiProviderEnum href \"../DoiProviderEnum\"\n\n  Doi : doi_value\n\n  Doi : type\n\n\n\n
"},{"location":"Doi/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance doi_value 1 Uriorcurie A digital object identifier, which is intended to persistantly identify some ... direct doi_provider 0..1 DoiProviderEnum The authority, or organization, the DOI is associated with direct doi_category 1 DoiCategoryEnum The resource type the corresponding doi resolves to direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"Doi/#usages","title":"Usages","text":"used by used in type used Study associated_dois range Doi"},{"location":"Doi/#aliases","title":"Aliases","text":""},{"location":"Doi/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Doi/#schema-source","title":"Schema Source","text":""},{"location":"Doi/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Doi native nmdc:Doi exact OBI:0002110"},{"location":"Doi/#linkml-source","title":"LinkML Source","text":""},{"location":"Doi/#direct","title":"Direct","text":"
name: Doi\ndescription: A centrally registered identifier symbol used to uniquely identify objects\n  given by the International DOI Foundation. The DOI system is particularly used for\n  electronic documents.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOIs\n- digital object identifiers\nexact_mappings:\n- OBI:0002110\nslots:\n- doi_value\n- doi_provider\n- doi_category\n- type\nclass_uri: nmdc:Doi\nrules:\n- preconditions:\n    slot_conditions:\n      doi_category:\n        name: doi_category\n        any_of:\n        - equals_string: dataset_doi\n        - equals_string: award_doi\n  postconditions:\n    slot_conditions:\n      doi_provider:\n        name: doi_provider\n        required: true\n  description: If doi_category is a publication_doi, then doi_provider is not required.\n    Otherwise, doi_provider is required.\n  title: dataset_award_dois_required\n\n
"},{"location":"Doi/#induced","title":"Induced","text":"
name: Doi\ndescription: A centrally registered identifier symbol used to uniquely identify objects\n  given by the International DOI Foundation. The DOI system is particularly used for\n  electronic documents.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOIs\n- digital object identifiers\nexact_mappings:\n- OBI:0002110\nattributes:\n  doi_value:\n    name: doi_value\n    description: A digital object identifier, which is intended to persistantly identify\n      some resource on the web.\n    examples:\n    - value: doi:10.46936/10.25585/60000880\n      description: The DOI links to an electronic document.\n    in_subset:\n    - data_portal_subset\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - DOI\n    - digital object identifier\n    exact_mappings:\n    - OBI:0002110\n    narrow_mappings:\n    - edam.data:1188\n    rank: 1000\n    alias: doi_value\n    owner: Doi\n    domain_of:\n    - Doi\n    range: uriorcurie\n    required: true\n    pattern: ^doi:10.\\d{2,9}/.*$\n  doi_provider:\n    name: doi_provider\n    description: The authority, or organization, the DOI is associated with.\n    examples:\n    - value: ess_dive\n      description: The corresponding DOI is associated with ESS-DIVE.\n    in_subset:\n    - data_portal_subset\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - NCIT:C74932\n    rank: 1000\n    alias: doi_provider\n    owner: Doi\n    domain_of:\n    - Doi\n    range: DoiProviderEnum\n  doi_category:\n    name: doi_category\n    description: The resource type the corresponding doi resolves to.\n    examples:\n    - value: dataset_doi\n      description: The corresponding DOI is a dataset resource type.\n    in_subset:\n    - data_portal_subset\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: doi_category\n    owner: Doi\n    domain_of:\n    - Doi\n    range: DoiCategoryEnum\n    required: true\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Doi\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Doi\nrules:\n- preconditions:\n    slot_conditions:\n      doi_category:\n        name: doi_category\n        any_of:\n        - equals_string: dataset_doi\n        - equals_string: award_doi\n  postconditions:\n    slot_conditions:\n      doi_provider:\n        name: doi_provider\n        required: true\n  description: If doi_category is a publication_doi, then doi_provider is not required.\n    Otherwise, doi_provider is required.\n  title: dataset_award_dois_required\n\n
"},{"location":"DoiCategoryEnum/","title":"Enum: DoiCategoryEnum","text":"

URI: DoiCategoryEnum

"},{"location":"DoiCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description award_doi None A type of DOI that resolves to a funding authority dataset_doi None A type of DOI that resolves to generated data publication_doi None A type of DOI that resolves to a publication data_management_plan_doi None A type of DOI that resolves to a data management plan"},{"location":"DoiCategoryEnum/#slots","title":"Slots","text":"Name Description doi_category The resource type the corresponding doi resolves to"},{"location":"DoiCategoryEnum/#comments","title":"Comments","text":""},{"location":"DoiCategoryEnum/#see-also","title":"See Also","text":""},{"location":"DoiCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoiCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoiCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: DoiCategoryEnum\ncomments:\n- See especially the resourceTypeGeneral section of the DataCite PDF, on pp48-53 as\n  of 2023-07-19\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://schema.datacite.org/meta/kernel-4.4/doc/DataCite-MetadataKernel_v4.4.pdf\n- https://api.crossref.org/types\nrank: 1000\npermissible_values:\n  award_doi:\n    text: award_doi\n    description: A type of DOI that resolves to a funding authority.\n  dataset_doi:\n    text: dataset_doi\n    description: A type of DOI that resolves to generated data.\n  publication_doi:\n    text: publication_doi\n    description: A type of DOI that resolves to a publication.\n  data_management_plan_doi:\n    text: data_management_plan_doi\n    description: A type of DOI that resolves to a data management plan.\n\n
"},{"location":"DoiProviderEnum/","title":"Enum: DoiProviderEnum","text":"

URI: DoiProviderEnum

"},{"location":"DoiProviderEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description emsl https://ror.org/04rc0xn13 jgi https://ror.org/04xm1d337 kbase https://ror.org/01znn6x10 osti https://ror.org/031478740 ess_dive https://ror.org/01t14bp54 massive None gsc None zenodo None edi https://ror.org/0330j0z60 figshare https://ror.org/041mxqs23"},{"location":"DoiProviderEnum/#slots","title":"Slots","text":"Name Description doi_provider The authority, or organization, the DOI is associated with"},{"location":"DoiProviderEnum/#see-also","title":"See Also","text":""},{"location":"DoiProviderEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoiProviderEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoiProviderEnum/#linkml-source","title":"LinkML Source","text":"
name: DoiProviderEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:DoiProviderEnum\n- nmdc:ProcessingInstitutionEnum\n- nmdc:ExecutionResourceEnum\nrank: 1000\npermissible_values:\n  emsl:\n    text: emsl\n    meaning: https://ror.org/04rc0xn13\n    title: EMSL\n    aliases:\n    - Environmental Molecular Sciences Laboratory\n    - EMSL\n  jgi:\n    text: jgi\n    meaning: https://ror.org/04xm1d337\n    title: JGI\n    aliases:\n    - Joint Genome Institute\n    - JGI\n  kbase:\n    text: kbase\n    meaning: https://ror.org/01znn6x10\n    title: KBase\n    aliases:\n    - KBase\n  osti:\n    text: osti\n    meaning: https://ror.org/031478740\n    title: OSTI\n    aliases:\n    - Office of Scientific and Technical Information\n    - OSTI\n  ess_dive:\n    text: ess_dive\n    meaning: https://ror.org/01t14bp54\n    title: ESS-DIVE\n    aliases:\n    - ESS-DIVE\n    - Environmental System Science Data Infrastructure for a Virtual Ecosystem\n  massive:\n    text: massive\n    title: MassIVE\n    aliases:\n    - MassIVE\n    - Mass Spectrometry Virtual Environment\n  gsc:\n    text: gsc\n    title: GSC\n    aliases:\n    - GSC\n    - Genomic Standards Consortium\n  zenodo:\n    text: zenodo\n    title: Zenodo\n    aliases:\n    - Zenodo\n  edi:\n    text: edi\n    meaning: https://ror.org/0330j0z60\n    title: EDI\n    aliases:\n    - EDI\n    - Environmental Data Initiative\n  figshare:\n    text: figshare\n    meaning: https://ror.org/041mxqs23\n    title: Figshare\n\n
"},{"location":"DoorCompTypeEnum/","title":"Enum: DoorCompTypeEnum","text":"

URI: DoorCompTypeEnum

"},{"location":"DoorCompTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metal covered None revolving None sliding None telescopic None"},{"location":"DoorCompTypeEnum/#slots","title":"Slots","text":"Name Description door_comp_type The composite type of the door"},{"location":"DoorCompTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCompTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorCompTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: door_comp_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  metal covered:\n    text: metal covered\n  revolving:\n    text: revolving\n  sliding:\n    text: sliding\n  telescopic:\n    text: telescopic\n\n
"},{"location":"DoorCondEnum/","title":"Enum: DoorCondEnum","text":"

URI: DoorCondEnum

"},{"location":"DoorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"DoorCondEnum/#slots","title":"Slots","text":"Name Description door_cond The phsical condition of the door"},{"location":"DoorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorCondEnum/#linkml-source","title":"LinkML Source","text":"
name: door_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  damaged:\n    text: damaged\n  needs repair:\n    text: needs repair\n  new:\n    text: new\n  rupture:\n    text: rupture\n  visible wear:\n    text: visible wear\n\n
"},{"location":"DoorDirectEnum/","title":"Enum: DoorDirectEnum","text":"

URI: DoorDirectEnum

"},{"location":"DoorDirectEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description inward None outward None sideways None"},{"location":"DoorDirectEnum/#slots","title":"Slots","text":"Name Description door_direct The direction the door opens"},{"location":"DoorDirectEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorDirectEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorDirectEnum/#linkml-source","title":"LinkML Source","text":"
name: door_direct_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  inward:\n    text: inward\n  outward:\n    text: outward\n  sideways:\n    text: sideways\n\n
"},{"location":"DoorLocEnum/","title":"Enum: DoorLocEnum","text":"

URI: DoorLocEnum

"},{"location":"DoorLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"DoorLocEnum/#slots","title":"Slots","text":"Name Description door_loc The relative location of the door in the room"},{"location":"DoorLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorLocEnum/#linkml-source","title":"LinkML Source","text":"
name: door_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n\n
"},{"location":"DoorMatEnum/","title":"Enum: DoorMatEnum","text":"

URI: DoorMatEnum

"},{"location":"DoorMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aluminum None cellular PVC None engineered plastic None fiberboard None fiberglass None metal None thermoplastic alloy None vinyl None wood None wood/plastic composite None"},{"location":"DoorMatEnum/#slots","title":"Slots","text":"Name Description door_mat The material the door is composed of"},{"location":"DoorMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorMatEnum/#linkml-source","title":"LinkML Source","text":"
name: door_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  aluminum:\n    text: aluminum\n  cellular PVC:\n    text: cellular PVC\n  engineered plastic:\n    text: engineered plastic\n  fiberboard:\n    text: fiberboard\n  fiberglass:\n    text: fiberglass\n  metal:\n    text: metal\n  thermoplastic alloy:\n    text: thermoplastic alloy\n  vinyl:\n    text: vinyl\n  wood:\n    text: wood\n  wood/plastic composite:\n    text: wood/plastic composite\n\n
"},{"location":"DoorMoveEnum/","title":"Enum: DoorMoveEnum","text":"

URI: DoorMoveEnum

"},{"location":"DoorMoveEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None folding None revolving None rolling shutter None sliding None swinging None"},{"location":"DoorMoveEnum/#slots","title":"Slots","text":"Name Description door_move The type of movement of the door"},{"location":"DoorMoveEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMoveEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorMoveEnum/#linkml-source","title":"LinkML Source","text":"
name: door_move_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  collapsible:\n    text: collapsible\n  folding:\n    text: folding\n  revolving:\n    text: revolving\n  rolling shutter:\n    text: rolling shutter\n  sliding:\n    text: sliding\n  swinging:\n    text: swinging\n\n
"},{"location":"DoorTypeEnum/","title":"Enum: DoorTypeEnum","text":"

URI: DoorTypeEnum

"},{"location":"DoorTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description composite None metal None wooden None"},{"location":"DoorTypeEnum/#slots","title":"Slots","text":"Name Description door_type The type of door material"},{"location":"DoorTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: door_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  composite:\n    text: composite\n  metal:\n    text: metal\n  wooden:\n    text: wooden\n\n
"},{"location":"DoorTypeMetalEnum/","title":"Enum: DoorTypeMetalEnum","text":"

URI: DoorTypeMetalEnum

"},{"location":"DoorTypeMetalEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None corrugated steel None hollow None rolling shutters None steel plate None"},{"location":"DoorTypeMetalEnum/#slots","title":"Slots","text":"Name Description door_type_metal The type of metal door"},{"location":"DoorTypeMetalEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeMetalEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorTypeMetalEnum/#linkml-source","title":"LinkML Source","text":"
name: door_type_metal_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  collapsible:\n    text: collapsible\n  corrugated steel:\n    text: corrugated steel\n  hollow:\n    text: hollow\n  rolling shutters:\n    text: rolling shutters\n  steel plate:\n    text: steel plate\n\n
"},{"location":"DoorTypeWoodEnum/","title":"Enum: DoorTypeWoodEnum","text":"

URI: DoorTypeWoodEnum

"},{"location":"DoorTypeWoodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bettened and ledged None battened None ledged and braced None ledged and framed None ledged, braced and frame None framed and paneled None glashed or sash None flush None louvered None wire gauged None"},{"location":"DoorTypeWoodEnum/#slots","title":"Slots","text":"Name Description door_type_wood The type of wood door"},{"location":"DoorTypeWoodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeWoodEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorTypeWoodEnum/#linkml-source","title":"LinkML Source","text":"
name: door_type_wood_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  bettened and ledged:\n    text: bettened and ledged\n  battened:\n    text: battened\n  ledged and braced:\n    text: ledged and braced\n  ledged and framed:\n    text: ledged and framed\n  ledged, braced and frame:\n    text: ledged, braced and frame\n  framed and paneled:\n    text: framed and paneled\n  glashed or sash:\n    text: glashed or sash\n  flush:\n    text: flush\n  louvered:\n    text: louvered\n  wire gauged:\n    text: wire gauged\n\n
"},{"location":"Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Double/#schema-source","title":"Schema Source","text":""},{"location":"Double/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:double native nmdc:double close schema:Float"},{"location":"DrainageClassEnum/","title":"Enum: DrainageClassEnum","text":"

URI: DrainageClassEnum

"},{"location":"DrainageClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description very poorly None poorly None somewhat poorly None moderately well None well None excessively drained None"},{"location":"DrainageClassEnum/#slots","title":"Slots","text":"Name Description drainage_class Drainage classification from a standard system such as the USDA system"},{"location":"DrainageClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrainageClassEnum/#schema-source","title":"Schema Source","text":""},{"location":"DrainageClassEnum/#linkml-source","title":"LinkML Source","text":"
name: drainage_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  very poorly:\n    text: very poorly\n  poorly:\n    text: poorly\n  somewhat poorly:\n    text: somewhat poorly\n  moderately well:\n    text: moderately well\n  well:\n    text: well\n  excessively drained:\n    text: excessively drained\n\n
"},{"location":"DrawingsEnum/","title":"Enum: DrawingsEnum","text":"

URI: DrawingsEnum

"},{"location":"DrawingsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None building navigation map None diagram None sketch None"},{"location":"DrawingsEnum/#slots","title":"Slots","text":"Name Description drawings The buildings architectural drawings; if design is chosen, indicate phase-con..."},{"location":"DrawingsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrawingsEnum/#schema-source","title":"Schema Source","text":""},{"location":"DrawingsEnum/#linkml-source","title":"LinkML Source","text":"
name: drawings_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  operation:\n    text: operation\n  as built:\n    text: as built\n  construction:\n    text: construction\n  bid:\n    text: bid\n  design:\n    text: design\n  building navigation map:\n    text: building navigation map\n  diagram:\n    text: diagram\n  sketch:\n    text: sketch\n\n
"},{"location":"EluentIntroductionCategoryEnum/","title":"Enum: EluentIntroductionCategoryEnum","text":"

URI: EluentIntroductionCategoryEnum

"},{"location":"EluentIntroductionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description liquid_chromatography None The processed sample is introduced into the mass spectrometer through a liqui... gas_chromatography None The processed sample is introduced into the mass spectrometer through a gas c... direct_infusion_syringe None The processed sample is introduced into the mass spectrometer through a direc... direct_infusion_autosampler None The processed sample is introduced into the mass spectrometer through a direc..."},{"location":"EluentIntroductionCategoryEnum/#slots","title":"Slots","text":"Name Description eluent_introduction_category A high-level categorization for how the processed sample is introduced into a..."},{"location":"EluentIntroductionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"EluentIntroductionCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"EluentIntroductionCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: EluentIntroductionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  liquid_chromatography:\n    text: liquid_chromatography\n    description: The processed sample is introduced into the mass spectrometer through\n      a liquid chromatography process.\n    aliases:\n    - LC\n  gas_chromatography:\n    text: gas_chromatography\n    description: The processed sample is introduced into the mass spectrometer through\n      a gas chromatography process.\n    aliases:\n    - GC\n  direct_infusion_syringe:\n    text: direct_infusion_syringe\n    description: The processed sample is introduced into the mass spectrometer through\n      a direct infusion process using a syringe.\n  direct_infusion_autosampler:\n    text: direct_infusion_autosampler\n    description: The processed sample is introduced into the mass spectrometer through\n      a direct infusion process using an autosampler.\n\n
"},{"location":"Environment/","title":"Subset: Environment","text":"

URI: Environment

"},{"location":"Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Environment/#schema-source","title":"Schema Source","text":""},{"location":"EnvironmentalMaterialTerm/","title":"Class: EnvironmentalMaterialTerm (DEPRECATED)

URI: nmdc:EnvironmentalMaterialTerm

classDiagram\n  class EnvironmentalMaterialTerm\n  click EnvironmentalMaterialTerm href \"../EnvironmentalMaterialTerm\"\n    OntologyClass <|-- EnvironmentalMaterialTerm\n      click OntologyClass href \"../OntologyClass\"\n\n\n\n  EnvironmentalMaterialTerm : alternative_identifiers\n\n  EnvironmentalMaterialTerm : description\n\n  EnvironmentalMaterialTerm : id\n\n  EnvironmentalMaterialTerm : name\n\n  EnvironmentalMaterialTerm : type\n\n\n\n
","text":""},{"location":"EnvironmentalMaterialTerm/#inheritance","title":"Inheritance","text":""},{"location":"EnvironmentalMaterialTerm/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"EnvironmentalMaterialTerm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"EnvironmentalMaterialTerm/#schema-source","title":"Schema Source","text":""},{"location":"EnvironmentalMaterialTerm/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:EnvironmentalMaterialTerm native nmdc:EnvironmentalMaterialTerm"},{"location":"EnvironmentalMaterialTerm/#linkml-source","title":"LinkML Source","text":""},{"location":"EnvironmentalMaterialTerm/#direct","title":"Direct","text":"
name: EnvironmentalMaterialTerm\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nclass_uri: nmdc:EnvironmentalMaterialTerm\n\n
"},{"location":"EnvironmentalMaterialTerm/#induced","title":"Induced","text":"
name: EnvironmentalMaterialTerm\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:EnvironmentalMaterialTerm\n\n
"},{"location":"EukEval/","title":"Class: EukEval","text":"

This class contains information pertaining to evaluating if a Metagenome-Assembled Genome (MAG) is eukaryotic.

URI: nmdc:EukEval

classDiagram\n  class EukEval\n  click EukEval href \"../EukEval\"\n\n  EukEval : completeness\n\n  EukEval : contamination\n\n  EukEval : ncbi_lineage\n\n  EukEval : ncbi_lineage_tax_ids\n\n  EukEval : type\n\n\n\n
"},{"location":"EukEval/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance type 1 Uriorcurie the class_uri of the class that has been instantiated direct completeness 0..1 Float direct contamination 0..1 Float direct ncbi_lineage_tax_ids 0..1 String Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId) direct ncbi_lineage 0..1 String Comma delimited ordered list of NCBI taxonomy names direct"},{"location":"EukEval/#usages","title":"Usages","text":"used by used in type used MagBin eukaryotic_evaluation range EukEval"},{"location":"EukEval/#comments","title":"Comments","text":""},{"location":"EukEval/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"EukEval/#schema-source","title":"Schema Source","text":""},{"location":"EukEval/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:EukEval native nmdc:EukEval"},{"location":"EukEval/#linkml-source","title":"LinkML Source","text":""},{"location":"EukEval/#direct","title":"Direct","text":"
name: EukEval\ndescription: This class contains information pertaining to evaluating if a Metagenome-Assembled\n  Genome (MAG) is eukaryotic.\ncomments:\n- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information\n  for this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- type\n- completeness\n- contamination\n- ncbi_lineage_tax_ids\n- ncbi_lineage\nclass_uri: nmdc:EukEval\n\n
"},{"location":"EukEval/#induced","title":"Induced","text":"
name: EukEval\ndescription: This class contains information pertaining to evaluating if a Metagenome-Assembled\n  Genome (MAG) is eukaryotic.\ncomments:\n- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information\n  for this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: EukEval\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  completeness:\n    name: completeness\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: completeness\n    owner: EukEval\n    domain_of:\n    - EukEval\n    - MagBin\n    range: float\n  contamination:\n    name: contamination\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: contamination\n    owner: EukEval\n    domain_of:\n    - EukEval\n    - MagBin\n    range: float\n  ncbi_lineage_tax_ids:\n    name: ncbi_lineage_tax_ids\n    description: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)\n    comments:\n    - Example 1-131567-2759-2611352-33682-191814-2603949\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: ncbi_lineage_tax_ids\n    owner: EukEval\n    domain_of:\n    - EukEval\n    range: string\n    pattern: ^\\d+(-\\d+)*$\n  ncbi_lineage:\n    name: ncbi_lineage\n    description: Comma delimited ordered list of NCBI taxonomy names.\n    comments:\n    - Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: ncbi_lineage\n    owner: EukEval\n    domain_of:\n    - EukEval\n    range: string\nclass_uri: nmdc:EukEval\n\n
"},{"location":"ExecutionResourceEnum/","title":"Enum: ExecutionResourceEnum","text":"

URI: ExecutionResourceEnum

"},{"location":"ExecutionResourceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description NERSC-Cori None NERSC Cori supercomputer NERSC-Perlmutter None NERSC Perlmutter supercomputer EMSL None Environmental Molecular Sciences Laboratory EMSL-RZR None Environmental Molecular Sciences Laboratory RZR cluster JGI None Joint Genome Institute LANL-B-div None LANL Bioscience Division"},{"location":"ExecutionResourceEnum/#slots","title":"Slots","text":"Name Description execution_resource The computing resource or facility where the workflow was executed"},{"location":"ExecutionResourceEnum/#see-also","title":"See Also","text":""},{"location":"ExecutionResourceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExecutionResourceEnum/#schema-source","title":"Schema Source","text":""},{"location":"ExecutionResourceEnum/#linkml-source","title":"LinkML Source","text":"
name: ExecutionResourceEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:DoiProviderEnum\n- nmdc:ProcessingInstitutionEnum\n- nmdc:ExecutionResourceEnum\nrank: 1000\npermissible_values:\n  NERSC-Cori:\n    text: NERSC-Cori\n    description: NERSC Cori supercomputer\n    aliases:\n    - Cori\n  NERSC-Perlmutter:\n    text: NERSC-Perlmutter\n    description: NERSC Perlmutter supercomputer\n    aliases:\n    - Perlmutter\n    - Saul\n  EMSL:\n    text: EMSL\n    description: Environmental Molecular Sciences Laboratory\n  EMSL-RZR:\n    text: EMSL-RZR\n    description: Environmental Molecular Sciences Laboratory RZR cluster\n    aliases:\n    - RZR\n  JGI:\n    text: JGI\n    description: Joint Genome Institute\n  LANL-B-div:\n    text: LANL-B-div\n    description: LANL Bioscience Division\n    aliases:\n    - B-div\n\n
"},{"location":"ExtWallOrientEnum/","title":"Enum: ExtWallOrientEnum","text":"

URI: ExtWallOrientEnum

"},{"location":"ExtWallOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWallOrientEnum/#slots","title":"Slots","text":"Name Description ext_wall_orient The orientation of the exterior wall"},{"location":"ExtWallOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWallOrientEnum/#schema-source","title":"Schema Source","text":""},{"location":"ExtWallOrientEnum/#linkml-source","title":"LinkML Source","text":"
name: ext_wall_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n  northeast:\n    text: northeast\n  southeast:\n    text: southeast\n  southwest:\n    text: southwest\n  northwest:\n    text: northwest\n\n
"},{"location":"ExtWindowOrientEnum/","title":"Enum: ExtWindowOrientEnum","text":"

URI: ExtWindowOrientEnum

"},{"location":"ExtWindowOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWindowOrientEnum/#slots","title":"Slots","text":"Name Description ext_window_orient The compass direction the exterior window of the room is facing"},{"location":"ExtWindowOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWindowOrientEnum/#schema-source","title":"Schema Source","text":""},{"location":"ExtWindowOrientEnum/#linkml-source","title":"LinkML Source","text":"
name: ext_window_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n  northeast:\n    text: northeast\n  southeast:\n    text: southeast\n  southwest:\n    text: southwest\n  northwest:\n    text: northwest\n\n
"},{"location":"ExternalIdentifier/","title":"Type: ExternalIdentifier","text":"

A CURIE representing an external identifier

URI: xsd:anyURI

"},{"location":"ExternalIdentifier/#see-also","title":"See Also","text":""},{"location":"ExternalIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExternalIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"ExternalIdentifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:anyURI native nmdc:external_identifier"},{"location":"Extraction/","title":"Class: Extraction","text":"

A material separation in which a desired component of an input material is separated from the remainder.

URI: nmdc:Extraction

classDiagram\n  class Extraction\n  click Extraction href \"../Extraction\"\n    MaterialProcessing <|-- Extraction\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  Extraction : alternative_identifiers\n\n  Extraction : description\n\n  Extraction : end_date\n\n  Extraction : extraction_targets\n\n      Extraction --> \"*\" ExtractionTargetEnum : extraction_targets\n    click ExtractionTargetEnum href \"../ExtractionTargetEnum\"\n\n  Extraction : has_failure_categorization\n\n      Extraction --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  Extraction : has_input\n\n      Extraction --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  Extraction : has_output\n\n      Extraction --> \"1..*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  Extraction : id\n\n  Extraction : input_mass\n\n      Extraction --> \"0..1\" QuantityValue : input_mass\n    click QuantityValue href \"../QuantityValue\"\n\n  Extraction : instrument_used\n\n      Extraction --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  Extraction : name\n\n  Extraction : processing_institution\n\n      Extraction --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  Extraction : protocol_link\n\n      Extraction --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  Extraction : qc_comment\n\n  Extraction : qc_status\n\n      Extraction --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  Extraction : start_date\n\n  Extraction : substances_used\n\n      Extraction --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  Extraction : type\n\n  Extraction : volume\n\n      Extraction --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"Extraction/#inheritance","title":"Inheritance","text":""},{"location":"Extraction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance substances_used * PortionOfSubstance The substances that are combined to enable a ChemicalConversionProcess direct extraction_targets * ExtractionTargetEnum Provides the target biomolecule that has been separated from a sample during ... direct input_mass 0..1 QuantityValue Total mass of sample used in activity direct volume 0..1 QuantityValue The volume of the solvent/solute being used, not the input direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output 1..* ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Extraction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Extraction/#schema-source","title":"Schema Source","text":""},{"location":"Extraction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Extraction native nmdc:Extraction exact OBI:0302884"},{"location":"Extraction/#linkml-source","title":"LinkML Source","text":""},{"location":"Extraction/#direct","title":"Direct","text":"
name: Extraction\ndescription: A material separation in which a desired component of an input material\n  is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: MaterialProcessing\nslots:\n- substances_used\n- extraction_targets\n- input_mass\n- volume\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The volume of the solvent/solute being used, not the input.\nclass_uri: nmdc:Extraction\n\n
"},{"location":"Extraction/#induced","title":"Induced","text":"
name: Extraction\ndescription: A material separation in which a desired component of an input material\n  is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: MaterialProcessing\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The volume of the solvent/solute being used, not the input.\nattributes:\n  substances_used:\n    name: substances_used\n    description: The substances that are combined to enable a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: Extraction\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  extraction_targets:\n    name: extraction_targets\n    description: Provides the target biomolecule that has been separated from a sample\n      during an extraction process.\n    notes:\n    - todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)\n    from_schema: https://w3id.org/nmdc/nmdc\n    narrow_mappings:\n    - NCIT:C177560\n    - MIXS:0000037\n    rank: 1000\n    alias: extraction_targets\n    owner: Extraction\n    domain_of:\n    - Extraction\n    range: ExtractionTargetEnum\n    multivalued: true\n  input_mass:\n    name: input_mass\n    description: Total mass of sample used in activity.\n    title: sample mass used\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample mass\n    - sample weight\n    exact_mappings:\n    - MS:1000004\n    narrow_mappings:\n    - MIXS:0000111\n    rank: 1000\n    alias: input_mass\n    owner: Extraction\n    domain_of:\n    - Extraction\n    range: QuantityValue\n  volume:\n    name: volume\n    description: The volume of the solvent/solute being used, not the input.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: Extraction\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: Extraction\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Extraction\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Extraction\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Extraction\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Extraction\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Extraction\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Extraction\n\n
"},{"location":"ExtractionTargetEnum/","title":"Enum: ExtractionTargetEnum","text":"

URI: ExtractionTargetEnum

"},{"location":"ExtractionTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None metabolite None protein None lipid None"},{"location":"ExtractionTargetEnum/#slots","title":"Slots","text":"Name Description extraction_targets Provides the target biomolecule that has been separated from a sample during ..."},{"location":"ExtractionTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtractionTargetEnum/#schema-source","title":"Schema Source","text":""},{"location":"ExtractionTargetEnum/#linkml-source","title":"LinkML Source","text":"
name: ExtractionTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  DNA:\n    text: DNA\n  RNA:\n    text: RNA\n  metabolite:\n    text: metabolite\n  protein:\n    text: protein\n  lipid:\n    text: lipid\n\n
"},{"location":"FailureCategorization/","title":"Class: FailureCategorization","text":"

URI: nmdc:FailureCategorization

classDiagram\n  class FailureCategorization\n  click FailureCategorization href \"../FailureCategorization\"\n\n  FailureCategorization : qc_failure_what\n\n      FailureCategorization --> \"0..1\" FailureWhatEnum : qc_failure_what\n    click FailureWhatEnum href \"../FailureWhatEnum\"\n\n  FailureCategorization : qc_failure_where\n\n      FailureCategorization --> \"0..1\" FailureWhereEnum : qc_failure_where\n    click FailureWhereEnum href \"../FailureWhereEnum\"\n\n  FailureCategorization : type\n\n\n\n
"},{"location":"FailureCategorization/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance qc_failure_what 0..1 FailureWhatEnum Provides a summary about what caused a lab or workflow process to fail direct qc_failure_where 0..1 FailureWhereEnum Describes the nmdc schema class that corresonds to where the failure occurred direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"FailureCategorization/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_failure_categorization range FailureCategorization MassSpectrometry has_failure_categorization range FailureCategorization Pooling has_failure_categorization range FailureCategorization Extraction has_failure_categorization range FailureCategorization LibraryPreparation has_failure_categorization range FailureCategorization CollectingBiosamplesFromSite has_failure_categorization range FailureCategorization ProtocolExecution has_failure_categorization range FailureCategorization SubSamplingProcess has_failure_categorization range FailureCategorization MixingProcess has_failure_categorization range FailureCategorization FiltrationProcess has_failure_categorization range FailureCategorization StorageProcess has_failure_categorization range FailureCategorization ChromatographicSeparationProcess has_failure_categorization range FailureCategorization DissolvingProcess has_failure_categorization range FailureCategorization ChemicalConversionProcess has_failure_categorization range FailureCategorization MetagenomeAnnotation has_failure_categorization range FailureCategorization MaterialProcessing has_failure_categorization range FailureCategorization PlannedProcess has_failure_categorization range FailureCategorization DataGeneration has_failure_categorization range FailureCategorization WorkflowExecution has_failure_categorization range FailureCategorization MetagenomeAssembly has_failure_categorization range FailureCategorization MetatranscriptomeAssembly has_failure_categorization range FailureCategorization MetatranscriptomeAnnotation has_failure_categorization range FailureCategorization MetatranscriptomeExpressionAnalysis has_failure_categorization range FailureCategorization MagsAnalysis has_failure_categorization range FailureCategorization MetagenomeSequencing has_failure_categorization range FailureCategorization ReadQcAnalysis has_failure_categorization range FailureCategorization ReadBasedTaxonomyAnalysis has_failure_categorization range FailureCategorization MetabolomicsAnalysis has_failure_categorization range FailureCategorization MetaproteomicsAnalysis has_failure_categorization range FailureCategorization NomAnalysis has_failure_categorization range FailureCategorization"},{"location":"FailureCategorization/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FailureCategorization/#schema-source","title":"Schema Source","text":""},{"location":"FailureCategorization/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FailureCategorization native nmdc:FailureCategorization"},{"location":"FailureCategorization/#linkml-source","title":"LinkML Source","text":""},{"location":"FailureCategorization/#direct","title":"Direct","text":"
name: FailureCategorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- qc_failure_what\n- qc_failure_where\n- type\nclass_uri: nmdc:FailureCategorization\n\n
"},{"location":"FailureCategorization/#induced","title":"Induced","text":"
name: FailureCategorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  qc_failure_what:\n    name: qc_failure_what\n    description: Provides a summary about what caused a lab or workflow process to\n      fail\n    comments:\n    - For example, low read count from a sequencer, malformed fastq files, etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_failure_what\n    owner: FailureCategorization\n    domain_of:\n    - FailureCategorization\n    range: FailureWhatEnum\n  qc_failure_where:\n    name: qc_failure_where\n    description: Describes the nmdc schema class that corresonds to where the failure\n      occurred. Most commonly this would be the same as Class that generated the results.\n    comments:\n    - If the assembly size was too small to proceed to annotation failure_where would\n      be MetagenomeAssembly.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_failure_where\n    owner: FailureCategorization\n    domain_of:\n    - FailureCategorization\n    range: FailureWhereEnum\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FailureCategorization\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FailureCategorization\n\n
"},{"location":"FailureWhatEnum/","title":"Enum: FailureWhatEnum","text":"

The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.

URI: FailureWhatEnum

"},{"location":"FailureWhatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low_read_count None Number of output reads is not sufficient to continue to the next analysis ste... malformed_data None Workflow failure reading input or writing the output file(s) assembly_size_too_small None The size of the metagenome or metatranscriptome assembly is too small to proc... no_valid_data_generated None A process ran but did not produce any output other None A lab process or analysis workflow has failed in a way that has not been capt..."},{"location":"FailureWhatEnum/#slots","title":"Slots","text":"Name Description qc_failure_what Provides a summary about what caused a lab or workflow process to fail"},{"location":"FailureWhatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FailureWhatEnum/#schema-source","title":"Schema Source","text":""},{"location":"FailureWhatEnum/#linkml-source","title":"LinkML Source","text":"
name: FailureWhatEnum\ndescription: The permitted values for describing where a failure occurred during processing\n  in the lab during analysis workflows.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  low_read_count:\n    text: low_read_count\n    description: Number of output reads is not sufficient to continue to the next\n      analysis step.\n  malformed_data:\n    text: malformed_data\n    description: Workflow failure reading input or writing the output file(s).\n  assembly_size_too_small:\n    text: assembly_size_too_small\n    description: The size of the metagenome or metatranscriptome assembly is too small\n      to proceed to the next analysis workflow.\n  no_valid_data_generated:\n    text: no_valid_data_generated\n    description: A process ran but did not produce any output. Ie binning ran but\n      did not produce any medium or high quality bins.\n  other:\n    text: other\n    description: A lab process or analysis workflow has failed in a way that has not\n      been captured by the available values yet. Please use slot 'qc_comment' to specify\n      details.\n\n
"},{"location":"FailureWhereEnum/","title":"Enum: FailureWhereEnum","text":"

The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.

URI: FailureWhereEnum

"},{"location":"FailureWhereEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description NucleotideSequencing None A failure has occurred during nucleotide sequencing, a data generation proces... MassSpectrometry None A failure has occurred during mass spectrometry, a data generation process Pooling None A failure has occurred in pooling, a lab process Extraction None A failure has occurred in extraction, a lab process LibraryPreparation None A failure has occurred in library preparation, a lab process MetagenomeAssembly None A failure has occurred in metagenome assembly, a workflow process MetatranscriptomeExpressionAnalysis None A failure has occurred in metatranscriptome expression analysis, a workflow p... MagsAnalysis None A failure has occurred in binning, a workflow process to generate metagenome-... ReadQcAnalysis None A failure has occurred in read qc, a workflow process ReadBasedTaxonomyAnalysis None A failure has occurred in reads based taxonomy, a workflow process MetagenomeAnnotation None A failure has occurred in annotation, a workflow process MetatranscriptomeAssembly None A failure has occurred in assembly, a workflow process MetatranscriptomeAnnotation None A failure has occurred in annotation, a workflow process MetabolomicsAnalysis None A failure has occurred in analyzing metabolomics data MetaproteomicsAnalysis None A failure has occurred in analyzing metaproteomics data NomAnalysis None A failure has occurred in analyzing NOM data"},{"location":"FailureWhereEnum/#slots","title":"Slots","text":"Name Description qc_failure_where Describes the nmdc schema class that corresonds to where the failure occurred"},{"location":"FailureWhereEnum/#comments","title":"Comments","text":""},{"location":"FailureWhereEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FailureWhereEnum/#schema-source","title":"Schema Source","text":""},{"location":"FailureWhereEnum/#linkml-source","title":"LinkML Source","text":"
name: FailureWhereEnum\ndescription: The permitted values for describing where in the process, either a lab\n  or analysis workflow step, the failure occurred.\ncomments:\n- At Chris' recommendation permissible values for this enumeration are the same as\n  Class names.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  NucleotideSequencing:\n    text: NucleotideSequencing\n    description: A failure has occurred during nucleotide sequencing, a data generation\n      process.\n  MassSpectrometry:\n    text: MassSpectrometry\n    description: A failure has occurred during mass spectrometry, a data generation\n      process.\n  Pooling:\n    text: Pooling\n    description: A failure has occurred in pooling, a lab process.\n  Extraction:\n    text: Extraction\n    description: A failure has occurred in extraction, a lab process.\n  LibraryPreparation:\n    text: LibraryPreparation\n    description: A failure has occurred in library preparation, a lab process.\n  MetagenomeAssembly:\n    text: MetagenomeAssembly\n    description: A failure has occurred in metagenome assembly, a workflow process.\n  MetatranscriptomeExpressionAnalysis:\n    text: MetatranscriptomeExpressionAnalysis\n    description: A failure has occurred in metatranscriptome expression analysis,\n      a workflow process.\n  MagsAnalysis:\n    text: MagsAnalysis\n    description: A failure has occurred in binning, a workflow process to generate\n      metagenome-assembled genomes (MAGS).\n  ReadQcAnalysis:\n    text: ReadQcAnalysis\n    description: A failure has occurred in read qc, a workflow process.\n  ReadBasedTaxonomyAnalysis:\n    text: ReadBasedTaxonomyAnalysis\n    description: A failure has occurred in reads based taxonomy, a workflow process.\n  MetagenomeAnnotation:\n    text: MetagenomeAnnotation\n    description: A failure has occurred in annotation, a workflow process.\n  MetatranscriptomeAssembly:\n    text: MetatranscriptomeAssembly\n    description: A failure has occurred in assembly, a workflow process.\n  MetatranscriptomeAnnotation:\n    text: MetatranscriptomeAnnotation\n    description: A failure has occurred in annotation, a workflow process.\n  MetabolomicsAnalysis:\n    text: MetabolomicsAnalysis\n    description: A failure has occurred in analyzing metabolomics data.\n  MetaproteomicsAnalysis:\n    text: MetaproteomicsAnalysis\n    description: A failure has occurred in analyzing metaproteomics data.\n  NomAnalysis:\n    text: NomAnalysis\n    description: A failure has occurred in analyzing NOM data.\n\n
"},{"location":"FaoClassEnum/","title":"Enum: FaoClassEnum","text":"

URI: FaoClassEnum

"},{"location":"FaoClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Acrisols None Andosols None Arenosols None Cambisols None Chernozems None Ferralsols None Fluvisols None Gleysols None Greyzems None Gypsisols None Histosols None Kastanozems None Lithosols None Luvisols None Nitosols None Phaeozems None Planosols None Podzols None Podzoluvisols None Rankers None Regosols None Rendzinas None Solonchaks None Solonetz None Vertisols None Yermosols None"},{"location":"FaoClassEnum/#slots","title":"Slots","text":"Name Description fao_class Soil classification from the FAO World Reference Database for Soil Resources"},{"location":"FaoClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FaoClassEnum/#schema-source","title":"Schema Source","text":""},{"location":"FaoClassEnum/#linkml-source","title":"LinkML Source","text":"
name: fao_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Acrisols:\n    text: Acrisols\n  Andosols:\n    text: Andosols\n  Arenosols:\n    text: Arenosols\n  Cambisols:\n    text: Cambisols\n  Chernozems:\n    text: Chernozems\n  Ferralsols:\n    text: Ferralsols\n  Fluvisols:\n    text: Fluvisols\n  Gleysols:\n    text: Gleysols\n  Greyzems:\n    text: Greyzems\n  Gypsisols:\n    text: Gypsisols\n  Histosols:\n    text: Histosols\n  Kastanozems:\n    text: Kastanozems\n  Lithosols:\n    text: Lithosols\n  Luvisols:\n    text: Luvisols\n  Nitosols:\n    text: Nitosols\n  Phaeozems:\n    text: Phaeozems\n  Planosols:\n    text: Planosols\n  Podzols:\n    text: Podzols\n  Podzoluvisols:\n    text: Podzoluvisols\n  Rankers:\n    text: Rankers\n  Regosols:\n    text: Regosols\n  Rendzinas:\n    text: Rendzinas\n  Solonchaks:\n    text: Solonchaks\n  Solonetz:\n    text: Solonetz\n  Vertisols:\n    text: Vertisols\n  Yermosols:\n    text: Yermosols\n\n
"},{"location":"FieldResearchSite/","title":"Class: Field Research Site (FieldResearchSite)","text":"

A site, outside of a laboratory, from which biosamples may be collected.

URI: nmdc:FieldResearchSite

classDiagram\n  class FieldResearchSite\n  click FieldResearchSite href \"../FieldResearchSite\"\n    Site <|-- FieldResearchSite\n      click Site href \"../Site\"\n\n\n\n  FieldResearchSite : alternative_identifiers\n\n  FieldResearchSite : cur_vegetation\n\n      FieldResearchSite --> \"0..1\" TextValue : cur_vegetation\n    click TextValue href \"../TextValue\"\n\n  FieldResearchSite : description\n\n  FieldResearchSite : elev\n\n  FieldResearchSite : geo_loc_name\n\n      FieldResearchSite --> \"0..1\" TextValue : geo_loc_name\n    click TextValue href \"../TextValue\"\n\n  FieldResearchSite : habitat\n\n  FieldResearchSite : id\n\n  FieldResearchSite : lat_lon\n\n      FieldResearchSite --> \"0..1\" GeolocationValue : lat_lon\n    click GeolocationValue href \"../GeolocationValue\"\n\n  FieldResearchSite : local_class\n\n      FieldResearchSite --> \"0..1\" TextValue : local_class\n    click TextValue href \"../TextValue\"\n\n  FieldResearchSite : name\n\n  FieldResearchSite : part_of\n\n      FieldResearchSite --> \"*\" FieldResearchSite : part_of\n    click FieldResearchSite href \"../FieldResearchSite\"\n\n  FieldResearchSite : soil_type\n\n      FieldResearchSite --> \"0..1\" TextValue : soil_type\n    click TextValue href \"../TextValue\"\n\n  FieldResearchSite : type\n\n\n\n
"},{"location":"FieldResearchSite/#inheritance","title":"Inheritance","text":""},{"location":"FieldResearchSite/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance cur_vegetation 0..1 TextValue Vegetation classification from one or more standard classification systems, o... direct elev 0..1 Float Elevation of the sampling site is its height above a fixed reference point, m... direct geo_loc_name 0..1 TextValue The geographical origin of the sample as defined by the country or sea name f... direct habitat 0..1 String direct lat_lon 0..1 GeolocationValue The geographical origin of the sample as defined by latitude and longitude direct local_class 0..1 TextValue Soil classification based on local soil classification system direct part_of * FieldResearchSite Links a resource to another resource that either logically or physically incl... direct soil_type 0..1 TextValue Description of the soil type or classification direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"FieldResearchSite/#usages","title":"Usages","text":"used by used in type used Database field_research_site_set range FieldResearchSite FieldResearchSite part_of range FieldResearchSite Biosample collected_from range FieldResearchSite"},{"location":"FieldResearchSite/#aliases","title":"Aliases","text":""},{"location":"FieldResearchSite/#comments","title":"Comments","text":""},{"location":"FieldResearchSite/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FieldResearchSite/#schema-source","title":"Schema Source","text":""},{"location":"FieldResearchSite/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FieldResearchSite native nmdc:FieldResearchSite"},{"location":"FieldResearchSite/#linkml-source","title":"LinkML Source","text":""},{"location":"FieldResearchSite/#direct","title":"Direct","text":"
name: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n  the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n  same plant were obtained at the same site. In this case, the site would correspond\n  to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslots:\n- cur_vegetation\n- elev\n- geo_loc_name\n- habitat\n- lat_lon\n- local_class\n- part_of\n- soil_type\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  part_of:\n    name: part_of\n    range: FieldResearchSite\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:FieldResearchSite\n\n
"},{"location":"FieldResearchSite/#induced","title":"Induced","text":"
name: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n  the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n  same plant were obtained at the same site. In this case, the site would correspond\n  to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  part_of:\n    name: part_of\n    range: FieldResearchSite\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  cur_vegetation:\n    name: cur_vegetation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: current vegetation type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Vegetation classification from one or more standard classification\n      systems, or agricultural crop\n    title: current vegetation\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - current vegetation\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000312\n    alias: cur_vegetation\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  elev:\n    name: elev\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n    description: Elevation of the sampling site is its height above a fixed reference\n      point, most commonly the mean sea level. Elevation is mainly used when referring\n      to points on the earth's surface, while altitude is used for points above the\n      surface, such as an aircraft in flight or a spacecraft in orbit.\n    title: elevation\n    examples:\n    - value: 100 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - elevation\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000093\n    alias: elev\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: float\n    multivalued: false\n  geo_loc_name:\n    name: geo_loc_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n          name'\n    description: The geographical origin of the sample as defined by the country or\n      sea name followed by specific region name. Country or sea names should be chosen\n      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n      (http://purl.bioontology.org/ontology/GAZ)\n    title: geographic location (country and/or sea,region)\n    examples:\n    - value: 'USA: Maryland, Bethesda'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - geographic location (country and/or sea,region)\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{term}: {term}, {text}'\n    slot_uri: MIXS:0000010\n    alias: geo_loc_name\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  habitat:\n    name: habitat\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: habitat\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: string\n  lat_lon:\n    name: lat_lon\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: decimal degrees,  limit to 8 decimal points\n    description: The geographical origin of the sample as defined by latitude and\n      longitude. The values should be reported in decimal degrees and in WGS84 system\n    title: geographic location (latitude and longitude)\n    examples:\n    - value: 50.586825 6.408977\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - geographic location (latitude and longitude)\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{float} {float}'\n    slot_uri: MIXS:0000009\n    alias: lat_lon\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: GeolocationValue\n    multivalued: false\n  local_class:\n    name: local_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: local classification name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Soil classification based on local soil classification system\n    title: soil_taxonomic/local classification\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil_taxonomic/local classification\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000330\n    alias: local_class\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  part_of:\n    name: part_of\n    description: Links a resource to another resource that either logically or physically\n      includes it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - is part of\n    rank: 1000\n    slot_uri: dcterms:isPartOf\n    alias: part_of\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Study\n    range: FieldResearchSite\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  soil_type:\n    name: soil_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: ENVO_00001998\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Description of the soil type or classification. This field accepts\n      terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms\n      can be separated by pipes.\n    title: soil type\n    examples:\n    - value: plinthosol [ENVO:00002250]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000332\n    alias: soil_type\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: FieldResearchSite\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: FieldResearchSite\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: FieldResearchSite\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: FieldResearchSite\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FieldResearchSite\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FieldResearchSite\n\n
"},{"location":"FileTypeEnum/","title":"Enum: FileTypeEnum","text":"

URI: FileTypeEnum

"},{"location":"FileTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Reference Calibration File None A file that contains data used to calibrate a natural organic matter or metab... Metagenome Raw Reads None Interleaved paired-end raw sequencing data Metagenome Raw Read 1 None Read 1 raw sequencing data, aka forward reads Metagenome Raw Read 2 None Read 2 raw sequencing data, aka reverse reads FT ICR-MS Analysis Results None FT ICR-MS-based molecular formula assignment results table GC-MS Metabolomics Results None GC-MS-based metabolite assignment results table Metaproteomics Workflow Statistics None Aggregate workflow statistics file Protein Report None Filtered protein report file Peptide Report None Filtered peptide report file Unfiltered Metaproteomics Results None MSGFjobs and MASIC output file Read Count and RPKM None Annotation read count and RPKM per feature JSON QC non-rRNA R2 None QC removed rRNA reads (R2) fastq QC non-rRNA R1 None QC removed rRNA reads (R1) fastq Metagenome Bins None Metagenome bin contigs fasta Metagenome HQMQ Bins Compression File None Compressed file containing high qulaity and medium quality metagenome bins an... Metagenome LQ Bins Compression File None Compressed file containing low quality metagenome bins and associated files Metagenome Bins Info File None File containing version information on the binning workflow CheckM Statistics None CheckM statistics report Metagenome Bins Heatmap None The Heatmap presents the pdf file containing the KO analysis results for meta... Metagenome Bins Barplot None The Bar chart presents the pdf file containing the KO analysis results for me... Metagenome Bins Krona Plot None The Krona plot presents the HTML file containing the KO analysis results for ... Read Based Analysis Info File None File containing reads based analysis information GTDBTK Bacterial Summary None GTDBTK bacterial summary GTDBTK Archaeal Summary None GTDBTK archaeal summary GOTTCHA2 Krona Plot None GOTTCHA2 krona plot HTML file GOTTCHA2 Classification Report None GOTTCHA2 classification report file GOTTCHA2 Report Full None GOTTCHA2 report file Kraken2 Krona Plot None Kraken2 krona plot HTML file Centrifuge Krona Plot None Centrifuge krona plot HTML file Centrifuge output report file None Centrifuge output report file Kraken2 Classification Report None Kraken2 output report file Kraken2 Taxonomic Classification None Kraken2 output read classification file Centrifuge Classification Report None Centrifuge output report file Centrifuge Taxonomic Classification None Centrifuge output read classification file Structural Annotation GFF None GFF3 format file with structural annotations Structural Annotation Stats Json None Structural annotations stats json Functional Annotation GFF None GFF3 format file with functional annotations Annotation Info File None File containing annotation info Annotation Amino Acid FASTA None FASTA amino acid file for annotated proteins Annotation Enzyme Commission None Tab delimited file for EC annotation Annotation KEGG Orthology None Tab delimited file for KO annotation Assembly Info File None File containing assembly info Assembly Coverage BAM None Sorted bam file of reads mapping back to the final assembly Assembly AGP None An AGP format file that describes the assembly Assembly Scaffolds None Final assembly scaffolds fasta Assembly Contigs None Final assembly contigs fasta Assembly Coverage Stats None Assembled contigs coverage information Contig Mapping File None Contig mappings between contigs and scaffolds Error Corrected Reads None Error corrected reads fastq Filtered Sequencing Reads None Reads QC result fastq (clean data) Read Filtering Info File None File containing read filtering information QC Statistics Extended None Extended report including methods and results for read filtering QC Statistics None Reads QC summary statistics TIGRFam Annotation GFF None GFF3 format file with TIGRfam CRT Annotation GFF None GFF3 format file with CRT Genemark Annotation GFF None GFF3 format file with Genemark Prodigal Annotation GFF None GFF3 format file with Prodigal TRNA Annotation GFF None GFF3 format file with TRNA Misc Annotation GFF None GFF3 format file with Misc RFAM Annotation GFF None GFF3 format file with RFAM TMRNA Annotation GFF None GFF3 format file with TMRNA Crispr Terms None Crispr Terms Product Names None Product names file Gene Phylogeny tsv None Gene Phylogeny tsv Scaffold Lineage tsv None phylogeny at the scaffold level Clusters of Orthologous Groups (COG) Annotation GFF None GFF3 format file with COGs KO_EC Annotation GFF None GFF3 format file with KO_EC CATH FunFams (Functional Families) Annotation GFF None GFF3 format file with CATH FunFams SUPERFam Annotation GFF None GFF3 format file with SUPERFam SMART Annotation GFF None GFF3 format file with SMART Pfam Annotation GFF None GFF3 format file with Pfam Annotation Statistics None Annotation statistics report Direct Infusion FT ICR-MS Raw Data None Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance mass spect... LC-DDA-MS/MS Raw Data None Liquid chromatographically separated MS1 and Data-Dependent MS2 binary instru... Configuration toml None A configuration toml file used by various programs to store settings that are... LC-MS Lipidomics Results None LC-MS-based lipid assignment results table Contaminants Amino Acid FASTA None FASTA amino acid file for contaminant proteins commonly observed in proteomic... Analysis Tool Parameter File None A configuration file used by a single computational software tool that stores... Workflow Operation Summary None A human readable record of analysis steps applied during an instance of a wor... Metatranscriptome Expression None Metatranscriptome expression values and read counts for gene features predict... Metatranscriptome Expression Intergenic None Metatranscriptome expression values and read counts for intergenic regions Metatranscriptome Expression Info File None File containing version information on the expression workflow rRNA Filtered Sequencing Reads None File containing ribosomal reads from the read qc filtering step BAI File None An index file found in the same directory as the binary alignment map (BAM) f..."},{"location":"FileTypeEnum/#slots","title":"Slots","text":"Name Description data_object_type The type of file represented by the data object"},{"location":"FileTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FileTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"FileTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: FileTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Reference Calibration File:\n    text: Reference Calibration File\n    description: A file that contains data used to calibrate a natural organic matter\n      or metabalomics analysis.\n  Metagenome Raw Reads:\n    text: Metagenome Raw Reads\n    description: Interleaved paired-end raw sequencing data\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: ^\\.fastq(\\.gz)?$\n  Metagenome Raw Read 1:\n    text: Metagenome Raw Read 1\n    description: Read 1 raw sequencing data, aka forward reads\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: ^.+_R1\\.fastq(\\.gz)?$\n    examples:\n    - value: BMI_H25VYBGXH_19S_31WellG1_R1.fastq.gz\n  Metagenome Raw Read 2:\n    text: Metagenome Raw Read 2\n    description: Read 2 raw sequencing data, aka reverse reads\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: ^.+_R2\\.fastq(\\.gz)?$\n    examples:\n    - value: BMI_H25VYBGXH_19S_31WellG1_R2.fastq.gz\n  FT ICR-MS Analysis Results:\n    text: FT ICR-MS Analysis Results\n    description: FT ICR-MS-based molecular formula assignment results table\n  GC-MS Metabolomics Results:\n    text: GC-MS Metabolomics Results\n    description: GC-MS-based metabolite assignment results table\n  Metaproteomics Workflow Statistics:\n    text: Metaproteomics Workflow Statistics\n    description: Aggregate workflow statistics file\n  Protein Report:\n    text: Protein Report\n    description: Filtered protein report file\n  Peptide Report:\n    text: Peptide Report\n    description: Filtered peptide report file\n  Unfiltered Metaproteomics Results:\n    text: Unfiltered Metaproteomics Results\n    description: MSGFjobs and MASIC output file\n  Read Count and RPKM:\n    text: Read Count and RPKM\n    description: Annotation read count and RPKM per feature JSON\n  QC non-rRNA R2:\n    text: QC non-rRNA R2\n    description: QC removed rRNA reads (R2) fastq\n  QC non-rRNA R1:\n    text: QC non-rRNA R1\n    description: QC removed rRNA reads (R1) fastq\n  Metagenome Bins:\n    text: Metagenome Bins\n    description: Metagenome bin contigs fasta\n  Metagenome HQMQ Bins Compression File:\n    text: Metagenome HQMQ Bins Compression File\n    description: Compressed file containing high qulaity and medium quality metagenome\n      bins and associated files\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_hqmq_bin.zip'\n  Metagenome LQ Bins Compression File:\n    text: Metagenome LQ Bins Compression File\n    description: Compressed file containing low quality metagenome bins and associated\n      files\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_lq_bin.zip'\n  Metagenome Bins Info File:\n    text: Metagenome Bins Info File\n    description: File containing version information on the binning workflow\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_bin.info'\n  CheckM Statistics:\n    text: CheckM Statistics\n    description: CheckM statistics report\n  Metagenome Bins Heatmap:\n    text: Metagenome Bins Heatmap\n    description: The Heatmap presents the pdf file containing the KO analysis results\n      for metagenome bins\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_heatmap.pdf'\n  Metagenome Bins Barplot:\n    text: Metagenome Bins Barplot\n    description: The Bar chart presents the pdf file containing the KO analysis results\n      for metagenome bins\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_barplot.pdf'\n  Metagenome Bins Krona Plot:\n    text: Metagenome Bins Krona Plot\n    description: The Krona plot presents the HTML file containing the KO analysis\n      results for metagenome bins\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_kronaplot.html'\n  Read Based Analysis Info File:\n    text: Read Based Analysis Info File\n    description: File containing reads based analysis information\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: profiler.info\n  GTDBTK Bacterial Summary:\n    text: GTDBTK Bacterial Summary\n    description: GTDBTK bacterial summary\n  GTDBTK Archaeal Summary:\n    text: GTDBTK Archaeal Summary\n    description: GTDBTK archaeal summary\n  GOTTCHA2 Krona Plot:\n    text: GOTTCHA2 Krona Plot\n    description: GOTTCHA2 krona plot HTML file\n  GOTTCHA2 Classification Report:\n    text: GOTTCHA2 Classification Report\n    description: GOTTCHA2 classification report file\n  GOTTCHA2 Report Full:\n    text: GOTTCHA2 Report Full\n    description: GOTTCHA2 report file\n  Kraken2 Krona Plot:\n    text: Kraken2 Krona Plot\n    description: Kraken2 krona plot HTML file\n  Centrifuge Krona Plot:\n    text: Centrifuge Krona Plot\n    description: Centrifuge krona plot HTML file\n  Centrifuge output report file:\n    text: Centrifuge output report file\n    description: Centrifuge output report file\n  Kraken2 Classification Report:\n    text: Kraken2 Classification Report\n    description: Kraken2 output report file\n  Kraken2 Taxonomic Classification:\n    text: Kraken2 Taxonomic Classification\n    description: Kraken2 output read classification file\n  Centrifuge Classification Report:\n    text: Centrifuge Classification Report\n    description: Centrifuge output report file\n  Centrifuge Taxonomic Classification:\n    text: Centrifuge Taxonomic Classification\n    description: Centrifuge output read classification file\n  Structural Annotation GFF:\n    text: Structural Annotation GFF\n    description: GFF3 format file with structural annotations\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_structural_annotation.gff'\n  Structural Annotation Stats Json:\n    text: Structural Annotation Stats Json\n    description: Structural annotations stats json\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_structural_annotation_stats.json'\n  Functional Annotation GFF:\n    text: Functional Annotation GFF\n    description: GFF3 format file with functional annotations\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_functional_annotation.gff'\n  Annotation Info File:\n    text: Annotation Info File\n    description: File containing annotation info\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_imgap.info'\n  Annotation Amino Acid FASTA:\n    text: Annotation Amino Acid FASTA\n    description: FASTA amino acid file for annotated proteins\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_proteins.faa'\n  Annotation Enzyme Commission:\n    text: Annotation Enzyme Commission\n    description: Tab delimited file for EC annotation\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_ec.tsv'\n  Annotation KEGG Orthology:\n    text: Annotation KEGG Orthology\n    description: Tab delimited file for KO annotation\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_ko.tsv'\n  Assembly Info File:\n    text: Assembly Info File\n    description: File containing assembly info\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: README.txt\n  Assembly Coverage BAM:\n    text: Assembly Coverage BAM\n    description: Sorted bam file of reads mapping back to the final assembly\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_pairedMapped.sam.gz'\n  Assembly AGP:\n    text: Assembly AGP\n    description: An AGP format file that describes the assembly\n  Assembly Scaffolds:\n    text: Assembly Scaffolds\n    description: Final assembly scaffolds fasta\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_assembly.contigs.fasta'\n  Assembly Contigs:\n    text: Assembly Contigs\n    description: Final assembly contigs fasta\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: assembly.contigs.fasta\n  Assembly Coverage Stats:\n    text: Assembly Coverage Stats\n    description: Assembled contigs coverage information\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_pairedMapped_sorted.bam.cov'\n  Contig Mapping File:\n    text: Contig Mapping File\n    description: Contig mappings between contigs and scaffolds\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_contig_names_mapping.tsv'\n  Error Corrected Reads:\n    text: Error Corrected Reads\n    description: Error corrected reads fastq\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: input.corr.fastq.gz\n  Filtered Sequencing Reads:\n    text: Filtered Sequencing Reads\n    description: Reads QC result fastq (clean data)\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '/.+?(?=filter)/filter-METAGENOME.fastq.gz '\n  Read Filtering Info File:\n    text: Read Filtering Info File\n    description: File containing read filtering information\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[rqc_wf_activity_id]_readsQC.info'\n  QC Statistics Extended:\n    text: QC Statistics Extended\n    description: Extended report including methods and results for read filtering\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: /.+?(?=filter)/filtered-report.txt\n  QC Statistics:\n    text: QC Statistics\n    description: Reads QC summary statistics\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[rqc_wf_activity_id]_filterStats2.txt'\n  TIGRFam Annotation GFF:\n    text: TIGRFam Annotation GFF\n    description: GFF3 format file with TIGRfam\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_tigrfam.gff'\n  CRT Annotation GFF:\n    text: CRT Annotation GFF\n    description: GFF3 format file with CRT\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_crt.gff'\n  Genemark Annotation GFF:\n    text: Genemark Annotation GFF\n    description: GFF3 format file with Genemark\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_genemark.gff'\n  Prodigal Annotation GFF:\n    text: Prodigal Annotation GFF\n    description: GFF3 format file with Prodigal\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_prodigal.gff'\n  TRNA Annotation GFF:\n    text: TRNA Annotation GFF\n    description: GFF3 format file with TRNA\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_trna.gff'\n  Misc Annotation GFF:\n    text: Misc Annotation GFF\n    description: GFF3 format file with Misc\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff'\n  RFAM Annotation GFF:\n    text: RFAM Annotation GFF\n    description: GFF3 format file with RFAM\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_rfam.gff'\n  TMRNA Annotation GFF:\n    text: TMRNA Annotation GFF\n    description: GFF3 format file with TMRNA\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_rfam_ncrna_tmrna.gff'\n  Crispr Terms:\n    text: Crispr Terms\n    description: Crispr Terms\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_crt.crisprs'\n  Product Names:\n    text: Product Names\n    description: Product names file\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_product_names.tsv'\n  Gene Phylogeny tsv:\n    text: Gene Phylogeny tsv\n    description: Gene Phylogeny tsv\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_gene_phylogeny.tsv'\n  Scaffold Lineage tsv:\n    text: Scaffold Lineage tsv\n    description: phylogeny at the scaffold level\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_scaffold_lineage.tsv'\n  Clusters of Orthologous Groups (COG) Annotation GFF:\n    text: Clusters of Orthologous Groups (COG) Annotation GFF\n    description: GFF3 format file with COGs\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_cog.gff'\n  KO_EC Annotation GFF:\n    text: KO_EC Annotation GFF\n    description: GFF3 format file with KO_EC\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_ko_ec.gff'\n  CATH FunFams (Functional Families) Annotation GFF:\n    text: CATH FunFams (Functional Families) Annotation GFF\n    description: GFF3 format file with CATH FunFams\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_cath_funfam.gff'\n  SUPERFam Annotation GFF:\n    text: SUPERFam Annotation GFF\n    description: GFF3 format file with SUPERFam\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_supfam.gff'\n  SMART Annotation GFF:\n    text: SMART Annotation GFF\n    description: GFF3 format file with SMART\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_smart.gff'\n  Pfam Annotation GFF:\n    text: Pfam Annotation GFF\n    description: GFF3 format file with Pfam\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_pfam.gff'\n  Annotation Statistics:\n    text: Annotation Statistics\n    description: Annotation statistics report\n  Direct Infusion FT ICR-MS Raw Data:\n    text: Direct Infusion FT ICR-MS Raw Data\n    description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance\n      mass spectrometry raw data acquired in broadband full scan mode\n  LC-DDA-MS/MS Raw Data:\n    text: LC-DDA-MS/MS Raw Data\n    description: Liquid chromatographically separated MS1 and Data-Dependent MS2 binary\n      instrument file\n  Configuration toml:\n    text: Configuration toml\n    description: A configuration toml file used by various programs to store settings\n      that are specific to their respective software.\n    broad_mappings:\n    - edam.format:4005\n  LC-MS Lipidomics Results:\n    text: LC-MS Lipidomics Results\n    description: LC-MS-based lipid assignment results table.\n  Contaminants Amino Acid FASTA:\n    text: Contaminants Amino Acid FASTA\n    description: FASTA amino acid file for contaminant proteins commonly observed\n      in proteomics data.\n  Analysis Tool Parameter File:\n    text: Analysis Tool Parameter File\n    description: A configuration file used by a single computational software tool\n      that stores settings that are specific to that tool.\n  Workflow Operation Summary:\n    text: Workflow Operation Summary\n    description: A human readable record of analysis steps applied during an instance\n      of a workflow operation.\n  Metatranscriptome Expression:\n    text: Metatranscriptome Expression\n    description: Metatranscriptome expression values and read counts for gene features\n      predicted on contigs\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*.rnaseq_gea.txt'\n  Metatranscriptome Expression Intergenic:\n    text: Metatranscriptome Expression Intergenic\n    description: Metatranscriptome expression values and read counts for intergenic\n      regions.\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*.rnaseq_gea.intergenic.txt'\n  Metatranscriptome Expression Info File:\n    text: Metatranscriptome Expression Info File\n    description: File containing version information on the expression workflow\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*_readcount.info'\n  rRNA Filtered Sequencing Reads:\n    text: rRNA Filtered Sequencing Reads\n    description: File containing ribosomal reads from the read qc filtering step.\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*.rRNA.fastq.gz'\n  BAI File:\n    text: BAI File\n    description: An index file found in the same directory as the binary alignment\n      map (BAM) file, a compressed binary version of a sequence alignment/map (SAM)\n      file.\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*.pairedMapped_sorted.bam.bai'\n    exact_mappings:\n    - NCIT:C190163\n\n
"},{"location":"FilterTypeEnum/","title":"Enum: FilterTypeEnum","text":"

URI: FilterTypeEnum

"},{"location":"FilterTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description particulate air filter None chemical air filter None low-MERV pleated media None HEPA None electrostatic None gas-phase or ultraviolet air treatments None"},{"location":"FilterTypeEnum/#slots","title":"Slots","text":"Name Description filter_type A device which removes solid particulates or airborne molecular contaminants"},{"location":"FilterTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FilterTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"FilterTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: filter_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  particulate air filter:\n    text: particulate air filter\n  chemical air filter:\n    text: chemical air filter\n  low-MERV pleated media:\n    text: low-MERV pleated media\n  HEPA:\n    text: HEPA\n  electrostatic:\n    text: electrostatic\n  gas-phase or ultraviolet air treatments:\n    text: gas-phase or ultraviolet air treatments\n\n
"},{"location":"FiltrationProcess/","title":"Class: FiltrationProcess","text":"

The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.

URI: nmdc:FiltrationProcess

classDiagram\n  class FiltrationProcess\n  click FiltrationProcess href \"../FiltrationProcess\"\n    MaterialProcessing <|-- FiltrationProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  FiltrationProcess : alternative_identifiers\n\n  FiltrationProcess : conditionings\n\n  FiltrationProcess : container_size\n\n      FiltrationProcess --> \"0..1\" QuantityValue : container_size\n    click QuantityValue href \"../QuantityValue\"\n\n  FiltrationProcess : description\n\n  FiltrationProcess : end_date\n\n  FiltrationProcess : filter_material\n\n  FiltrationProcess : filter_pore_size\n\n      FiltrationProcess --> \"0..1\" QuantityValue : filter_pore_size\n    click QuantityValue href \"../QuantityValue\"\n\n  FiltrationProcess : filtration_category\n\n  FiltrationProcess : has_failure_categorization\n\n      FiltrationProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  FiltrationProcess : has_input\n\n      FiltrationProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  FiltrationProcess : has_output\n\n      FiltrationProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  FiltrationProcess : id\n\n  FiltrationProcess : instrument_used\n\n      FiltrationProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  FiltrationProcess : is_pressurized\n\n  FiltrationProcess : name\n\n  FiltrationProcess : processing_institution\n\n      FiltrationProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  FiltrationProcess : protocol_link\n\n      FiltrationProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  FiltrationProcess : qc_comment\n\n  FiltrationProcess : qc_status\n\n      FiltrationProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  FiltrationProcess : separation_method\n\n      FiltrationProcess --> \"0..1\" SeparationMethodEnum : separation_method\n    click SeparationMethodEnum href \"../SeparationMethodEnum\"\n\n  FiltrationProcess : start_date\n\n  FiltrationProcess : type\n\n  FiltrationProcess : volume\n\n      FiltrationProcess --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"FiltrationProcess/#inheritance","title":"Inheritance","text":""},{"location":"FiltrationProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance conditionings * String Preliminary treatment of either phase with a suitable solution of the other p... direct container_size 0..1 QuantityValue The volume of the container an analyte is stored in or an activity takes plac... direct filter_material 0..1 String A porous material on which solid particles present in air or other fluid whic... direct filter_pore_size 0..1 QuantityValue A quantitative or qualitative measurement of the physical dimensions of the p... direct filtration_category 0..1 String The type of conditioning applied to a filter, device, etc direct is_pressurized 0..1 Boolean Whether or not pressure was applied to a thing or process direct separation_method 0..1 SeparationMethodEnum The method that was used to separate a substance from a solution or mixture direct volume 0..1 QuantityValue The volume of sample filtered direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"FiltrationProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FiltrationProcess/#schema-source","title":"Schema Source","text":""},{"location":"FiltrationProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FiltrationProcess native nmdc:FiltrationProcess related CHMO:0001640"},{"location":"FiltrationProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"FiltrationProcess/#direct","title":"Direct","text":"
name: FiltrationProcess\ndescription: The process of segregation of phases; e.g. the separation of suspended\n  solids from a liquid or gas, usually by forcing a carrier gas or liquid through\n  a porous medium.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- CHMO:0001640\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslots:\n- conditionings\n- container_size\n- filter_material\n- filter_pore_size\n- filtration_category\n- is_pressurized\n- separation_method\n- volume\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The volume of sample filtered.\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:FiltrationProcess\n\n
"},{"location":"FiltrationProcess/#induced","title":"Induced","text":"
name: FiltrationProcess\ndescription: The process of segregation of phases; e.g. the separation of suspended\n  solids from a liquid or gas, usually by forcing a carrier gas or liquid through\n  a porous medium.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- CHMO:0001640\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The volume of sample filtered.\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  conditionings:\n    name: conditionings\n    description: Preliminary treatment of either phase with a suitable solution of\n      the other phase (in the absence of main extractable solute(s)) so that when\n      the subsequent equilibration is carried out changes in the (volume) phase ratio\n      or in the concentrations of other components are minimized.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    list_elements_ordered: true\n    alias: conditionings\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: string\n    multivalued: true\n  container_size:\n    name: container_size\n    description: The volume of the container an analyte is stored in or an activity\n      takes place in\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: container_size\n    owner: FiltrationProcess\n    domain_of:\n    - SubSamplingProcess\n    - FiltrationProcess\n    range: QuantityValue\n  filter_material:\n    name: filter_material\n    description: A porous material on which solid particles present in air or other\n      fluid which flows through it are largely caught and retained.\n    comments:\n    - 'Filters are made with a variety of materials: cellulose and derivatives, glass\n      fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous\n      or be made so by mechanical or other means. Membrane/ceramic filters are prepared\n      with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene,\n      polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement.\n      The pores constitute 80\u201385% of the filter volume commonly and several pore sizes\n      are available for air sampling (0.45\u22120.8 \u03bcm are commonly employed).'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: filter_material\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: string\n  filter_pore_size:\n    name: filter_pore_size\n    description: A quantitative or qualitative measurement of the physical dimensions\n      of the pores in a material.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: filter_pore_size\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: QuantityValue\n  filtration_category:\n    name: filtration_category\n    description: The type of conditioning applied to a filter, device, etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: filtration_category\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: string\n  is_pressurized:\n    name: is_pressurized\n    description: Whether or not pressure was applied to a thing or process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: is_pressurized\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: boolean\n  separation_method:\n    name: separation_method\n    description: The method that was used to separate a substance from a solution\n      or mixture.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: separation_method\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: SeparationMethodEnum\n  volume:\n    name: volume\n    description: The volume of sample filtered.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: FiltrationProcess\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: FiltrationProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: FiltrationProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: FiltrationProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: FiltrationProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: FiltrationProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FiltrationProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FiltrationProcess\n\n
"},{"location":"Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Float/#schema-source","title":"Schema Source","text":""},{"location":"Float/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:float native nmdc:float exact schema:Float"},{"location":"FloorCondEnum/","title":"Enum: FloorCondEnum","text":"

URI: FloorCondEnum

"},{"location":"FloorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"FloorCondEnum/#slots","title":"Slots","text":"Name Description floor_cond The physical condition of the floor at the time of sampling; photos or video ..."},{"location":"FloorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"FloorCondEnum/#linkml-source","title":"LinkML Source","text":"
name: floor_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  new:\n    text: new\n  visible wear:\n    text: visible wear\n  needs repair:\n    text: needs repair\n  damaged:\n    text: damaged\n  rupture:\n    text: rupture\n\n
"},{"location":"FloorFinishMatEnum/","title":"Enum: FloorFinishMatEnum","text":"

URI: FloorFinishMatEnum

"},{"location":"FloorFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description tile None wood strip or parquet None carpet None rug None laminate wood None lineoleum None vinyl composition tile None sheet vinyl None stone None bamboo None cork None terrazo None concrete None none None sealed None clear finish None paint None none or unfinished None"},{"location":"FloorFinishMatEnum/#slots","title":"Slots","text":"Name Description floor_finish_mat The floor covering type; the finished surface that is walked on"},{"location":"FloorFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorFinishMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"FloorFinishMatEnum/#linkml-source","title":"LinkML Source","text":"
name: floor_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  tile:\n    text: tile\n  wood strip or parquet:\n    text: wood strip or parquet\n  carpet:\n    text: carpet\n  rug:\n    text: rug\n  laminate wood:\n    text: laminate wood\n  lineoleum:\n    text: lineoleum\n  vinyl composition tile:\n    text: vinyl composition tile\n  sheet vinyl:\n    text: sheet vinyl\n  stone:\n    text: stone\n  bamboo:\n    text: bamboo\n  cork:\n    text: cork\n  terrazo:\n    text: terrazo\n  concrete:\n    text: concrete\n  none:\n    text: none\n  sealed:\n    text: sealed\n  clear finish:\n    text: clear finish\n  paint:\n    text: paint\n  none or unfinished:\n    text: none or unfinished\n\n
"},{"location":"FloorStrucEnum/","title":"Enum: FloorStrucEnum","text":"

URI: FloorStrucEnum

"},{"location":"FloorStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description balcony None floating floor None glass floor None raised floor None sprung floor None wood-framed None concrete None"},{"location":"FloorStrucEnum/#slots","title":"Slots","text":"Name Description floor_struc Refers to the structural elements and subfloor upon which the finish flooring..."},{"location":"FloorStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorStrucEnum/#schema-source","title":"Schema Source","text":""},{"location":"FloorStrucEnum/#linkml-source","title":"LinkML Source","text":"
name: floor_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  balcony:\n    text: balcony\n  floating floor:\n    text: floating floor\n  glass floor:\n    text: glass floor\n  raised floor:\n    text: raised floor\n  sprung floor:\n    text: sprung floor\n  wood-framed:\n    text: wood-framed\n  concrete:\n    text: concrete\n\n
"},{"location":"FloorWaterMoldEnum/","title":"Enum: FloorWaterMoldEnum","text":"

URI: FloorWaterMoldEnum

"},{"location":"FloorWaterMoldEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mold odor None wet floor None water stains None wall discoloration None floor discoloration None ceiling discoloration None peeling paint or wallpaper None bulging walls None condensation None"},{"location":"FloorWaterMoldEnum/#slots","title":"Slots","text":"Name Description floor_water_mold Signs of the presence of mold or mildew in a room"},{"location":"FloorWaterMoldEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorWaterMoldEnum/#schema-source","title":"Schema Source","text":""},{"location":"FloorWaterMoldEnum/#linkml-source","title":"LinkML Source","text":"
name: floor_water_mold_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  mold odor:\n    text: mold odor\n  wet floor:\n    text: wet floor\n  water stains:\n    text: water stains\n  wall discoloration:\n    text: wall discoloration\n  floor discoloration:\n    text: floor discoloration\n  ceiling discoloration:\n    text: ceiling discoloration\n  peeling paint or wallpaper:\n    text: peeling paint or wallpaper\n  bulging walls:\n    text: bulging walls\n  condensation:\n    text: condensation\n\n
"},{"location":"FreqCleanEnum/","title":"Enum: FreqCleanEnum","text":"

URI: FreqCleanEnum

"},{"location":"FreqCleanEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Daily None Weekly None Monthly None Quarterly None Annually None other None"},{"location":"FreqCleanEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FreqCleanEnum/#schema-source","title":"Schema Source","text":""},{"location":"FreqCleanEnum/#linkml-source","title":"LinkML Source","text":"
name: freq_clean_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Daily:\n    text: Daily\n  Weekly:\n    text: Weekly\n  Monthly:\n    text: Monthly\n  Quarterly:\n    text: Quarterly\n  Annually:\n    text: Annually\n  other:\n    text: other\n\n
"},{"location":"FunctionalAnnotation/","title":"Class: FunctionalAnnotation","text":"

An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods

URI: nmdc:FunctionalAnnotation

classDiagram\n  class FunctionalAnnotation\n  click FunctionalAnnotation href \"../FunctionalAnnotation\"\n\n  FunctionalAnnotation : feature_category\n\n      FunctionalAnnotation --> \"0..1\" ControlledIdentifiedTermValue : feature_category\n    click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n  FunctionalAnnotation : has_function\n\n  FunctionalAnnotation : subject\n\n      FunctionalAnnotation --> \"0..1\" GeneProduct : subject\n    click GeneProduct href \"../GeneProduct\"\n\n  FunctionalAnnotation : type\n\n  FunctionalAnnotation : was_generated_by\n\n      FunctionalAnnotation --> \"0..1\" MetagenomeAnnotation : was_generated_by\n    click MetagenomeAnnotation href \"../MetagenomeAnnotation\"\n\n\n\n
"},{"location":"FunctionalAnnotation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_function 0..1 String direct subject 0..1 GeneProduct direct was_generated_by 0..1 MetagenomeAnnotation\u00a0or\u00a0WorkflowExecution\u00a0or\u00a0DataGeneration provenance for the annotation direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct feature_category 0..1 ControlledIdentifiedTermValue A Sequence Ontology term that describes the category of a feature direct"},{"location":"FunctionalAnnotation/#usages","title":"Usages","text":"used by used in type used Database functional_annotation_set range FunctionalAnnotation"},{"location":"FunctionalAnnotation/#see-also","title":"See Also","text":""},{"location":"FunctionalAnnotation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FunctionalAnnotation/#schema-source","title":"Schema Source","text":""},{"location":"FunctionalAnnotation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FunctionalAnnotation native nmdc:FunctionalAnnotation narrow biolink:GeneToGoTermAssociation"},{"location":"FunctionalAnnotation/#linkml-source","title":"LinkML Source","text":""},{"location":"FunctionalAnnotation/#direct","title":"Direct","text":"
name: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n  by a gene product,  or which the gene product plays an active role in. Functional\n  annotations can be assigned manually by curators, or automatically in workflows.  In\n  the context of NMDC, all function annotation is performed automatically, typically\n  using HMM or Blast type methods\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslots:\n- has_function\n- subject\n- was_generated_by\n- type\n- feature_category\nslot_usage:\n  has_function:\n    name: has_function\n    notes:\n    - Still missing patterns for COG and RetroRules\n    - These patterns are not yet tied to the listed prefixes. A discussion about that\n      possibility had been started, including the question of whether these lists\n      are intended to be open examples or closed\n  was_generated_by:\n    name: was_generated_by\n    description: provenance for the annotation.\n    notes:\n    - To be consistent with the rest of the NMDC schema we use the PROV annotation\n      model, rather than GPAD\n    range: MetagenomeAnnotation\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\nclass_uri: nmdc:FunctionalAnnotation\n\n
"},{"location":"FunctionalAnnotation/#induced","title":"Induced","text":"
name: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n  by a gene product,  or which the gene product plays an active role in. Functional\n  annotations can be assigned manually by curators, or automatically in workflows.  In\n  the context of NMDC, all function annotation is performed automatically, typically\n  using HMM or Blast type methods\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslot_usage:\n  has_function:\n    name: has_function\n    notes:\n    - Still missing patterns for COG and RetroRules\n    - These patterns are not yet tied to the listed prefixes. A discussion about that\n      possibility had been started, including the question of whether these lists\n      are intended to be open examples or closed\n  was_generated_by:\n    name: was_generated_by\n    description: provenance for the annotation.\n    notes:\n    - To be consistent with the rest of the NMDC schema we use the PROV annotation\n      model, rather than GPAD\n    range: MetagenomeAnnotation\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\nattributes:\n  has_function:\n    name: has_function\n    notes:\n    - Still missing patterns for COG and RetroRules\n    - These patterns are not yet tied to the listed prefixes. A discussion about that\n      possibility had been started, including the question of whether these lists\n      are intended to be open examples or closed\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_function\n    owner: FunctionalAnnotation\n    domain_of:\n    - FunctionalAnnotation\n    range: string\n    pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n  subject:\n    name: subject\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: subject\n    owner: FunctionalAnnotation\n    domain_of:\n    - FunctionalAnnotation\n    range: GeneProduct\n  was_generated_by:\n    name: was_generated_by\n    description: provenance for the annotation.\n    notes:\n    - To be consistent with the rest of the NMDC schema we use the PROV annotation\n      model, rather than GPAD\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasGeneratedBy\n    rank: 1000\n    alias: was_generated_by\n    owner: FunctionalAnnotation\n    domain_of:\n    - FunctionalAnnotation\n    - DataObject\n    range: MetagenomeAnnotation\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n    any_of:\n    - range: WorkflowExecution\n    - range: DataGeneration\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FunctionalAnnotation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  feature_category:\n    name: feature_category\n    description: A Sequence Ontology term that describes the category of a feature\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: feature_category\n    owner: FunctionalAnnotation\n    domain_of:\n    - GenomeFeature\n    - FunctionalAnnotation\n    range: ControlledIdentifiedTermValue\nclass_uri: nmdc:FunctionalAnnotation\n\n
"},{"location":"FunctionalAnnotationAggMember/","title":"Class: FunctionalAnnotationAggMember","text":"

URI: nmdc:FunctionalAnnotationAggMember

classDiagram\n  class FunctionalAnnotationAggMember\n  click FunctionalAnnotationAggMember href \"../FunctionalAnnotationAggMember\"\n\n  FunctionalAnnotationAggMember : count\n\n  FunctionalAnnotationAggMember : gene_function_id\n\n  FunctionalAnnotationAggMember : metagenome_annotation_id\n\n      FunctionalAnnotationAggMember --> \"1\" WorkflowExecution : metagenome_annotation_id\n    click WorkflowExecution href \"../WorkflowExecution\"\n\n  FunctionalAnnotationAggMember : type\n\n\n\n
"},{"location":"FunctionalAnnotationAggMember/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance metagenome_annotation_id 1 WorkflowExecution\u00a0or\u00a0MetagenomeAnnotation\u00a0or\u00a0MetatranscriptomeAnnotation The identifier for the analysis activity that generated the functional annota... direct gene_function_id 1 Uriorcurie The identifier for the gene function direct count 1 Integer direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"FunctionalAnnotationAggMember/#usages","title":"Usages","text":"used by used in type used Database functional_annotation_agg range FunctionalAnnotationAggMember"},{"location":"FunctionalAnnotationAggMember/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FunctionalAnnotationAggMember/#schema-source","title":"Schema Source","text":""},{"location":"FunctionalAnnotationAggMember/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FunctionalAnnotationAggMember native nmdc:FunctionalAnnotationAggMember"},{"location":"FunctionalAnnotationAggMember/#linkml-source","title":"LinkML Source","text":""},{"location":"FunctionalAnnotationAggMember/#direct","title":"Direct","text":"
name: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- metagenome_annotation_id\n- gene_function_id\n- count\n- type\nslot_usage:\n  metagenome_annotation_id:\n    name: metagenome_annotation_id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\nclass_uri: nmdc:FunctionalAnnotationAggMember\n\n
"},{"location":"FunctionalAnnotationAggMember/#induced","title":"Induced","text":"
name: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n  metagenome_annotation_id:\n    name: metagenome_annotation_id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\nattributes:\n  metagenome_annotation_id:\n    name: metagenome_annotation_id\n    description: The identifier for the analysis activity that generated the functional\n      annotation results, where the analysis activity is an instance of the/an appropriate\n      subclass of WorkflowExecution\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: metagenome_annotation_id\n    owner: FunctionalAnnotationAggMember\n    domain_of:\n    - FunctionalAnnotationAggMember\n    range: WorkflowExecution\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n    any_of:\n    - range: MetagenomeAnnotation\n    - range: MetatranscriptomeAnnotation\n  gene_function_id:\n    name: gene_function_id\n    description: The identifier for the gene function.\n    examples:\n    - value: KEGG.ORTHOLOGY:K00627\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gene_function_id\n    owner: FunctionalAnnotationAggMember\n    domain_of:\n    - FunctionalAnnotationAggMember\n    range: uriorcurie\n    required: true\n  count:\n    name: count\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: count\n    owner: FunctionalAnnotationAggMember\n    domain_of:\n    - FunctionalAnnotationAggMember\n    range: integer\n    required: true\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FunctionalAnnotationAggMember\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FunctionalAnnotationAggMember\n\n
"},{"location":"FunctionalAnnotationTerm/","title":"Class: FunctionalAnnotationTerm","text":"

Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:FunctionalAnnotationTerm

classDiagram\n  class FunctionalAnnotationTerm\n  click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n    OntologyClass <|-- FunctionalAnnotationTerm\n      click OntologyClass href \"../OntologyClass\"\n\n\n    FunctionalAnnotationTerm <|-- Pathway\n      click Pathway href \"../Pathway\"\n    FunctionalAnnotationTerm <|-- OrthologyGroup\n      click OrthologyGroup href \"../OrthologyGroup\"\n\n\n\n  FunctionalAnnotationTerm : alternative_identifiers\n\n  FunctionalAnnotationTerm : description\n\n  FunctionalAnnotationTerm : id\n\n  FunctionalAnnotationTerm : name\n\n  FunctionalAnnotationTerm : type\n\n\n\n
"},{"location":"FunctionalAnnotationTerm/#inheritance","title":"Inheritance","text":""},{"location":"FunctionalAnnotationTerm/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"FunctionalAnnotationTerm/#aliases","title":"Aliases","text":""},{"location":"FunctionalAnnotationTerm/#todos","title":"TODOs","text":""},{"location":"FunctionalAnnotationTerm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FunctionalAnnotationTerm/#schema-source","title":"Schema Source","text":""},{"location":"FunctionalAnnotationTerm/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FunctionalAnnotationTerm native nmdc:FunctionalAnnotationTerm"},{"location":"FunctionalAnnotationTerm/#linkml-source","title":"LinkML Source","text":""},{"location":"FunctionalAnnotationTerm/#direct","title":"Direct","text":"
name: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n  a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming (Duncan, 2021-04-02)\n- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup\n  subclasses.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nclass_uri: nmdc:FunctionalAnnotationTerm\n\n
"},{"location":"FunctionalAnnotationTerm/#induced","title":"Induced","text":"
name: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n  a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming (Duncan, 2021-04-02)\n- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup\n  subclasses.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FunctionalAnnotationTerm\n\n
"},{"location":"FurnitureEnum/","title":"Enum: FurnitureEnum","text":"

URI: FurnitureEnum

"},{"location":"FurnitureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None chair None desks None"},{"location":"FurnitureEnum/#slots","title":"Slots","text":"Name Description furniture The types of furniture present in the sampled room"},{"location":"FurnitureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FurnitureEnum/#schema-source","title":"Schema Source","text":""},{"location":"FurnitureEnum/#linkml-source","title":"LinkML Source","text":"
name: furniture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  cabinet:\n    text: cabinet\n  chair:\n    text: chair\n  desks:\n    text: desks\n\n
"},{"location":"GenderRestroomEnum/","title":"Enum: GenderRestroomEnum","text":"

URI: GenderRestroomEnum

"},{"location":"GenderRestroomEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description all gender None female None gender neurtral None male None male and female None unisex None"},{"location":"GenderRestroomEnum/#slots","title":"Slots","text":"Name Description gender_restroom The gender type of the restroom"},{"location":"GenderRestroomEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GenderRestroomEnum/#schema-source","title":"Schema Source","text":""},{"location":"GenderRestroomEnum/#linkml-source","title":"LinkML Source","text":"
name: gender_restroom_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  all gender:\n    text: all gender\n  female:\n    text: female\n  gender neurtral:\n    text: gender neurtral\n  male:\n    text: male\n  male and female:\n    text: male and female\n  unisex:\n    text: unisex\n\n
"},{"location":"GeneProduct/","title":"Class: GeneProduct","text":"

A molecule encoded by a gene that has an evolved function

URI: nmdc:GeneProduct

classDiagram\n  class GeneProduct\n  click GeneProduct href \"../GeneProduct\"\n    NamedThing <|-- GeneProduct\n      click NamedThing href \"../NamedThing\"\n\n\n\n  GeneProduct : alternative_identifiers\n\n  GeneProduct : description\n\n  GeneProduct : id\n\n  GeneProduct : name\n\n  GeneProduct : type\n\n\n\n
"},{"location":"GeneProduct/#inheritance","title":"Inheritance","text":""},{"location":"GeneProduct/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"GeneProduct/#usages","title":"Usages","text":"used by used in type used PeptideQuantification all_proteins range GeneProduct PeptideQuantification best_protein range GeneProduct ProteinQuantification all_proteins range GeneProduct ProteinQuantification best_protein range GeneProduct GenomeFeature encodes range GeneProduct FunctionalAnnotation subject range GeneProduct"},{"location":"GeneProduct/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GeneProduct/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"GeneProduct/#schema-source","title":"Schema Source","text":""},{"location":"GeneProduct/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:GeneProduct native nmdc:GeneProduct exact biolink:GeneProduct"},{"location":"GeneProduct/#linkml-source","title":"LinkML Source","text":""},{"location":"GeneProduct/#direct","title":"Direct","text":"
name: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nclass_uri: nmdc:GeneProduct\n\n
"},{"location":"GeneProduct/#induced","title":"Induced","text":"
name: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: GeneProduct\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: GeneProduct\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: GeneProduct\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: GeneProduct\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: GeneProduct\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:GeneProduct\n\n
"},{"location":"GenomeFeature/","title":"Class: GenomeFeature","text":"

A feature localized to an interval along a genome

URI: nmdc:GenomeFeature

classDiagram\n  class GenomeFeature\n  click GenomeFeature href \"../GenomeFeature\"\n\n  GenomeFeature : encodes\n\n      GenomeFeature --> \"0..1\" GeneProduct : encodes\n    click GeneProduct href \"../GeneProduct\"\n\n  GenomeFeature : end\n\n  GenomeFeature : feature_category\n\n      GenomeFeature --> \"0..1\" ControlledIdentifiedTermValue : feature_category\n    click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n  GenomeFeature : feature_type\n\n  GenomeFeature : phase\n\n  GenomeFeature : seqid\n\n  GenomeFeature : start\n\n  GenomeFeature : strand\n\n  GenomeFeature : type\n\n\n\n
"},{"location":"GenomeFeature/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance encodes 0..1 GeneProduct The gene product encoded by this feature direct end 1 Integer The end of the feature in positive 1-based integer coordinates direct feature_type 0..1 String TODO: Yuri to write direct phase 0..1 Integer The phase for a coding sequence entity direct seqid 1 String The ID of the landmark used to establish the coordinate system for the curren... direct start 1 Integer The start of the feature in positive 1-based integer coordinates direct strand 0..1 String The strand on which a feature is located direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct feature_category 0..1 ControlledIdentifiedTermValue A Sequence Ontology term that describes the category of a feature direct"},{"location":"GenomeFeature/#usages","title":"Usages","text":"used by used in type used Database genome_feature_set range GenomeFeature"},{"location":"GenomeFeature/#comments","title":"Comments","text":""},{"location":"GenomeFeature/#see-also","title":"See Also","text":""},{"location":"GenomeFeature/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GenomeFeature/#schema-source","title":"Schema Source","text":""},{"location":"GenomeFeature/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:GenomeFeature native nmdc:GenomeFeature"},{"location":"GenomeFeature/#linkml-source","title":"LinkML Source","text":""},{"location":"GenomeFeature/#direct","title":"Direct","text":"
name: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslots:\n- encodes\n- end\n- feature_type\n- phase\n- seqid\n- start\n- strand\n- type\n- feature_category\nslot_usage:\n  seqid:\n    name: seqid\n    required: true\n  start:\n    name: start\n    required: true\n  end:\n    name: end\n    required: true\nclass_uri: nmdc:GenomeFeature\n\n
"},{"location":"GenomeFeature/#induced","title":"Induced","text":"
name: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslot_usage:\n  seqid:\n    name: seqid\n    required: true\n  start:\n    name: start\n    required: true\n  end:\n    name: end\n    required: true\nattributes:\n  encodes:\n    name: encodes\n    description: The gene product encoded by this feature. Typically this is used\n      for a CDS feature or gene feature which will encode a protein. It can also be\n      used by a nc transcript ot gene feature that encoded a ncRNA\n    todos:\n    - If we revert Reaction back into the schema, that would be a reasonable domain\n      for this slot\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: encodes\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: GeneProduct\n  end:\n    name: end\n    description: The end of the feature in positive 1-based integer coordinates\n    comments:\n    - '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n      feature,  end = the position of the end + the length of the landmark feature.\"'\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - biolink:end_interbase_coordinate\n    rank: 1000\n    is_a: gff_coordinate\n    alias: end\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: integer\n    required: true\n    minimum_value: 1\n  feature_type:\n    name: feature_type\n    description: 'TODO: Yuri to write'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: feature_type\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: string\n  phase:\n    name: phase\n    description: The phase for a coding sequence entity. For example, phase of a CDS\n      as represented in a GFF3 with a value of 0, 1 or 2.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - biolink:phase\n    rank: 1000\n    alias: phase\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: integer\n    minimum_value: 0\n    maximum_value: 2\n  seqid:\n    name: seqid\n    description: The ID of the landmark used to establish the coordinate system for\n      the current feature.\n    todos:\n    - change range from string to object\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: seqid\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: string\n    required: true\n  start:\n    name: start\n    description: The start of the feature in positive 1-based integer coordinates\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - biolink:start_interbase_coordinate\n    rank: 1000\n    is_a: gff_coordinate\n    alias: start\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: integer\n    required: true\n    minimum_value: 1\n  strand:\n    name: strand\n    description: The strand on which a feature is located. Has a value of '+' (sense\n      strand or forward strand) or  '-' (anti-sense strand or reverse strand).\n    todos:\n    - set the range to an enum?\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - biolink:strand\n    rank: 1000\n    alias: strand\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: GenomeFeature\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  feature_category:\n    name: feature_category\n    description: A Sequence Ontology term that describes the category of a feature\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: feature_category\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    - FunctionalAnnotation\n    range: ControlledIdentifiedTermValue\nclass_uri: nmdc:GenomeFeature\n\n
"},{"location":"GeolocationValue/","title":"Class: GeolocationValue","text":"

A normalized value for a location on the earth's surface

URI: nmdc:GeolocationValue

classDiagram\n  class GeolocationValue\n  click GeolocationValue href \"../GeolocationValue\"\n    AttributeValue <|-- GeolocationValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  GeolocationValue : has_raw_value\n\n  GeolocationValue : latitude\n\n  GeolocationValue : longitude\n\n  GeolocationValue : type\n\n\n\n
"},{"location":"GeolocationValue/#inheritance","title":"Inheritance","text":""},{"location":"GeolocationValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance latitude 1 DecimalDegree latitude direct longitude 1 DecimalDegree longitude direct has_raw_value 0..1 String The raw value for a geolocation should follow {latitude} {longitude} AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"GeolocationValue/#usages","title":"Usages","text":"used by used in type used FieldResearchSite lat_lon range GeolocationValue Biosample lat_lon range GeolocationValue"},{"location":"GeolocationValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GeolocationValue/#schema-source","title":"Schema Source","text":""},{"location":"GeolocationValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:GeolocationValue native nmdc:GeolocationValue undefined schema:GeoCoordinates"},{"location":"GeolocationValue/#linkml-source","title":"LinkML Source","text":""},{"location":"GeolocationValue/#direct","title":"Direct","text":"
name: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslots:\n- latitude\n- longitude\nslot_usage:\n  has_raw_value:\n    name: has_raw_value\n    description: The raw value for a geolocation should follow {latitude} {longitude}\n  latitude:\n    name: latitude\n    required: true\n  longitude:\n    name: longitude\n    required: true\nclass_uri: nmdc:GeolocationValue\n\n
"},{"location":"GeolocationValue/#induced","title":"Induced","text":"
name: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslot_usage:\n  has_raw_value:\n    name: has_raw_value\n    description: The raw value for a geolocation should follow {latitude} {longitude}\n  latitude:\n    name: latitude\n    required: true\n  longitude:\n    name: longitude\n    required: true\nattributes:\n  latitude:\n    name: latitude\n    description: latitude\n    examples:\n    - value: '-33.460524'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - schema:latitude\n    rank: 1000\n    slot_uri: wgs84:lat\n    alias: latitude\n    owner: GeolocationValue\n    domain_of:\n    - GeolocationValue\n    range: decimal degree\n    required: true\n  longitude:\n    name: longitude\n    description: longitude\n    examples:\n    - value: '150.168149'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - schema:longitude\n    rank: 1000\n    slot_uri: wgs84:long\n    alias: longitude\n    owner: GeolocationValue\n    domain_of:\n    - GeolocationValue\n    range: decimal degree\n    required: true\n  has_raw_value:\n    name: has_raw_value\n    description: The raw value for a geolocation should follow {latitude} {longitude}\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: GeolocationValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: GeolocationValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:GeolocationValue\n\n
"},{"location":"GrowthHabitEnum/","title":"Enum: GrowthHabitEnum","text":"

URI: GrowthHabitEnum

"},{"location":"GrowthHabitEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description erect None semi-erect None spreading None prostrate None"},{"location":"GrowthHabitEnum/#slots","title":"Slots","text":"Name Description growth_habit Characteristic shape, appearance or growth form of a plant species"},{"location":"GrowthHabitEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GrowthHabitEnum/#schema-source","title":"Schema Source","text":""},{"location":"GrowthHabitEnum/#linkml-source","title":"LinkML Source","text":"
name: growth_habit_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  erect:\n    text: erect\n  semi-erect:\n    text: semi-erect\n  spreading:\n    text: spreading\n  prostrate:\n    text: prostrate\n\n
"},{"location":"HandidnessEnum/","title":"Enum: HandidnessEnum","text":"

URI: HandidnessEnum

"},{"location":"HandidnessEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ambidexterity None left handedness None mixed-handedness None right handedness None"},{"location":"HandidnessEnum/#slots","title":"Slots","text":"Name Description handidness The handidness of the individual sampled"},{"location":"HandidnessEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HandidnessEnum/#schema-source","title":"Schema Source","text":""},{"location":"HandidnessEnum/#linkml-source","title":"LinkML Source","text":"
name: handidness_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  ambidexterity:\n    text: ambidexterity\n  left handedness:\n    text: left handedness\n  mixed-handedness:\n    text: mixed-handedness\n  right handedness:\n    text: right handedness\n\n
"},{"location":"HcProducedEnum/","title":"Enum: HcProducedEnum","text":"

URI: HcProducedEnum

"},{"location":"HcProducedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil None Gas-Condensate None Gas None Bitumen None Coalbed Methane None other None"},{"location":"HcProducedEnum/#slots","title":"Slots","text":"Name Description hc_produced Main hydrocarbon type produced from resource (i"},{"location":"HcProducedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcProducedEnum/#schema-source","title":"Schema Source","text":""},{"location":"HcProducedEnum/#linkml-source","title":"LinkML Source","text":"
name: hc_produced_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Oil:\n    text: Oil\n  Gas-Condensate:\n    text: Gas-Condensate\n  Gas:\n    text: Gas\n  Bitumen:\n    text: Bitumen\n  Coalbed Methane:\n    text: Coalbed Methane\n  other:\n    text: other\n\n
"},{"location":"HcrEnum/","title":"Enum: HcrEnum","text":"

URI: HcrEnum

"},{"location":"HcrEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil Reservoir None Gas Reservoir None Oil Sand None Coalbed None Shale None Tight Oil Reservoir None Tight Gas Reservoir None other None"},{"location":"HcrEnum/#slots","title":"Slots","text":"Name Description hcr Main Hydrocarbon Resource type"},{"location":"HcrEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrEnum/#schema-source","title":"Schema Source","text":""},{"location":"HcrEnum/#linkml-source","title":"LinkML Source","text":"
name: hcr_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Oil Reservoir:\n    text: Oil Reservoir\n  Gas Reservoir:\n    text: Gas Reservoir\n  Oil Sand:\n    text: Oil Sand\n  Coalbed:\n    text: Coalbed\n  Shale:\n    text: Shale\n  Tight Oil Reservoir:\n    text: Tight Oil Reservoir\n  Tight Gas Reservoir:\n    text: Tight Gas Reservoir\n  other:\n    text: other\n\n
"},{"location":"HcrGeolAgeEnum/","title":"Enum: HcrGeolAgeEnum","text":"

URI: HcrGeolAgeEnum

"},{"location":"HcrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"HcrGeolAgeEnum/#slots","title":"Slots","text":"Name Description hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en"},{"location":"HcrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrGeolAgeEnum/#schema-source","title":"Schema Source","text":""},{"location":"HcrGeolAgeEnum/#linkml-source","title":"LinkML Source","text":"
name: hcr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Archean:\n    text: Archean\n  Cambrian:\n    text: Cambrian\n  Carboniferous:\n    text: Carboniferous\n  Cenozoic:\n    text: Cenozoic\n  Cretaceous:\n    text: Cretaceous\n  Devonian:\n    text: Devonian\n  Jurassic:\n    text: Jurassic\n  Mesozoic:\n    text: Mesozoic\n  Neogene:\n    text: Neogene\n  Ordovician:\n    text: Ordovician\n  Paleogene:\n    text: Paleogene\n  Paleozoic:\n    text: Paleozoic\n  Permian:\n    text: Permian\n  Precambrian:\n    text: Precambrian\n  Proterozoic:\n    text: Proterozoic\n  Silurian:\n    text: Silurian\n  Triassic:\n    text: Triassic\n  other:\n    text: other\n\n
"},{"location":"HeatCoolTypeEnum/","title":"Enum: HeatCoolTypeEnum","text":"

URI: HeatCoolTypeEnum

"},{"location":"HeatCoolTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description radiant system None heat pump None forced air system None steam forced heat None wood stove None"},{"location":"HeatCoolTypeEnum/#slots","title":"Slots","text":"Name Description heat_cool_type Methods of conditioning or heating a room or building"},{"location":"HeatCoolTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatCoolTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"HeatCoolTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: heat_cool_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  radiant system:\n    text: radiant system\n  heat pump:\n    text: heat pump\n  forced air system:\n    text: forced air system\n  steam forced heat:\n    text: steam forced heat\n  wood stove:\n    text: wood stove\n\n
"},{"location":"HeatDelivLocEnum/","title":"Enum: HeatDelivLocEnum","text":"

URI: HeatDelivLocEnum

"},{"location":"HeatDelivLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"HeatDelivLocEnum/#slots","title":"Slots","text":"Name Description heat_deliv_loc The location of heat delivery within the room"},{"location":"HeatDelivLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatDelivLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"HeatDelivLocEnum/#linkml-source","title":"LinkML Source","text":"
name: heat_deliv_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n\n
"},{"location":"HostSexEnum/","title":"Enum: HostSexEnum","text":"

URI: HostSexEnum

"},{"location":"HostSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description female None hermaphrodite None male None neuter None"},{"location":"HostSexEnum/#slots","title":"Slots","text":"Name Description host_sex Gender or physical sex of the host"},{"location":"HostSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HostSexEnum/#schema-source","title":"Schema Source","text":""},{"location":"HostSexEnum/#linkml-source","title":"LinkML Source","text":"
name: host_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  female:\n    text: female\n  hermaphrodite:\n    text: hermaphrodite\n  male:\n    text: male\n  neuter:\n    text: neuter\n\n
"},{"location":"ImageValue/","title":"Class: ImageValue","text":"

An attribute value representing an image.

URI: nmdc:ImageValue

classDiagram\n  class ImageValue\n  click ImageValue href \"../ImageValue\"\n    AttributeValue <|-- ImageValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  ImageValue : description\n\n  ImageValue : display_order\n\n  ImageValue : has_raw_value\n\n  ImageValue : type\n\n  ImageValue : url\n\n\n\n
"},{"location":"ImageValue/#inheritance","title":"Inheritance","text":""},{"location":"ImageValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance url 0..1 String direct description 0..1 String a human-readable description of a thing direct display_order 0..1 Integer When rendering information, this attribute to specify the order in which the ... direct has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"ImageValue/#usages","title":"Usages","text":"used by used in type used Study study_image range ImageValue"},{"location":"ImageValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ImageValue/#schema-source","title":"Schema Source","text":""},{"location":"ImageValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ImageValue native nmdc:ImageValue"},{"location":"ImageValue/#linkml-source","title":"LinkML Source","text":""},{"location":"ImageValue/#direct","title":"Direct","text":"
name: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- url\n- description\n- display_order\nclass_uri: nmdc:ImageValue\n\n
"},{"location":"ImageValue/#induced","title":"Induced","text":"
name: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n  url:\n    name: url\n    notes:\n    - See issue 207 - this clashes with the mixs field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: url\n    owner: ImageValue\n    domain_of:\n    - ImageValue\n    - Protocol\n    - DataObject\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ImageValue\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  display_order:\n    name: display_order\n    description: When rendering information, this attribute to specify the order in\n      which the information should be rendered.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: display_order\n    owner: ImageValue\n    domain_of:\n    - ImageValue\n    range: integer\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: ImageValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ImageValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ImageValue\n\n
"},{"location":"IndoorSpaceEnum/","title":"Enum: IndoorSpaceEnum","text":"

URI: IndoorSpaceEnum

"},{"location":"IndoorSpaceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bedroom None office None bathroom None foyer None kitchen None locker room None hallway None elevator None"},{"location":"IndoorSpaceEnum/#slots","title":"Slots","text":"Name Description indoor_space A distinguishable space within a structure, the purpose for which discrete ar..."},{"location":"IndoorSpaceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSpaceEnum/#schema-source","title":"Schema Source","text":""},{"location":"IndoorSpaceEnum/#linkml-source","title":"LinkML Source","text":"
name: indoor_space_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  bedroom:\n    text: bedroom\n  office:\n    text: office\n  bathroom:\n    text: bathroom\n  foyer:\n    text: foyer\n  kitchen:\n    text: kitchen\n  locker room:\n    text: locker room\n  hallway:\n    text: hallway\n  elevator:\n    text: elevator\n\n
"},{"location":"IndoorSurfEnum/","title":"Enum: IndoorSurfEnum","text":"

URI: IndoorSurfEnum

"},{"location":"IndoorSurfEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None ceiling None counter top None door None shelving None vent cover None window None wall None"},{"location":"IndoorSurfEnum/#slots","title":"Slots","text":"Name Description indoor_surf Type of indoor surface"},{"location":"IndoorSurfEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSurfEnum/#schema-source","title":"Schema Source","text":""},{"location":"IndoorSurfEnum/#linkml-source","title":"LinkML Source","text":"
name: indoor_surf_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  cabinet:\n    text: cabinet\n  ceiling:\n    text: ceiling\n  counter top:\n    text: counter top\n  door:\n    text: door\n  shelving:\n    text: shelving\n  vent cover:\n    text: vent cover\n  window:\n    text: window\n  wall:\n    text: wall\n\n
"},{"location":"InformationObject/","title":"Class: InformationObject","text":"

Any data or knowledge that reduces uncertainty or enhances understanding about a system, process, or entity.

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:InformationObject

classDiagram\n  class InformationObject\n  click InformationObject href \"../InformationObject\"\n    NamedThing <|-- InformationObject\n      click NamedThing href \"../NamedThing\"\n\n\n    InformationObject <|-- Configuration\n      click Configuration href \"../Configuration\"\n    InformationObject <|-- Manifest\n      click Manifest href \"../Manifest\"\n    InformationObject <|-- DataObject\n      click DataObject href \"../DataObject\"\n    InformationObject <|-- CalibrationInformation\n      click CalibrationInformation href \"../CalibrationInformation\"\n\n\n\n  InformationObject : alternative_identifiers\n\n  InformationObject : description\n\n  InformationObject : id\n\n  InformationObject : name\n\n  InformationObject : type\n\n\n\n
"},{"location":"InformationObject/#inheritance","title":"Inheritance","text":""},{"location":"InformationObject/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"InformationObject/#comments","title":"Comments","text":""},{"location":"InformationObject/#see-also","title":"See Also","text":""},{"location":"InformationObject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InformationObject/#schema-source","title":"Schema Source","text":""},{"location":"InformationObject/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:InformationObject native nmdc:InformationObject"},{"location":"InformationObject/#linkml-source","title":"LinkML Source","text":""},{"location":"InformationObject/#direct","title":"Direct","text":"
name: InformationObject\ndescription: Any data or knowledge that reduces uncertainty or enhances understanding\n  about a system, process, or entity.\ncomments:\n- The direct subclasses of NamedThing should aggregate the relevant classes and make\n  them uniform. PlannedProcess and MaterialEntity are clearly disjoint. Let's do the\n  same thing for our modelling of things that don't consist of matter and aren't processes.\n- InformationObjects may include embedded data or links to external resources via\n  the url slot\n- May appear as output from a process, inputs into a process, or both\n- All slots relating one class to a InformationObject should be is_a sub-properties\n  of has_input or has_output, if they are multivalued or otherwise organized\n- Historically information about many classes has been inlined into the class. This\n  is an alternative pattern.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:AttributeValue\nis_a: NamedThing\nabstract: true\nclass_uri: nmdc:InformationObject\n\n
"},{"location":"InformationObject/#induced","title":"Induced","text":"
name: InformationObject\ndescription: Any data or knowledge that reduces uncertainty or enhances understanding\n  about a system, process, or entity.\ncomments:\n- The direct subclasses of NamedThing should aggregate the relevant classes and make\n  them uniform. PlannedProcess and MaterialEntity are clearly disjoint. Let's do the\n  same thing for our modelling of things that don't consist of matter and aren't processes.\n- InformationObjects may include embedded data or links to external resources via\n  the url slot\n- May appear as output from a process, inputs into a process, or both\n- All slots relating one class to a InformationObject should be is_a sub-properties\n  of has_input or has_output, if they are multivalued or otherwise organized\n- Historically information about many classes has been inlined into the class. This\n  is an alternative pattern.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:AttributeValue\nis_a: NamedThing\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: InformationObject\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: InformationObject\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: InformationObject\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: InformationObject\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: InformationObject\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:InformationObject\n\n
"},{"location":"Instrument/","title":"Class: Instrument","text":"

A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.

URI: nmdc:Instrument

classDiagram\n  class Instrument\n  click Instrument href \"../Instrument\"\n    MaterialEntity <|-- Instrument\n      click MaterialEntity href \"../MaterialEntity\"\n\n\n\n  Instrument : alternative_identifiers\n\n  Instrument : description\n\n  Instrument : id\n\n  Instrument : model\n\n      Instrument --> \"0..1\" InstrumentModelEnum : model\n    click InstrumentModelEnum href \"../InstrumentModelEnum\"\n\n  Instrument : name\n\n  Instrument : type\n\n  Instrument : vendor\n\n      Instrument --> \"0..1\" InstrumentVendorEnum : vendor\n    click InstrumentVendorEnum href \"../InstrumentVendorEnum\"\n\n\n\n
"},{"location":"Instrument/#inheritance","title":"Inheritance","text":""},{"location":"Instrument/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance vendor 0..1 InstrumentVendorEnum direct model 0..1 InstrumentModelEnum direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Instrument/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing instrument_used range Instrument MassSpectrometry instrument_used range Instrument Database instrument_set range Instrument Pooling instrument_used range Instrument Extraction instrument_used range Instrument LibraryPreparation instrument_used range Instrument SubSamplingProcess instrument_used range Instrument MixingProcess instrument_used range Instrument FiltrationProcess instrument_used range Instrument ChromatographicSeparationProcess instrument_used range Instrument DissolvingProcess instrument_used range Instrument ChemicalConversionProcess instrument_used range Instrument MaterialProcessing instrument_used range Instrument DataGeneration instrument_used range Instrument"},{"location":"Instrument/#aliases","title":"Aliases","text":""},{"location":"Instrument/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Instrument/#schema-source","title":"Schema Source","text":""},{"location":"Instrument/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Instrument native nmdc:Instrument exact OBI:0000968"},{"location":"Instrument/#linkml-source","title":"LinkML Source","text":""},{"location":"Instrument/#direct","title":"Direct","text":"
name: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n  investigation, but is not a reagent.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000968\nis_a: MaterialEntity\nslots:\n- vendor\n- model\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:Instrument\n\n
"},{"location":"Instrument/#induced","title":"Induced","text":"
name: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n  investigation, but is not a reagent.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000968\nis_a: MaterialEntity\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  vendor:\n    name: vendor\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: vendor\n    owner: Instrument\n    domain_of:\n    - Instrument\n    range: InstrumentVendorEnum\n  model:\n    name: model\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: model\n    owner: Instrument\n    domain_of:\n    - Instrument\n    range: InstrumentModelEnum\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Instrument\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Instrument\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Instrument\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Instrument\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Instrument\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Instrument\n\n
"},{"location":"InstrumentModelEnum/","title":"Enum: InstrumentModelEnum","text":"

URI: InstrumentModelEnum

"},{"location":"InstrumentModelEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description exploris_21T None exploris_240 None exploris_480 None ltq_orbitrap_velos None orbitrap_fusion_lumos None orbitrap_eclipse_tribid None orbitrap_q_exactive None solarix_7T None solarix_12T None solarix_15T None agilent_8890A None agilent_7980A None vortex_genie_2 None novaseq None novaseq_6000 OBI:0002630 novaseq_x None hiseq None hiseq_1000 OBI:0002022 hiseq_1500 OBI:0003386 hiseq_2000 OBI:0002001 hiseq_2500 OBI:0002002 hiseq_3000 OBI:0002048 hiseq_4000 OBI:0002049 hiseq_x_ten OBI:0002129 miniseq OBI:0003114 miseq OBI:0002003 nextseq_1000 OBI:0003606 nextseq None nextseq_500 OBI:0002021 nextseq_550 OBI:0003387 gridion OBI:0002751 minion OBI:0002750 promethion OBI:0002752 rs_II OBI:0002012 sequel OBI:0002632 sequel_II OBI:0002633 revio None"},{"location":"InstrumentModelEnum/#slots","title":"Slots","text":"Name Description model"},{"location":"InstrumentModelEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InstrumentModelEnum/#schema-source","title":"Schema Source","text":""},{"location":"InstrumentModelEnum/#linkml-source","title":"LinkML Source","text":"
name: InstrumentModelEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  exploris_21T:\n    text: exploris_21T\n    aliases:\n    - Exploris 21T\n  exploris_240:\n    text: exploris_240\n    aliases:\n    - Orbitrap Exploris 240\n  exploris_480:\n    text: exploris_480\n    aliases:\n    - Orbitrap Exploris 480\n  ltq_orbitrap_velos:\n    text: ltq_orbitrap_velos\n    aliases:\n    - LTQ Orbitrap Velos\n    - LTQ Orbitrap Velos ETD\n    - Velos\n  orbitrap_fusion_lumos:\n    text: orbitrap_fusion_lumos\n    aliases:\n    - Orbitrap Fusion Lumos\n    - Fusion\n  orbitrap_eclipse_tribid:\n    text: orbitrap_eclipse_tribid\n    aliases:\n    - Orbitrap Eclipse Tribid\n    - Eclipse\n  orbitrap_q_exactive:\n    text: orbitrap_q_exactive\n    aliases:\n    - Orbitrap Q-Exactive HF\n    - Orbitrap Q-Exactive HF-X\n  solarix_7T:\n    text: solarix_7T\n    aliases:\n    - 7T Solarix\n    - 7T FT-ICR MS\n    - 7T MRMS\n  solarix_12T:\n    text: solarix_12T\n    aliases:\n    - 12T Solarix\n    - 12T FT-ICR MS\n    - 12T MRMS\n  solarix_15T:\n    text: solarix_15T\n    aliases:\n    - 15T Solarix\n    - 15T FT-ICR MS\n    - 15T MRMS\n  agilent_8890A:\n    text: agilent_8890A\n    aliases:\n    - 8890A GC-MS\n    - Agilent GC MS\n  agilent_7980A:\n    text: agilent_7980A\n    aliases:\n    - 7980A GC-MS\n    - Agilent GC MS\n  vortex_genie_2:\n    text: vortex_genie_2\n    aliases:\n    - VortexGenie2\n  novaseq:\n    text: novaseq\n    aliases:\n    - NovaSeq\n    - Illumina NovaSeq\n  novaseq_6000:\n    text: novaseq_6000\n    meaning: OBI:0002630\n    comments:\n    - Possible flowcell versions are SP, S1, S2, S4.\n    see_also:\n    - https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html\n    aliases:\n    - NovaSeq 6000\n    - Illumina NovaSeq 6000\n    structured_aliases:\n      Illumina NovaSeq S2:\n        literal_form: Illumina NovaSeq S2\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n      Illumina NovaSeq S4:\n        literal_form: Illumina NovaSeq S4\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n      Illumina NovaSeq SP:\n        literal_form: Illumina NovaSeq SP\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n  novaseq_x:\n    text: novaseq_x\n    comments:\n    - Possible flowcell versions are 1.5B, 10B, 25B. Only difference between X and\n      X Plus is 2 flowcells for X Plus versus 1 flowcell for X.\n    see_also:\n    - https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html\n    aliases:\n    - Illumina NovaSeq X\n    - Illumina NovaSeq X Plus\n  hiseq:\n    text: hiseq\n    aliases:\n    - Illumina HiSeq\n  hiseq_1000:\n    text: hiseq_1000\n    meaning: OBI:0002022\n    aliases:\n    - Illumina HiSeq 1000\n  hiseq_1500:\n    text: hiseq_1500\n    meaning: OBI:0003386\n    aliases:\n    - Illumina HiSeq 1500\n  hiseq_2000:\n    text: hiseq_2000\n    meaning: OBI:0002001\n    aliases:\n    - Illumina HiSeq 2000\n  hiseq_2500:\n    text: hiseq_2500\n    meaning: OBI:0002002\n    aliases:\n    - Illumina HiSeq 2500\n    structured_aliases:\n      Illumina HiSeq 2500-1TB:\n        literal_form: Illumina HiSeq 2500-1TB\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n      Illumina HiSeq 2500-Rapid:\n        literal_form: Illumina HiSeq 2500-Rapid\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n  hiseq_3000:\n    text: hiseq_3000\n    meaning: OBI:0002048\n    aliases:\n    - Illumina HiSeq 3000\n  hiseq_4000:\n    text: hiseq_4000\n    meaning: OBI:0002049\n    aliases:\n    - Illumina HiSeq 4000\n  hiseq_x_ten:\n    text: hiseq_x_ten\n    meaning: OBI:0002129\n    aliases:\n    - Illumina HiSeq X Ten\n  miniseq:\n    text: miniseq\n    meaning: OBI:0003114\n    aliases:\n    - Illumina MiniSeq\n  miseq:\n    text: miseq\n    meaning: OBI:0002003\n    aliases:\n    - MiSeq\n    - Illumina MiSeq\n  nextseq_1000:\n    text: nextseq_1000\n    meaning: OBI:0003606\n    aliases:\n    - Illumina NextSeq 1000\n  nextseq:\n    text: nextseq\n    aliases:\n    - NextSeq\n    - Illumina NextSeq\n    structured_aliases:\n      Illumina NextSeq-HO:\n        literal_form: Illumina NextSeq-HO\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n      Illumina NextSeq-MO:\n        literal_form: Illumina NextSeq-MO\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n  nextseq_500:\n    text: nextseq_500\n    meaning: OBI:0002021\n    aliases:\n    - NextSeq 500\n    - Illumina NextSeq 500\n  nextseq_550:\n    text: nextseq_550\n    meaning: OBI:0003387\n    aliases:\n    - NextSeq 550\n    - Illumina NextSeq 550\n  gridion:\n    text: gridion\n    meaning: OBI:0002751\n    aliases:\n    - Oxford Nanopore GridION Mk1\n  minion:\n    text: minion\n    meaning: OBI:0002750\n    aliases:\n    - Oxford Nanopore MinION\n  promethion:\n    text: promethion\n    meaning: OBI:0002752\n    aliases:\n    - Oxford Nanopore PromethION\n  rs_II:\n    text: rs_II\n    meaning: OBI:0002012\n    aliases:\n    - PacBio RS II\n  sequel:\n    text: sequel\n    meaning: OBI:0002632\n    aliases:\n    - PacBio Sequel\n  sequel_II:\n    text: sequel_II\n    meaning: OBI:0002633\n    aliases:\n    - PacBio Sequel II\n  revio:\n    text: revio\n    aliases:\n    - PacBio Revio\n    - Revio\n\n
"},{"location":"InstrumentVendorEnum/","title":"Enum: InstrumentVendorEnum","text":"

URI: InstrumentVendorEnum

"},{"location":"InstrumentVendorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description waters None agilent None bruker None thermo_fisher None vwr None perkin_elmer None gilson None scientific_industries None illumina OBI:0000759 pacbio OBI:0001856 oxford_nanopore OBI:0002755 pnnl None"},{"location":"InstrumentVendorEnum/#slots","title":"Slots","text":"Name Description vendor"},{"location":"InstrumentVendorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InstrumentVendorEnum/#schema-source","title":"Schema Source","text":""},{"location":"InstrumentVendorEnum/#linkml-source","title":"LinkML Source","text":"
name: InstrumentVendorEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  waters:\n    text: waters\n    aliases:\n    - Waters Corporation\n  agilent:\n    text: agilent\n    aliases:\n    - Agilent Technologies\n  bruker:\n    text: bruker\n    aliases:\n    - Bruker Corporation\n    - Bruker Daltonics\n  thermo_fisher:\n    text: thermo_fisher\n    aliases:\n    - ThermoFisher\n    - Thermo Fisher Scientific\n  vwr:\n    text: vwr\n  perkin_elmer:\n    text: perkin_elmer\n  gilson:\n    text: gilson\n  scientific_industries:\n    text: scientific_industries\n  illumina:\n    text: illumina\n    meaning: OBI:0000759\n    aliases:\n    - Illumina\n  pacbio:\n    text: pacbio\n    meaning: OBI:0001856\n    aliases:\n    - PacBio\n    - Pacific Biosciences\n  oxford_nanopore:\n    text: oxford_nanopore\n    meaning: OBI:0002755\n    aliases:\n    - Oxford Nanopore Technologies\n  pnnl:\n    text: pnnl\n    aliases:\n    - PNNL\n\n
"},{"location":"IntWallCondEnum/","title":"Enum: IntWallCondEnum","text":"

URI: IntWallCondEnum

"},{"location":"IntWallCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"IntWallCondEnum/#slots","title":"Slots","text":"Name Description int_wall_cond The physical condition of the wall at the time of sampling; photos or video p..."},{"location":"IntWallCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IntWallCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"IntWallCondEnum/#linkml-source","title":"LinkML Source","text":"
name: int_wall_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  new:\n    text: new\n  visible wear:\n    text: visible wear\n  needs repair:\n    text: needs repair\n  damaged:\n    text: damaged\n  rupture:\n    text: rupture\n\n
"},{"location":"Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Integer/#schema-source","title":"Schema Source","text":""},{"location":"Integer/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:integer native nmdc:integer exact schema:Integer"},{"location":"Investigation/","title":"Subset: Investigation","text":"

URI: Investigation

"},{"location":"Investigation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Investigation/#schema-source","title":"Schema Source","text":""},{"location":"IonizationSourceEnum/","title":"Enum: IonizationSourceEnum","text":"

URI: IonizationSourceEnum

"},{"location":"IonizationSourceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description electrospray_ionization None matrix_assisted_laser_desorption_ionization None atmospheric_pressure_photo_ionization None atmospheric_pressure_chemical_ionization None electron_ionization None"},{"location":"IonizationSourceEnum/#slots","title":"Slots","text":"Name Description ionization_source The ionization source used to introduce processed samples into a mass spectro..."},{"location":"IonizationSourceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IonizationSourceEnum/#schema-source","title":"Schema Source","text":""},{"location":"IonizationSourceEnum/#linkml-source","title":"LinkML Source","text":"
name: IonizationSourceEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  electrospray_ionization:\n    text: electrospray_ionization\n    aliases:\n    - ESI\n  matrix_assisted_laser_desorption_ionization:\n    text: matrix_assisted_laser_desorption_ionization\n    aliases:\n    - MALDI\n  atmospheric_pressure_photo_ionization:\n    text: atmospheric_pressure_photo_ionization\n    aliases:\n    - APPI\n  atmospheric_pressure_chemical_ionization:\n    text: atmospheric_pressure_chemical_ionization\n    aliases:\n    - APCI\n  electron_ionization:\n    text: electron_ionization\n    aliases:\n    - EI\n\n
"},{"location":"JgiContTypeEnum/","title":"Enum: JgiContTypeEnum","text":"

URI: JgiContTypeEnum

"},{"location":"JgiContTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plate None tube None"},{"location":"JgiContTypeEnum/#slots","title":"Slots","text":"Name Description dna_cont_type Tube or plate (96-well) rna_cont_type Tube or plate (96-well)"},{"location":"JgiContTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"JgiContTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"JgiContTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: JgiContTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  plate:\n    text: plate\n  tube:\n    text: tube\n\n
"},{"location":"Jsonpath/","title":"Type: Jsonpath","text":"

A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.

URI: xsd:string

"},{"location":"Jsonpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Jsonpath/#schema-source","title":"Schema Source","text":""},{"location":"Jsonpath/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:jsonpath"},{"location":"Jsonpointer/","title":"Type: Jsonpointer","text":"

A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.

URI: xsd:string

"},{"location":"Jsonpointer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Jsonpointer/#schema-source","title":"Schema Source","text":""},{"location":"Jsonpointer/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:jsonpointer"},{"location":"LanguageCode/","title":"Type: LanguageCode","text":"

A language code conforming to ISO_639-1

URI: xsd:language

"},{"location":"LanguageCode/#see-also","title":"See Also","text":""},{"location":"LanguageCode/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LanguageCode/#schema-source","title":"Schema Source","text":""},{"location":"LanguageCode/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:language native nmdc:language_code"},{"location":"LibraryPreparation/","title":"Class: LibraryPreparation","text":"

URI: nmdc:LibraryPreparation

classDiagram\n  class LibraryPreparation\n  click LibraryPreparation href \"../LibraryPreparation\"\n    MaterialProcessing <|-- LibraryPreparation\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  LibraryPreparation : alternative_identifiers\n\n  LibraryPreparation : description\n\n  LibraryPreparation : end_date\n\n  LibraryPreparation : has_failure_categorization\n\n      LibraryPreparation --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  LibraryPreparation : has_input\n\n      LibraryPreparation --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  LibraryPreparation : has_output\n\n      LibraryPreparation --> \"1..*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  LibraryPreparation : id\n\n  LibraryPreparation : instrument_used\n\n      LibraryPreparation --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  LibraryPreparation : is_stranded\n\n  LibraryPreparation : library_preparation_kit\n\n  LibraryPreparation : library_type\n\n      LibraryPreparation --> \"0..1\" LibraryTypeEnum : library_type\n    click LibraryTypeEnum href \"../LibraryTypeEnum\"\n\n  LibraryPreparation : name\n\n  LibraryPreparation : nucl_acid_amp\n\n      LibraryPreparation --> \"0..1\" TextValue : nucl_acid_amp\n    click TextValue href \"../TextValue\"\n\n  LibraryPreparation : pcr_cond\n\n      LibraryPreparation --> \"0..1\" TextValue : pcr_cond\n    click TextValue href \"../TextValue\"\n\n  LibraryPreparation : pcr_cycles\n\n  LibraryPreparation : pcr_primers\n\n      LibraryPreparation --> \"0..1\" TextValue : pcr_primers\n    click TextValue href \"../TextValue\"\n\n  LibraryPreparation : processing_institution\n\n      LibraryPreparation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  LibraryPreparation : protocol_link\n\n      LibraryPreparation --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  LibraryPreparation : qc_comment\n\n  LibraryPreparation : qc_status\n\n      LibraryPreparation --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  LibraryPreparation : start_date\n\n  LibraryPreparation : stranded_orientation\n\n      LibraryPreparation --> \"0..1\" StrandedOrientationEnum : stranded_orientation\n    click StrandedOrientationEnum href \"../StrandedOrientationEnum\"\n\n  LibraryPreparation : type\n\n\n\n
"},{"location":"LibraryPreparation/#inheritance","title":"Inheritance","text":""},{"location":"LibraryPreparation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance is_stranded 0..1 Boolean Is the (RNA) library stranded or non-stranded (unstranded) direct library_preparation_kit 0..1 String direct library_type 0..1 LibraryTypeEnum direct nucl_acid_amp 0..1 TextValue A link to a literature reference, electronic resource or a standard operating... direct pcr_cond 0..1 TextValue Description of reaction conditions and components of polymerase chain reactio... direct pcr_cycles 0..1 Integer direct pcr_primers 0..1 TextValue PCR primers that were used to amplify the sequence of the targeted gene, locu... direct stranded_orientation 0..1 StrandedOrientationEnum Lists the strand orientiation for a stranded RNA library preparation direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output 1..* ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"LibraryPreparation/#aliases","title":"Aliases","text":""},{"location":"LibraryPreparation/#comments","title":"Comments","text":""},{"location":"LibraryPreparation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LibraryPreparation/#schema-source","title":"Schema Source","text":""},{"location":"LibraryPreparation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:LibraryPreparation native nmdc:LibraryPreparation close OBI:0000711"},{"location":"LibraryPreparation/#linkml-source","title":"LinkML Source","text":""},{"location":"LibraryPreparation/#direct","title":"Direct","text":"
name: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: MaterialProcessing\nslots:\n- is_stranded\n- library_preparation_kit\n- library_type\n- nucl_acid_amp\n- pcr_cond\n- pcr_cycles\n- pcr_primers\n- stranded_orientation\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  pcr_cond:\n    name: pcr_cond\n    description: Description of reaction conditions and components of polymerase chain\n      reaction performed during library preparation\nclass_uri: nmdc:LibraryPreparation\n\n
"},{"location":"LibraryPreparation/#induced","title":"Induced","text":"
name: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: MaterialProcessing\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  pcr_cond:\n    name: pcr_cond\n    description: Description of reaction conditions and components of polymerase chain\n      reaction performed during library preparation\nattributes:\n  is_stranded:\n    name: is_stranded\n    description: Is the (RNA) library stranded or non-stranded (unstranded).\n    comments:\n    - A value of true means the library is stranded, flase means non-stranded.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: is_stranded\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: boolean\n  library_preparation_kit:\n    name: library_preparation_kit\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: library_preparation_kit\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: string\n  library_type:\n    name: library_type\n    title: library type\n    examples:\n    - value: DNA\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: library_type\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: LibraryTypeEnum\n  nucl_acid_amp:\n    name: nucl_acid_amp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID, DOI or URL\n    description: A link to a literature reference, electronic resource or a standard\n      operating procedure (SOP), that describes the enzymatic amplification (PCR,\n      TMA, NASBA) of specific nucleic acids\n    title: nucleic acid amplification\n    examples:\n    - value: https://phylogenomics.me/protocols/16s-pcr-protocol/\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - nucleic acid amplification\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000038\n    alias: nucl_acid_amp\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: TextValue\n    multivalued: false\n  pcr_cond:\n    name: pcr_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n          elongation:degrees_minutes;total cycles\n    description: Description of reaction conditions and components of polymerase chain\n      reaction performed during library preparation\n    title: pcr conditions\n    examples:\n    - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pcr conditions\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n      elongation:degrees_minutes;total cycles\n    slot_uri: MIXS:0000049\n    alias: pcr_cond\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: TextValue\n    multivalued: false\n  pcr_cycles:\n    name: pcr_cycles\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - OBI:0002475\n    rank: 1000\n    alias: pcr_cycles\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: integer\n  pcr_primers:\n    name: pcr_primers\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: 'FWD: forward primer sequence;REV:reverse primer sequence'\n    description: PCR primers that were used to amplify the sequence of the targeted\n      gene, locus or subfragment. This field should contain all the primers used for\n      a single PCR reaction if multiple forward or reverse primers are present in\n      a single PCR reaction. The primer sequence should be reported in uppercase letters\n    title: pcr primers\n    examples:\n    - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pcr primers\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: FWD:{dna};REV:{dna}\n    slot_uri: MIXS:0000046\n    alias: pcr_primers\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: TextValue\n    multivalued: false\n  stranded_orientation:\n    name: stranded_orientation\n    description: Lists the strand orientiation for a stranded RNA library preparation.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: stranded_orientation\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: StrandedOrientationEnum\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: LibraryPreparation\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: LibraryPreparation\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: LibraryPreparation\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: LibraryPreparation\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: LibraryPreparation\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: LibraryPreparation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:LibraryPreparation\n\n
"},{"location":"LibraryTypeEnum/","title":"Enum: LibraryTypeEnum","text":"

URI: LibraryTypeEnum

"},{"location":"LibraryTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None"},{"location":"LibraryTypeEnum/#slots","title":"Slots","text":"Name Description library_type"},{"location":"LibraryTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LibraryTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"LibraryTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: LibraryTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  DNA:\n    text: DNA\n  RNA:\n    text: RNA\n\n
"},{"location":"LightTypeEnum/","title":"Enum: LightTypeEnum","text":"

URI: LightTypeEnum

"},{"location":"LightTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description natural light None electric light None desk lamp None flourescent lights None none None"},{"location":"LightTypeEnum/#slots","title":"Slots","text":"Name Description light_type Application of light to achieve some practical or aesthetic effect"},{"location":"LightTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LightTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"LightTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: light_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  natural light:\n    text: natural light\n  electric light:\n    text: electric light\n  desk lamp:\n    text: desk lamp\n  flourescent lights:\n    text: flourescent lights\n  none:\n    text: none\n\n
"},{"location":"LithologyEnum/","title":"Enum: LithologyEnum","text":"

URI: LithologyEnum

"},{"location":"LithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Basement None Chalk None Chert None Coal None Conglomerate None Diatomite None Dolomite None Limestone None Sandstone None Shale None Siltstone None Volcanic None other None"},{"location":"LithologyEnum/#slots","title":"Slots","text":"Name Description lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki"},{"location":"LithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LithologyEnum/#schema-source","title":"Schema Source","text":""},{"location":"LithologyEnum/#linkml-source","title":"LinkML Source","text":"
name: lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Basement:\n    text: Basement\n  Chalk:\n    text: Chalk\n  Chert:\n    text: Chert\n  Coal:\n    text: Coal\n  Conglomerate:\n    text: Conglomerate\n  Diatomite:\n    text: Diatomite\n  Dolomite:\n    text: Dolomite\n  Limestone:\n    text: Limestone\n  Sandstone:\n    text: Sandstone\n  Shale:\n    text: Shale\n  Siltstone:\n    text: Siltstone\n  Volcanic:\n    text: Volcanic\n  other:\n    text: other\n\n
"},{"location":"MagBin/","title":"Class: MagBin","text":"

URI: nmdc:MagBin

classDiagram\n  class MagBin\n  click MagBin href \"../MagBin\"\n\n  MagBin : bin_name\n\n  MagBin : bin_quality\n\n  MagBin : completeness\n\n  MagBin : contamination\n\n  MagBin : eukaryotic_evaluation\n\n      MagBin --> \"0..1\" EukEval : eukaryotic_evaluation\n    click EukEval href \"../EukEval\"\n\n  MagBin : gene_count\n\n  MagBin : gtdbtk_class\n\n  MagBin : gtdbtk_domain\n\n  MagBin : gtdbtk_family\n\n  MagBin : gtdbtk_genus\n\n  MagBin : gtdbtk_order\n\n  MagBin : gtdbtk_phylum\n\n  MagBin : gtdbtk_species\n\n  MagBin : members_id\n\n  MagBin : num_16s\n\n  MagBin : num_23s\n\n  MagBin : num_5s\n\n  MagBin : num_t_rna\n\n  MagBin : number_of_contig\n\n  MagBin : total_bases\n\n  MagBin : type\n\n\n\n
"},{"location":"MagBin/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance bin_name 0..1 String direct bin_quality 0..1 String direct completeness 0..1 Float direct contamination 0..1 Float direct gene_count 0..1 Integer direct gtdbtk_class 0..1 String direct gtdbtk_domain 0..1 String direct gtdbtk_family 0..1 String direct gtdbtk_genus 0..1 String direct gtdbtk_order 0..1 String direct gtdbtk_phylum 0..1 String direct gtdbtk_species 0..1 String direct members_id * String direct num_16s 0..1 Integer direct num_23s 0..1 Integer direct num_5s 0..1 Integer direct num_t_rna 0..1 Integer direct number_of_contig 0..1 Integer direct total_bases 0..1 Integer direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct eukaryotic_evaluation 0..1 EukEval Contains results from evaluating if a Metagenome-Assembled Genome is of eukar... direct"},{"location":"MagBin/#usages","title":"Usages","text":"used by used in type used MagsAnalysis mags_list range MagBin"},{"location":"MagBin/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MagBin/#schema-source","title":"Schema Source","text":""},{"location":"MagBin/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MagBin native nmdc:MagBin"},{"location":"MagBin/#linkml-source","title":"LinkML Source","text":""},{"location":"MagBin/#direct","title":"Direct","text":"
name: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- bin_name\n- bin_quality\n- completeness\n- contamination\n- gene_count\n- gtdbtk_class\n- gtdbtk_domain\n- gtdbtk_family\n- gtdbtk_genus\n- gtdbtk_order\n- gtdbtk_phylum\n- gtdbtk_species\n- members_id\n- num_16s\n- num_23s\n- num_5s\n- num_t_rna\n- number_of_contig\n- total_bases\n- type\n- eukaryotic_evaluation\nclass_uri: nmdc:MagBin\n\n
"},{"location":"MagBin/#induced","title":"Induced","text":"
name: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  bin_name:\n    name: bin_name\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: bin_name\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  bin_quality:\n    name: bin_quality\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: bin_quality\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  completeness:\n    name: completeness\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: completeness\n    owner: MagBin\n    domain_of:\n    - EukEval\n    - MagBin\n    range: float\n  contamination:\n    name: contamination\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: contamination\n    owner: MagBin\n    domain_of:\n    - EukEval\n    - MagBin\n    range: float\n  gene_count:\n    name: gene_count\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gene_count\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  gtdbtk_class:\n    name: gtdbtk_class\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_class\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_domain:\n    name: gtdbtk_domain\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_domain\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_family:\n    name: gtdbtk_family\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_family\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_genus:\n    name: gtdbtk_genus\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_genus\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_order:\n    name: gtdbtk_order\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_order\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_phylum:\n    name: gtdbtk_phylum\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_phylum\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_species:\n    name: gtdbtk_species\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_species\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  members_id:\n    name: members_id\n    todos:\n    - this slot needs some basic textual annotations and constraints\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: members_id\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n    multivalued: true\n  num_16s:\n    name: num_16s\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: num_16s\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  num_23s:\n    name: num_23s\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: num_23s\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  num_5s:\n    name: num_5s\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: num_5s\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  num_t_rna:\n    name: num_t_rna\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: num_t_rna\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  number_of_contig:\n    name: number_of_contig\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: number_of_contig\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  total_bases:\n    name: total_bases\n    todos:\n    - this slot needs some basic textual annotations and constraints\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: total_bases\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MagBin\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  eukaryotic_evaluation:\n    name: eukaryotic_evaluation\n    description: Contains results from evaluating if a Metagenome-Assembled Genome\n      is of eukaryotic lineage.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: eukaryotic_evaluation\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: EukEval\nclass_uri: nmdc:MagBin\n\n
"},{"location":"MagsAnalysis/","title":"Class: Metagenome-Assembled Genome analysis activity (MagsAnalysis)","text":"

A workflow execution activity that uses computational binning tools to group assembled contigs into genomes

URI: nmdc:MagsAnalysis

classDiagram\n  class MagsAnalysis\n  click MagsAnalysis href \"../MagsAnalysis\"\n    WorkflowExecution <|-- MagsAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MagsAnalysis : alternative_identifiers\n\n  MagsAnalysis : binned_contig_num\n\n  MagsAnalysis : description\n\n  MagsAnalysis : end_date\n\n  MagsAnalysis : ended_at_time\n\n  MagsAnalysis : execution_resource\n\n      MagsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MagsAnalysis : git_url\n\n  MagsAnalysis : has_failure_categorization\n\n      MagsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MagsAnalysis : has_input\n\n      MagsAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MagsAnalysis : has_output\n\n      MagsAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MagsAnalysis : id\n\n  MagsAnalysis : img_identifiers\n\n  MagsAnalysis : input_contig_num\n\n  MagsAnalysis : low_depth_contig_num\n\n  MagsAnalysis : mags_list\n\n      MagsAnalysis --> \"*\" MagBin : mags_list\n    click MagBin href \"../MagBin\"\n\n  MagsAnalysis : name\n\n  MagsAnalysis : processing_institution\n\n      MagsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MagsAnalysis : protocol_link\n\n      MagsAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MagsAnalysis : qc_comment\n\n  MagsAnalysis : qc_status\n\n      MagsAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MagsAnalysis : start_date\n\n  MagsAnalysis : started_at_time\n\n  MagsAnalysis : too_short_contig_num\n\n  MagsAnalysis : type\n\n  MagsAnalysis : unbinned_contig_num\n\n  MagsAnalysis : version\n\n  MagsAnalysis : was_informed_by\n\n      MagsAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MagsAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"MagsAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance binned_contig_num 0..1 Integer direct input_contig_num 0..1 Integer direct low_depth_contig_num 0..1 Integer direct mags_list * MagBin direct too_short_contig_num 0..1 Integer direct unbinned_contig_num 0..1 Integer direct img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MagsAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MagsAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"MagsAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MagsAnalysis native nmdc:MagsAnalysis"},{"location":"MagsAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"MagsAnalysis/#direct","title":"Direct","text":"
name: MagsAnalysis\ndescription: A workflow execution activity that uses computational binning tools to\n  group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- binned_contig_num\n- input_contig_num\n- low_depth_contig_num\n- mags_list\n- too_short_contig_num\n- unbinned_contig_num\n- img_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MagsAnalysis\n\n
"},{"location":"MagsAnalysis/#induced","title":"Induced","text":"
name: MagsAnalysis\ndescription: A workflow execution activity that uses computational binning tools to\n  group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  binned_contig_num:\n    name: binned_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: binned_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  input_contig_num:\n    name: input_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: input_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  low_depth_contig_num:\n    name: low_depth_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: low_depth_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  mags_list:\n    name: mags_list\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mags_list\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: MagBin\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  too_short_contig_num:\n    name: too_short_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: too_short_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  unbinned_contig_num:\n    name: unbinned_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: unbinned_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: MagsAnalysis\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n    maximum_cardinality: 1\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MagsAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MagsAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MagsAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MagsAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MagsAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MagsAnalysis\n\n
"},{"location":"Manifest/","title":"Class: Manifest","text":"

URI: nmdc:Manifest

classDiagram\n  class Manifest\n  click Manifest href \"../Manifest\"\n    InformationObject <|-- Manifest\n      click InformationObject href \"../InformationObject\"\n\n\n\n  Manifest : alternative_identifiers\n\n  Manifest : description\n\n  Manifest : id\n\n  Manifest : manifest_category\n\n      Manifest --> \"1\" ManifestCategoryEnum : manifest_category\n    click ManifestCategoryEnum href \"../ManifestCategoryEnum\"\n\n  Manifest : name\n\n  Manifest : type\n\n\n\n
"},{"location":"Manifest/#inheritance","title":"Inheritance","text":""},{"location":"Manifest/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance manifest_category 1 ManifestCategoryEnum The type of collection that describes the data in the collection direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Manifest/#usages","title":"Usages","text":"used by used in type used Database manifest_set range Manifest DataObject in_manifest range Manifest"},{"location":"Manifest/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Manifest/#schema-source","title":"Schema Source","text":""},{"location":"Manifest/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Manifest native nmdc:Manifest"},{"location":"Manifest/#linkml-source","title":"LinkML Source","text":""},{"location":"Manifest/#direct","title":"Direct","text":"
name: Manifest\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- manifest_category\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\nclass_uri: nmdc:Manifest\n\n
"},{"location":"Manifest/#induced","title":"Induced","text":"
name: Manifest\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\nattributes:\n  manifest_category:\n    name: manifest_category\n    description: The type of collection that describes the data in the collection.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: manifest_category\n    owner: Manifest\n    domain_of:\n    - Manifest\n    range: ManifestCategoryEnum\n    required: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Manifest\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Manifest\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Manifest\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Manifest\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Manifest\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Manifest\n\n
"},{"location":"ManifestCategoryEnum/","title":"Enum: ManifestCategoryEnum","text":"

URI: ManifestCategoryEnum

"},{"location":"ManifestCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description instrument_run None A collection of data generation records from a single run of an instrument technical_replicates None A collection of data generation records that represent technical replicates o... fractions None A collection of data generation records that represent fractions of a single ..."},{"location":"ManifestCategoryEnum/#slots","title":"Slots","text":"Name Description manifest_category The type of collection that describes the data in the collection"},{"location":"ManifestCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ManifestCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ManifestCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ManifestCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  instrument_run:\n    text: instrument_run\n    description: A collection of data generation records from a single run of an instrument.\n  technical_replicates:\n    text: technical_replicates\n    description: A collection of data generation records that represent technical\n      replicates of a single sample.\n  fractions:\n    text: fractions\n    description: A collection of data generation records that represent fractions\n      of a single sample.\n\n
"},{"location":"MassAnalyzerEnum/","title":"Enum: MassAnalyzerEnum","text":"

URI: MassAnalyzerEnum

"},{"location":"MassAnalyzerEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description time_of_flight None Instrument that separates ions by m/z in a field-free region after accelerati... quadrupole None A mass spectrometer that consists of four parallel rods whose centers form th... Orbitrap None An ion trapping device that consists of an outer barrel-like electrode and a ... ion_cyclotron_resonance None A mass spectrometer based on the principle of ion cyclotron resonance in whic... ion_trap None A device for spatially confining ions using electric and magnetic fields alon..."},{"location":"MassAnalyzerEnum/#slots","title":"Slots","text":"Name Description mass_analyzers The kind of mass analyzer(s) used during the spectra collection"},{"location":"MassAnalyzerEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassAnalyzerEnum/#schema-source","title":"Schema Source","text":""},{"location":"MassAnalyzerEnum/#linkml-source","title":"LinkML Source","text":"
name: MassAnalyzerEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  time_of_flight:\n    text: time_of_flight\n    description: Instrument that separates ions by m/z in a field-free region after\n      acceleration to a fixed acceleration energy.\n    aliases:\n    - TOF\n    exact_mappings:\n    - MS:1000084\n  quadrupole:\n    text: quadrupole\n    description: A mass spectrometer that consists of four parallel rods whose centers\n      form the corners of a square and whose opposing poles are connected. The voltage\n      applied to the rods is a superposition of a static potential and a sinusoidal\n      radio frequency potential. The motion of an ion in the x and y dimensions is\n      described by the Matthieu equation whose solutions show that ions in a particular\n      m/z range can be transmitted along the z axis.\n    aliases:\n    - Quad\n    - Q\n    exact_mappings:\n    - MS:1000081\n  Orbitrap:\n    text: Orbitrap\n    description: An ion trapping device that consists of an outer barrel-like electrode\n      and a coaxial inner spindle-like electrode that form an electrostatic field\n      with quadro-logarithmic potential distribution. The frequency of harmonic oscillations\n      of the orbitally trapped ions along the axis of the electrostatic field is independent\n      of the ion velocity and is inversely proportional to the square root of m/z\n      so that the trap can be used as a mass analyzer.\n    aliases:\n    - Orbi\n    exact_mappings:\n    - MS:1000484\n  ion_cyclotron_resonance:\n    text: ion_cyclotron_resonance\n    description: A mass spectrometer based on the principle of ion cyclotron resonance\n      in which an ion in a magnetic field moves in a circular orbit at a frequency\n      characteristic of its m/z value. Ions are coherently excited to a larger radius\n      orbit using a pulse of radio frequency energy and their image charge is detected\n      on receiver plates as a time domain signal. Fourier transformation of the time\n      domain signal results in a frequency domain signal which is converted to a mass\n      spectrum based in the inverse relationship between frequency and m/z.\n    aliases:\n    - ICR\n    exact_mappings:\n    - MS:1000079\n  ion_trap:\n    text: ion_trap\n    description: A device for spatially confining ions using electric and magnetic\n      fields alone or in combination.\n    aliases:\n    - LTQ\n    - Ion Trap\n    - Paul Trap\n    exact_mappings:\n    - MS:1000264\n\n
"},{"location":"MassSpectrometry/","title":"Class: MassSpectrometry","text":"

Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.

URI: nmdc:MassSpectrometry

classDiagram\n  class MassSpectrometry\n  click MassSpectrometry href \"../MassSpectrometry\"\n    DataGeneration <|-- MassSpectrometry\n      click DataGeneration href \"../DataGeneration\"\n\n\n\n  MassSpectrometry : add_date\n\n  MassSpectrometry : alternative_identifiers\n\n  MassSpectrometry : analyte_category\n\n      MassSpectrometry --> \"1\" AnalyteCategoryEnum : analyte_category\n    click AnalyteCategoryEnum href \"../AnalyteCategoryEnum\"\n\n  MassSpectrometry : associated_studies\n\n      MassSpectrometry --> \"1..*\" Study : associated_studies\n    click Study href \"../Study\"\n\n  MassSpectrometry : description\n\n  MassSpectrometry : eluent_introduction_category\n\n      MassSpectrometry --> \"0..1\" EluentIntroductionCategoryEnum : eluent_introduction_category\n    click EluentIntroductionCategoryEnum href \"../EluentIntroductionCategoryEnum\"\n\n  MassSpectrometry : end_date\n\n  MassSpectrometry : has_calibration\n\n  MassSpectrometry : has_chromatography_configuration\n\n      MassSpectrometry --> \"0..1\" ChromatographyConfiguration : has_chromatography_configuration\n    click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n\n  MassSpectrometry : has_failure_categorization\n\n      MassSpectrometry --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MassSpectrometry : has_input\n\n      MassSpectrometry --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MassSpectrometry : has_mass_spectrometry_configuration\n\n      MassSpectrometry --> \"0..1\" MassSpectrometryConfiguration : has_mass_spectrometry_configuration\n    click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n\n  MassSpectrometry : has_output\n\n      MassSpectrometry --> \"*\" DataObject : has_output\n    click DataObject href \"../DataObject\"\n\n  MassSpectrometry : id\n\n  MassSpectrometry : instrument_used\n\n      MassSpectrometry --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  MassSpectrometry : mod_date\n\n  MassSpectrometry : name\n\n  MassSpectrometry : principal_investigator\n\n      MassSpectrometry --> \"0..1\" PersonValue : principal_investigator\n    click PersonValue href \"../PersonValue\"\n\n  MassSpectrometry : processing_institution\n\n      MassSpectrometry --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MassSpectrometry : protocol_link\n\n      MassSpectrometry --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MassSpectrometry : qc_comment\n\n  MassSpectrometry : qc_status\n\n      MassSpectrometry --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MassSpectrometry : start_date\n\n  MassSpectrometry : type\n\n\n\n
"},{"location":"MassSpectrometry/#inheritance","title":"Inheritance","text":""},{"location":"MassSpectrometry/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance eluent_introduction_category 0..1 EluentIntroductionCategoryEnum A high-level categorization for how the processed sample is introduced into a... direct has_calibration 0..1 String\u00a0or\u00a0CalibrationInformation\u00a0or\u00a0String a calibration instance associated with a process direct has_chromatography_configuration 0..1 ChromatographyConfiguration The identifier of the associated ChromatographyConfiguration, providing infor... direct has_mass_spectrometry_configuration 0..1 MassSpectrometryConfiguration The identifier of the associated MassSpectrometryConfiguration direct add_date 0..1 String The date on which the information was added to the database DataGeneration analyte_category 1 AnalyteCategoryEnum The type of analyte(s) that were measured in the data generation process and ... DataGeneration associated_studies 1..* Study The study associated with a resource DataGeneration instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing DataGeneration mod_date 0..1 String The last date on which the database information was modified DataGeneration principal_investigator 0..1 PersonValue Principal Investigator who led the study and/or generated the dataset DataGeneration has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * DataObject An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MassSpectrometry/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometry/#schema-source","title":"Schema Source","text":""},{"location":"MassSpectrometry/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MassSpectrometry native nmdc:MassSpectrometry exact CHMO:0000470"},{"location":"MassSpectrometry/#linkml-source","title":"LinkML Source","text":""},{"location":"MassSpectrometry/#direct","title":"Direct","text":"
name: MassSpectrometry\ndescription: Spectrometry where the sample is converted into gaseous ions which are\n  characterised by their mass-to-charge ratio and relative abundance.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- CHMO:0000470\nis_a: DataGeneration\nslots:\n- eluent_introduction_category\n- has_calibration\n- has_chromatography_configuration\n- has_mass_spectrometry_configuration\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_calibration:\n    name: has_calibration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_chromatography_configuration:\n    name: has_chromatography_configuration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_mass_spectrometry_configuration:\n    name: has_mass_spectrometry_configuration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MassSpectrometry\nrules:\n- preconditions:\n    slot_conditions:\n      eluent_introduction_category:\n        name: eluent_introduction_category\n        equals_string: gas_chromatography\n  postconditions:\n    slot_conditions:\n      has_calibration:\n        name: has_calibration\n        required: true\n  description: If eluent_introduction_category is gas_chromatography, then has_calibration\n    is required.\n  title: has_calibration_required_if_gc\n- preconditions:\n    slot_conditions:\n      eluent_introduction_category:\n        name: eluent_introduction_category\n        any_of:\n        - equals_string: liquid_chromatography\n        - equals_string: gas_chromatography\n  postconditions:\n    slot_conditions:\n      has_chromatography_configuration:\n        name: has_chromatography_configuration\n        required: true\n  description: If eluent_introduction_category is liquid_chromatography or gas_chromatography,\n    then has_chromatography_configuration is required.\n  title: has_chromatography_configuration_required_if_lc_or_gc\n\n
"},{"location":"MassSpectrometry/#induced","title":"Induced","text":"
name: MassSpectrometry\ndescription: Spectrometry where the sample is converted into gaseous ions which are\n  characterised by their mass-to-charge ratio and relative abundance.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- CHMO:0000470\nis_a: DataGeneration\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_calibration:\n    name: has_calibration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_chromatography_configuration:\n    name: has_chromatography_configuration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_mass_spectrometry_configuration:\n    name: has_mass_spectrometry_configuration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  eluent_introduction_category:\n    name: eluent_introduction_category\n    description: A high-level categorization for how the processed sample is introduced\n      into a mass spectrometer.\n    examples:\n    - value: liquid_chromatography\n    - value: direct_infusion_syringe\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: eluent_introduction_category\n    owner: MassSpectrometry\n    domain_of:\n    - MassSpectrometry\n    range: EluentIntroductionCategoryEnum\n  has_calibration:\n    name: has_calibration\n    description: a calibration instance associated with a process\n    notes:\n    - 'has_calibration slot will be removed from all WorkflowExecution classes but\n      remain on the MassSpectrometry class after an ingest of the appropriate set\n      has occurred.  Once this has occurred, this slot''s range can be updated to\n      CalibrationInformation and class/slot definitions can move to nmdc.yaml.   See\n      PR #29 in Berkeley schema.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_calibration\n    owner: MassSpectrometry\n    domain_of:\n    - MassSpectrometry\n    - MetabolomicsAnalysis\n    - NomAnalysis\n    range: string\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: CalibrationInformation\n    - range: string\n  has_chromatography_configuration:\n    name: has_chromatography_configuration\n    description: The identifier of the associated ChromatographyConfiguration, providing\n      information about how a sample was introduced into the mass spectrometer.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_chromatography_configuration\n    owner: MassSpectrometry\n    domain_of:\n    - MassSpectrometry\n    range: ChromatographyConfiguration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_mass_spectrometry_configuration:\n    name: has_mass_spectrometry_configuration\n    description: The identifier of the associated MassSpectrometryConfiguration.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_mass_spectrometry_configuration\n    owner: MassSpectrometry\n    domain_of:\n    - MassSpectrometry\n    range: MassSpectrometryConfiguration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  add_date:\n    name: add_date\n    description: The date on which the information was added to the database.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: add_date\n    owner: MassSpectrometry\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  analyte_category:\n    name: analyte_category\n    description: \"The type of analyte(s) that were measured in the data generation\\\n      \\ process and analyzed\\n  in the Workflow Chain\\n\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: analyte_category\n    owner: MassSpectrometry\n    domain_of:\n    - DataGeneration\n    range: AnalyteCategoryEnum\n    required: true\n  associated_studies:\n    name: associated_studies\n    description: The study associated with a resource.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: associated_studies\n    owner: MassSpectrometry\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: Study\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: MassSpectrometry\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  mod_date:\n    name: mod_date\n    description: The last date on which the database information was modified.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mod_date\n    owner: MassSpectrometry\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  principal_investigator:\n    name: principal_investigator\n    description: Principal Investigator who led the study and/or generated the dataset.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - PI\n    rank: 1000\n    alias: principal_investigator\n    owner: MassSpectrometry\n    domain_of:\n    - Study\n    - DataGeneration\n    range: PersonValue\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: DataObject\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MassSpectrometry\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MassSpectrometry\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MassSpectrometry\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MassSpectrometry\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MassSpectrometry\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MassSpectrometry\nrules:\n- preconditions:\n    slot_conditions:\n      eluent_introduction_category:\n        name: eluent_introduction_category\n        equals_string: gas_chromatography\n  postconditions:\n    slot_conditions:\n      has_calibration:\n        name: has_calibration\n        required: true\n  description: If eluent_introduction_category is gas_chromatography, then has_calibration\n    is required.\n  title: has_calibration_required_if_gc\n- preconditions:\n    slot_conditions:\n      eluent_introduction_category:\n        name: eluent_introduction_category\n        any_of:\n        - equals_string: liquid_chromatography\n        - equals_string: gas_chromatography\n  postconditions:\n    slot_conditions:\n      has_chromatography_configuration:\n        name: has_chromatography_configuration\n        required: true\n  description: If eluent_introduction_category is liquid_chromatography or gas_chromatography,\n    then has_chromatography_configuration is required.\n  title: has_chromatography_configuration_required_if_lc_or_gc\n\n
"},{"location":"MassSpectrometryAcquisitionStrategyEnum/","title":"Enum: MassSpectrometryAcquisitionStrategyEnum","text":"

URI: MassSpectrometryAcquisitionStrategyEnum

"},{"location":"MassSpectrometryAcquisitionStrategyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description data_independent_acquisition None ['Data independent mass spectrometer acquisition method wherein the full mass... data_dependent_acquisition None Mass spectrometer data acquisition method wherein MSn spectra are triggered b... full_scan_only None Mass spectrometer data acquisition method wherein only MS1 data are acquired"},{"location":"MassSpectrometryAcquisitionStrategyEnum/#slots","title":"Slots","text":"Name Description mass_spectrometry_acquisition_strategy Mode of running a mass spectrometer method by which m/z ranges are selected a..."},{"location":"MassSpectrometryAcquisitionStrategyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometryAcquisitionStrategyEnum/#schema-source","title":"Schema Source","text":""},{"location":"MassSpectrometryAcquisitionStrategyEnum/#linkml-source","title":"LinkML Source","text":"
name: MassSpectrometryAcquisitionStrategyEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  data_independent_acquisition:\n    text: data_independent_acquisition\n    description: '[''Data independent mass spectrometer acquisition method wherein\n      the full mass range is fragmented. Examples of such an approach include MS^E,\n      AIF, and bbCID.'']'\n    aliases:\n    - DIA\n    - data independent acquisition from dissociation of full mass range\n    exact_mappings:\n    - MS:1003227\n  data_dependent_acquisition:\n    text: data_dependent_acquisition\n    description: Mass spectrometer data acquisition method wherein MSn spectra are\n      triggered based on the m/z of precursor ions detected in the same run.\n    aliases:\n    - -DDA\n    exact_mappings:\n    - MS:1003221\n  full_scan_only:\n    text: full_scan_only\n    description: Mass spectrometer data acquisition method wherein only MS1 data are\n      acquired.\n    aliases:\n    - MS\n\n
"},{"location":"MassSpectrometryConfiguration/","title":"Class: MassSpectrometryConfiguration","text":"

A set of parameters that define and control the actions of a mass spectrometry process.

URI: nmdc:MassSpectrometryConfiguration

classDiagram\n  class MassSpectrometryConfiguration\n  click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n    Configuration <|-- MassSpectrometryConfiguration\n      click Configuration href \"../Configuration\"\n\n\n\n  MassSpectrometryConfiguration : alternative_identifiers\n\n  MassSpectrometryConfiguration : description\n\n  MassSpectrometryConfiguration : id\n\n  MassSpectrometryConfiguration : ionization_source\n\n      MassSpectrometryConfiguration --> \"0..1\" IonizationSourceEnum : ionization_source\n    click IonizationSourceEnum href \"../IonizationSourceEnum\"\n\n  MassSpectrometryConfiguration : mass_analyzers\n\n      MassSpectrometryConfiguration --> \"*\" MassAnalyzerEnum : mass_analyzers\n    click MassAnalyzerEnum href \"../MassAnalyzerEnum\"\n\n  MassSpectrometryConfiguration : mass_spectrometry_acquisition_strategy\n\n      MassSpectrometryConfiguration --> \"0..1\" MassSpectrometryAcquisitionStrategyEnum : mass_spectrometry_acquisition_strategy\n    click MassSpectrometryAcquisitionStrategyEnum href \"../MassSpectrometryAcquisitionStrategyEnum\"\n\n  MassSpectrometryConfiguration : mass_spectrum_collection_modes\n\n      MassSpectrometryConfiguration --> \"*\" MassSpectrumCollectionModeEnum : mass_spectrum_collection_modes\n    click MassSpectrumCollectionModeEnum href \"../MassSpectrumCollectionModeEnum\"\n\n  MassSpectrometryConfiguration : name\n\n  MassSpectrometryConfiguration : polarity_mode\n\n      MassSpectrometryConfiguration --> \"0..1\" PolarityModeEnum : polarity_mode\n    click PolarityModeEnum href \"../PolarityModeEnum\"\n\n  MassSpectrometryConfiguration : resolution_categories\n\n      MassSpectrometryConfiguration --> \"*\" ResolutionCategoryEnum : resolution_categories\n    click ResolutionCategoryEnum href \"../ResolutionCategoryEnum\"\n\n  MassSpectrometryConfiguration : type\n\n\n\n
"},{"location":"MassSpectrometryConfiguration/#inheritance","title":"Inheritance","text":""},{"location":"MassSpectrometryConfiguration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance mass_spectrometry_acquisition_strategy 0..1 MassSpectrometryAcquisitionStrategyEnum Mode of running a mass spectrometer method by which m/z ranges are selected a... direct resolution_categories * ResolutionCategoryEnum The relative resolution at which spectra were collected direct mass_analyzers * MassAnalyzerEnum The kind of mass analyzer(s) used during the spectra collection direct ionization_source 0..1 IonizationSourceEnum The ionization source used to introduce processed samples into a mass spectro... direct mass_spectrum_collection_modes * MassSpectrumCollectionModeEnum Indicates whether mass spectra were collected in full profile, reduced profil... direct polarity_mode 0..1 PolarityModeEnum the polarity of which ions are generated and detected direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 1 String A human readable label for an entity NamedThing description 1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MassSpectrometryConfiguration/#usages","title":"Usages","text":"used by used in type used MassSpectrometry has_mass_spectrometry_configuration range MassSpectrometryConfiguration"},{"location":"MassSpectrometryConfiguration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometryConfiguration/#schema-source","title":"Schema Source","text":""},{"location":"MassSpectrometryConfiguration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MassSpectrometryConfiguration native nmdc:MassSpectrometryConfiguration"},{"location":"MassSpectrometryConfiguration/#linkml-source","title":"LinkML Source","text":""},{"location":"MassSpectrometryConfiguration/#direct","title":"Direct","text":"
name: MassSpectrometryConfiguration\ndescription: A set of parameters that define and control the actions of a mass spectrometry\n  process.\nnotes:\n- This class is intended to represent a mass spectrometry method file that controls\n  a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslots:\n- mass_spectrometry_acquisition_strategy\n- resolution_categories\n- mass_analyzers\n- ionization_source\n- mass_spectrum_collection_modes\n- polarity_mode\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MassSpectrometryConfiguration\n\n
"},{"location":"MassSpectrometryConfiguration/#induced","title":"Induced","text":"
name: MassSpectrometryConfiguration\ndescription: A set of parameters that define and control the actions of a mass spectrometry\n  process.\nnotes:\n- This class is intended to represent a mass spectrometry method file that controls\n  a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  mass_spectrometry_acquisition_strategy:\n    name: mass_spectrometry_acquisition_strategy\n    description: Mode of running a mass spectrometer method by which m/z ranges are\n      selected and ions possibly fragment.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - MS:1003213\n    rank: 1000\n    alias: mass_spectrometry_acquisition_strategy\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: MassSpectrometryAcquisitionStrategyEnum\n  resolution_categories:\n    name: resolution_categories\n    description: The relative resolution at which spectra were collected.\n    examples:\n    - value: '[''high'', ''low'']'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: resolution_categories\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: ResolutionCategoryEnum\n    multivalued: true\n  mass_analyzers:\n    name: mass_analyzers\n    description: The kind of mass analyzer(s) used during the spectra collection.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - MS:1000443\n    rank: 1000\n    alias: mass_analyzers\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: MassAnalyzerEnum\n    multivalued: true\n  ionization_source:\n    name: ionization_source\n    description: The ionization source used to introduce processed samples into a\n      mass spectrometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - MS:1000008\n    rank: 1000\n    alias: ionization_source\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: IonizationSourceEnum\n  mass_spectrum_collection_modes:\n    name: mass_spectrum_collection_modes\n    description: Indicates whether mass spectra were collected in full profile, reduced\n      profile, or centroid mode during acquisition.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mass_spectrum_collection_modes\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: MassSpectrumCollectionModeEnum\n    multivalued: true\n  polarity_mode:\n    name: polarity_mode\n    description: the polarity of which ions are generated and detected\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: polarity_mode\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: PolarityModeEnum\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n    required: true\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n    required: true\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MassSpectrometryConfiguration\n\n
"},{"location":"MassSpectrumCollectionModeEnum/","title":"Enum: MassSpectrumCollectionModeEnum","text":"

URI: MassSpectrumCollectionModeEnum

"},{"location":"MassSpectrumCollectionModeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description full_profile None reduced_profile None centroid None"},{"location":"MassSpectrumCollectionModeEnum/#slots","title":"Slots","text":"Name Description mass_spectrum_collection_modes Indicates whether mass spectra were collected in full profile, reduced profil..."},{"location":"MassSpectrumCollectionModeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrumCollectionModeEnum/#schema-source","title":"Schema Source","text":""},{"location":"MassSpectrumCollectionModeEnum/#linkml-source","title":"LinkML Source","text":"
name: MassSpectrumCollectionModeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  full_profile:\n    text: full_profile\n  reduced_profile:\n    text: reduced_profile\n  centroid:\n    text: centroid\n\n
"},{"location":"MaterialEntity/","title":"Class: Material Entity (MaterialEntity)","text":"

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:MaterialEntity

classDiagram\n  class MaterialEntity\n  click MaterialEntity href \"../MaterialEntity\"\n    NamedThing <|-- MaterialEntity\n      click NamedThing href \"../NamedThing\"\n\n\n    MaterialEntity <|-- Biosample\n      click Biosample href \"../Biosample\"\n    MaterialEntity <|-- ProcessedSample\n      click ProcessedSample href \"../ProcessedSample\"\n    MaterialEntity <|-- Site\n      click Site href \"../Site\"\n    MaterialEntity <|-- Instrument\n      click Instrument href \"../Instrument\"\n\n\n\n  MaterialEntity : alternative_identifiers\n\n  MaterialEntity : description\n\n  MaterialEntity : id\n\n  MaterialEntity : name\n\n  MaterialEntity : type\n\n\n\n
"},{"location":"MaterialEntity/#inheritance","title":"Inheritance","text":""},{"location":"MaterialEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MaterialEntity/#aliases","title":"Aliases","text":""},{"location":"MaterialEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MaterialEntity/#schema-source","title":"Schema Source","text":""},{"location":"MaterialEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MaterialEntity native nmdc:MaterialEntity"},{"location":"MaterialEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"MaterialEntity/#direct","title":"Direct","text":"
name: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nclass_uri: nmdc:MaterialEntity\n\n
"},{"location":"MaterialEntity/#induced","title":"Induced","text":"
name: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MaterialEntity\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MaterialEntity\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MaterialEntity\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MaterialEntity\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MaterialEntity\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MaterialEntity\n\n
"},{"location":"MaterialProcessing/","title":"Class: MaterialProcessing","text":"

A process that takes one or more samples as inputs and generates one or more samples as outputs.

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:MaterialProcessing

classDiagram\n  class MaterialProcessing\n  click MaterialProcessing href \"../MaterialProcessing\"\n    PlannedProcess <|-- MaterialProcessing\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n    MaterialProcessing <|-- Pooling\n      click Pooling href \"../Pooling\"\n    MaterialProcessing <|-- Extraction\n      click Extraction href \"../Extraction\"\n    MaterialProcessing <|-- LibraryPreparation\n      click LibraryPreparation href \"../LibraryPreparation\"\n    MaterialProcessing <|-- SubSamplingProcess\n      click SubSamplingProcess href \"../SubSamplingProcess\"\n    MaterialProcessing <|-- MixingProcess\n      click MixingProcess href \"../MixingProcess\"\n    MaterialProcessing <|-- FiltrationProcess\n      click FiltrationProcess href \"../FiltrationProcess\"\n    MaterialProcessing <|-- ChromatographicSeparationProcess\n      click ChromatographicSeparationProcess href \"../ChromatographicSeparationProcess\"\n    MaterialProcessing <|-- DissolvingProcess\n      click DissolvingProcess href \"../DissolvingProcess\"\n    MaterialProcessing <|-- ChemicalConversionProcess\n      click ChemicalConversionProcess href \"../ChemicalConversionProcess\"\n\n\n\n  MaterialProcessing : alternative_identifiers\n\n  MaterialProcessing : description\n\n  MaterialProcessing : end_date\n\n  MaterialProcessing : has_failure_categorization\n\n      MaterialProcessing --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MaterialProcessing : has_input\n\n      MaterialProcessing --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MaterialProcessing : has_output\n\n      MaterialProcessing --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  MaterialProcessing : id\n\n  MaterialProcessing : instrument_used\n\n      MaterialProcessing --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  MaterialProcessing : name\n\n  MaterialProcessing : processing_institution\n\n      MaterialProcessing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MaterialProcessing : protocol_link\n\n      MaterialProcessing --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MaterialProcessing : qc_comment\n\n  MaterialProcessing : qc_status\n\n      MaterialProcessing --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MaterialProcessing : start_date\n\n  MaterialProcessing : type\n\n\n\n
"},{"location":"MaterialProcessing/#inheritance","title":"Inheritance","text":""},{"location":"MaterialProcessing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing direct has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MaterialProcessing/#usages","title":"Usages","text":"used by used in type used Database material_processing_set range MaterialProcessing"},{"location":"MaterialProcessing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MaterialProcessing/#schema-source","title":"Schema Source","text":""},{"location":"MaterialProcessing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MaterialProcessing native nmdc:MaterialProcessing broad OBI:0000094"},{"location":"MaterialProcessing/#linkml-source","title":"LinkML Source","text":""},{"location":"MaterialProcessing/#direct","title":"Direct","text":"
name: MaterialProcessing\ndescription: A process that takes one or more samples as inputs and generates one\n  or more samples as outputs.\nnotes:\n- This class is a replacement for BiosampleProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nabstract: true\nslots:\n- instrument_used\nslot_usage:\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MaterialProcessing\n\n
"},{"location":"MaterialProcessing/#induced","title":"Induced","text":"
name: MaterialProcessing\ndescription: A process that takes one or more samples as inputs and generates one\n  or more samples as outputs.\nnotes:\n- This class is a replacement for BiosampleProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: MaterialProcessing\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MaterialProcessing\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MaterialProcessing\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MaterialProcessing\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MaterialProcessing\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MaterialProcessing\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MaterialProcessing\n\n
"},{"location":"MechStrucEnum/","title":"Enum: MechStrucEnum","text":"

URI: MechStrucEnum

"},{"location":"MechStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description subway None coach None carriage None elevator None escalator None boat None train None car None bus None"},{"location":"MechStrucEnum/#slots","title":"Slots","text":"Name Description mech_struc mechanical structure: a moving structure"},{"location":"MechStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MechStrucEnum/#schema-source","title":"Schema Source","text":""},{"location":"MechStrucEnum/#linkml-source","title":"LinkML Source","text":"
name: mech_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  subway:\n    text: subway\n  coach:\n    text: coach\n  carriage:\n    text: carriage\n  elevator:\n    text: elevator\n  escalator:\n    text: escalator\n  boat:\n    text: boat\n  train:\n    text: train\n  car:\n    text: car\n  bus:\n    text: bus\n\n
"},{"location":"MetaboliteIdentification/","title":"Class: MetaboliteIdentification","text":"

This is used to link a metabolomics analysis workflow to a specific metabolite

URI: nmdc:MetaboliteIdentification

classDiagram\n  class MetaboliteIdentification\n  click MetaboliteIdentification href \"../MetaboliteIdentification\"\n\n  MetaboliteIdentification : alternative_identifiers\n\n  MetaboliteIdentification : highest_similarity_score\n\n  MetaboliteIdentification : metabolite_identified\n\n      MetaboliteIdentification --> \"0..1\" ChemicalEntity : metabolite_identified\n    click ChemicalEntity href \"../ChemicalEntity\"\n\n  MetaboliteIdentification : type\n\n\n\n
"},{"location":"MetaboliteIdentification/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity direct highest_similarity_score 0..1 Float direct metabolite_identified 0..1 ChemicalEntity the specific metabolite identifier direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"MetaboliteIdentification/#usages","title":"Usages","text":"used by used in type used MetabolomicsAnalysis has_metabolite_identifications range MetaboliteIdentification"},{"location":"MetaboliteIdentification/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetaboliteIdentification/#schema-source","title":"Schema Source","text":""},{"location":"MetaboliteIdentification/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetaboliteIdentification native nmdc:MetaboliteIdentification"},{"location":"MetaboliteIdentification/#linkml-source","title":"LinkML Source","text":""},{"location":"MetaboliteIdentification/#direct","title":"Direct","text":"
name: MetaboliteIdentification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- alternative_identifiers\n- highest_similarity_score\n- metabolite_identified\n- type\nclass_uri: nmdc:MetaboliteIdentification\n\n
"},{"location":"MetaboliteIdentification/#induced","title":"Induced","text":"
name: MetaboliteIdentification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetaboliteIdentification\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  highest_similarity_score:\n    name: highest_similarity_score\n    todos:\n    - Yuri to fill in description\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: highest_similarity_score\n    owner: MetaboliteIdentification\n    domain_of:\n    - MetaboliteIdentification\n    range: float\n  metabolite_identified:\n    name: metabolite_identified\n    description: the specific metabolite identifier\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: metabolite_identified\n    owner: MetaboliteIdentification\n    domain_of:\n    - MetaboliteIdentification\n    range: ChemicalEntity\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetaboliteIdentification\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetaboliteIdentification\n\n
"},{"location":"MetabolomicsAnalysis/","title":"Class: MetabolomicsAnalysis","text":"

URI: nmdc:MetabolomicsAnalysis

classDiagram\n  class MetabolomicsAnalysis\n  click MetabolomicsAnalysis href \"../MetabolomicsAnalysis\"\n    WorkflowExecution <|-- MetabolomicsAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetabolomicsAnalysis : alternative_identifiers\n\n  MetabolomicsAnalysis : description\n\n  MetabolomicsAnalysis : end_date\n\n  MetabolomicsAnalysis : ended_at_time\n\n  MetabolomicsAnalysis : execution_resource\n\n      MetabolomicsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetabolomicsAnalysis : git_url\n\n  MetabolomicsAnalysis : has_calibration\n\n  MetabolomicsAnalysis : has_failure_categorization\n\n      MetabolomicsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetabolomicsAnalysis : has_input\n\n      MetabolomicsAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetabolomicsAnalysis : has_metabolite_identifications\n\n      MetabolomicsAnalysis --> \"*\" MetaboliteIdentification : has_metabolite_identifications\n    click MetaboliteIdentification href \"../MetaboliteIdentification\"\n\n  MetabolomicsAnalysis : has_output\n\n      MetabolomicsAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetabolomicsAnalysis : id\n\n  MetabolomicsAnalysis : name\n\n  MetabolomicsAnalysis : processing_institution\n\n      MetabolomicsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetabolomicsAnalysis : protocol_link\n\n      MetabolomicsAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetabolomicsAnalysis : qc_comment\n\n  MetabolomicsAnalysis : qc_status\n\n      MetabolomicsAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetabolomicsAnalysis : start_date\n\n  MetabolomicsAnalysis : started_at_time\n\n  MetabolomicsAnalysis : type\n\n  MetabolomicsAnalysis : version\n\n  MetabolomicsAnalysis : was_informed_by\n\n      MetabolomicsAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetabolomicsAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"MetabolomicsAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_calibration 0..1 String\u00a0or\u00a0CalibrationInformation\u00a0or\u00a0String a calibration instance associated with a process direct has_metabolite_identifications * MetaboliteIdentification direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetabolomicsAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetabolomicsAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"MetabolomicsAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetabolomicsAnalysis native nmdc:MetabolomicsAnalysis"},{"location":"MetabolomicsAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"MetabolomicsAnalysis/#direct","title":"Direct","text":"
name: MetabolomicsAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- has_calibration\n- has_metabolite_identifications\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetabolomicsAnalysis\n\n
"},{"location":"MetabolomicsAnalysis/#induced","title":"Induced","text":"
name: MetabolomicsAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_calibration:\n    name: has_calibration\n    description: a calibration instance associated with a process\n    notes:\n    - 'has_calibration slot will be removed from all WorkflowExecution classes but\n      remain on the MassSpectrometry class after an ingest of the appropriate set\n      has occurred.  Once this has occurred, this slot''s range can be updated to\n      CalibrationInformation and class/slot definitions can move to nmdc.yaml.   See\n      PR #29 in Berkeley schema.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_calibration\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - MassSpectrometry\n    - MetabolomicsAnalysis\n    - NomAnalysis\n    range: string\n    any_of:\n    - range: CalibrationInformation\n    - range: string\n  has_metabolite_identifications:\n    name: has_metabolite_identifications\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_metabolite_identifications\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - MetabolomicsAnalysis\n    range: MetaboliteIdentification\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetabolomicsAnalysis\n\n
"},{"location":"Metadata_Documentation_Overview/","title":"The NMDC Metadata Standards Documentation","text":""},{"location":"Metadata_Documentation_Overview/#introduction","title":"Introduction","text":"

This documentation provides details on the National Microbiome Data Collaborative\u2019s (NMDC) approach to sample and data processing metadata. These are key features that drive the data search and discovery aspect of the NMDC data portal (https://microbiomedata.org/data/). If you are unfamiliar with these types of metadata (Figure 1), we recommend you begin with an Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask) (https://doi.org/10.25979/1607365).

Figure 1: Microbiome metadata types: Information that contextualizes sample including its geographic location and collection date, sample preparation, data processing methods, and data products produced from a biological sample (Luke et al., 2020. Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask). DOI: 10.25979/1607365).

All data integrated into the NMDC data portal must adhere to existing metadata standards for proper indexing and display, and to ensure accurate search results are returned. This documentation outlines the standards and ontologies that were included in the NMDC data schema, a framework that defines how data were defined and linked. For the 2019-2022 pilot initiative, the NMDC Metadata Standards Team (see the NMDC Team page) leveraged existing community-driven standards developed by the Genomics Standards Consortium (GSC), the Joint Genome Institute (JGI) Genomes Online Database (GOLD), and OBO Foundry\u2019s Environmental Ontology (EnvO). In collaboration with these organizations, the NMDC has created a framework for mapping these standards into an interoperable framework that can be expanded to include additional standards and ontologies in the future.

Additional information on the activities by the NMDC Metadata Standards team can be found on the NMDC website at: https://microbiomedata.org/metadata/

"},{"location":"Metadata_Documentation_Overview/#standards-and-ontologies-used-by-the-nmdc","title":"Standards and Ontologies used by the NMDC","text":""},{"location":"Metadata_Documentation_Overview/#sample-metadata","title":"Sample Metadata","text":""},{"location":"Metadata_Documentation_Overview/#gsc-minimum-information-about-any-x-sequence-mixs","title":"GSC Minimum Information about any (x) Sequence (MIxS)","text":"

The GSC has developed standards for describing genomic and metagenomic sequences, including the \u201cminimum information about a genome sequence\u201d (MIGS), the \u201cminimum information about a metagenome sequence\u201d (MIMS), and the \u201cminimum information about a marker gene sequence\u201d (MIMARKS). To complement this community-driven standard effort, the GSC has also developed a system for describing the environment from which a biological sample originates, as \u201cenvironmental packages\u201d and established a unified standard set of checklists through the minimum information about any (x) sequence (MIxS). MIxS provides a standardized data dictionary of sample descriptors (e.g., location, environment, elevation, altitude, depth, etc.) organized into different packages for 17 different sample environments.

To standardize how physical samples are described (i.e., sample metadata, Figure 1), the NMDC schema includes environmental descriptors from the GSC MIxS standards.

Explore how to create a MIxS-compliant sample metadata spreadsheet

"},{"location":"Metadata_Documentation_Overview/#genomes-online-database-gold","title":"Genomes Online Database (GOLD)","text":"

The JGI Genomes OnLine Database (GOLD, Mukherjee 2021) is an open-access repository of genome, metagenome, and metatranscriptome sequencing projects with their associated metadata. GOLD data are organized based on Study, Biosample/Organism, Sequencing Project and Analysis Project (Mukherjee 2017). Biosamples (defined as the physical material collected from an environment) are described using a five-level ecosystem classification path (Figure 2); the NMDC schema also uses this ecosystem classification to describe sample environments.

Figure 2. The GOLD five-level ecosystem classification paths (Mukherjee 2019).

Overview of the GOLD ecosystem paths

Explore how to map sample environments using the GOLD ecosystem classification

"},{"location":"Metadata_Documentation_Overview/#environmental-ontology-envo","title":"Environmental Ontology (EnvO)","text":"

The Environment Ontology (EnvO, Buttigieg 2016) is a community-led ontology that represents environmental entities such as biomes, environmental features, and environmental materials. Each EnvO term is identified using a unique resource identifier (e.g., CURIE or IRI) that resolves in a web browser. This ensures that EnvO\u2019s terms (and their definitions) are easy to find, reference, and share amongst collaborators. It also ensures that datasets described using EnvO terms can be more easily integrated and analyzed in a reproducible manner. And since the meanings of the terms are precisely defined and accessible, humans and computers can easily connect EnvO terms across datasets.

EnvO terms are the recommended values for several of the mandatory terms in the MIxS packages, often referred to as the \"MIxS triad\u201d.

Explore how to map sample environments using the EnvO ecosystem classification

Review a step-by-step example of how to assign EnvO terms to an oligotrophic lake sediment sample below.

env_broad_scale (Biome)

Using EnvO biome categories, aquatic is appropriate. However, since the EnvO is a hierarchical system, the aquatic biome has two sub-categories: freshwater and marine biomes. The freshwater biome is further divided into freshwater lake biome and freshwater river biome. Therefore, for a lake sediment sample, freshwater lake biome is the appropriate EnvO biome category.

env_local_scale (Feature)

Next, we describe the local environmental feature in the vicinity of and likely having a strong causal influence on the sample. Using the EnvO astronomical body part categories, we step through the relevant categories (see figure on the right) until we reach the EnvO term oligotrophic lake.

env_medium (Material)

Finally, since the sample is oligotrophic lake sediment, the EnvO environmental material could be assigned sediment. But because the EnvO hierarchy provides sub-categories within sediment, the environmenta material will be assigned lake sediment.

Therefore, the EnvO triad for oligotrophic lake sediment is:

Env_broad_scale: freshwater lake biome [ENVO_01000252]

Env_local_scale: oligotrophic lake [ENVO_01000774]

Env_medium: lake sediment [ENVO_00000546]

"},{"location":"Metadata_Documentation_Overview/#classifying-samples-with-gold-and-mixsenvo","title":"Classifying samples with GOLD and MIxS/EnvO","text":"

The five-level GOLD ecosystem classification path and EnvO triad each have unique advantages in describing the environmental context of a biosample. The NMDC leverages the strengths of both the GOLD ecosystem classification path and MIxS/EnvO triad. The assignment of MIxS/EnvO triad for the biosamples currently in the NMDC data portal was achieved through a manual curation process using various metadata fields of GOLD biosamples fields, such as name, description, habitat, sample collection site, identifier, ecosystem classification path, and study description. The NMDC team is currently working on exploring solutions for automated mapping between GOLD and MIxS/EnvO.

Figure 3: Mapping between the MIxS/EnvO triad and the GOLD ecosystem classification enables integration of sample environments defined with GOLD and MIxS/EnvO.

"},{"location":"Metadata_Documentation_Overview/#data-processing-metadata","title":"Data Processing Metadata","text":"

In addition, the NMDC is adopting the MIxS standards for sequence data types (e.g., sequencing method, pcr primers and conditions, etc.), and are building on previous efforts by the Proteomics Standards Initiative and Metabolomics Standards Initiative to develop standards and controlled vocabularies for mass spectrometry data types (e.g., ionization mode, mass resolution, scan rate, etc.). Additional details on the processing metadata are coming soon.

"},{"location":"Metadata_Documentation_Overview/#overview-of-the-nmdc-data-schema","title":"Overview of the NMDC Data Schema","text":"

The NMDC has developed a normalized metadata schema (available in the NMDC GitHub) for representing studies, samples, relationships between samples, and associated data objects. The schema is organized into object classes, which act as nodes. Each class has associated slots, which are fields that contain metadata that describe the object. For more in-depth information, full documentation of the NMDC schema can be found here.

For the NMDC pilot, a python toolkit for generating NMDC-compliant JavaScript Object Notation (JSON) objects was developed to create ETL (Extract-Transform-Load) software to ingest metadata from the DOE User Facilities. Read more about the data in the NMDC pilot here.

"},{"location":"MetagenomeAnnotation/","title":"Class: MetagenomeAnnotation","text":"

A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs

URI: nmdc:MetagenomeAnnotation

classDiagram\n  class MetagenomeAnnotation\n  click MetagenomeAnnotation href \"../MetagenomeAnnotation\"\n    WorkflowExecution <|-- MetagenomeAnnotation\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetagenomeAnnotation : alternative_identifiers\n\n  MetagenomeAnnotation : description\n\n  MetagenomeAnnotation : end_date\n\n  MetagenomeAnnotation : ended_at_time\n\n  MetagenomeAnnotation : execution_resource\n\n      MetagenomeAnnotation --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetagenomeAnnotation : git_url\n\n  MetagenomeAnnotation : gold_analysis_project_identifiers\n\n  MetagenomeAnnotation : has_failure_categorization\n\n      MetagenomeAnnotation --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetagenomeAnnotation : has_input\n\n      MetagenomeAnnotation --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeAnnotation : has_output\n\n      MetagenomeAnnotation --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeAnnotation : id\n\n  MetagenomeAnnotation : img_identifiers\n\n  MetagenomeAnnotation : name\n\n  MetagenomeAnnotation : processing_institution\n\n      MetagenomeAnnotation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetagenomeAnnotation : protocol_link\n\n      MetagenomeAnnotation --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetagenomeAnnotation : qc_comment\n\n  MetagenomeAnnotation : qc_status\n\n      MetagenomeAnnotation --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetagenomeAnnotation : start_date\n\n  MetagenomeAnnotation : started_at_time\n\n  MetagenomeAnnotation : type\n\n  MetagenomeAnnotation : version\n\n  MetagenomeAnnotation : was_informed_by\n\n      MetagenomeAnnotation --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetagenomeAnnotation/#inheritance","title":"Inheritance","text":""},{"location":"MetagenomeAnnotation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct gold_analysis_project_identifiers * ExternalIdentifier identifiers for corresponding analysis projects in GOLD direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetagenomeAnnotation/#usages","title":"Usages","text":"used by used in type used FunctionalAnnotationAggMember metagenome_annotation_id any_of[range] MetagenomeAnnotation FunctionalAnnotation was_generated_by range MetagenomeAnnotation"},{"location":"MetagenomeAnnotation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetagenomeAnnotation/#schema-source","title":"Schema Source","text":""},{"location":"MetagenomeAnnotation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetagenomeAnnotation native nmdc:MetagenomeAnnotation"},{"location":"MetagenomeAnnotation/#linkml-source","title":"LinkML Source","text":""},{"location":"MetagenomeAnnotation/#direct","title":"Direct","text":"
name: MetagenomeAnnotation\ndescription: A workflow execution activity that provides functional and structural\n  annotation of assembled metagenome contigs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\n- gold_analysis_project_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\nclass_uri: nmdc:MetagenomeAnnotation\n\n
"},{"location":"MetagenomeAnnotation/#induced","title":"Induced","text":"
name: MetagenomeAnnotation\ndescription: A workflow execution activity that provides functional and structural\n  annotation of assembled metagenome contigs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\nattributes:\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: MetagenomeAnnotation\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n    maximum_cardinality: 1\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    description: identifiers for corresponding analysis projects in GOLD\n    examples:\n    - value: https://bioregistry.io/gold:Ga0526289\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: analysis_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_analysis_project_identifiers\n    owner: MetagenomeAnnotation\n    domain_of:\n    - MetagenomeAnnotation\n    - MetatranscriptomeAnnotation\n    range: external_identifier\n    multivalued: true\n    pattern: ^gold:Ga[0-9]+$\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetagenomeAnnotation\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetagenomeAnnotation\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetagenomeAnnotation\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetagenomeAnnotation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetagenomeAnnotation\n\n
"},{"location":"MetagenomeAssembly/","title":"Class: MetagenomeAssembly","text":"

A workflow execution activity that converts sequencing reads into an assembled metagenome.

URI: nmdc:MetagenomeAssembly

classDiagram\n  class MetagenomeAssembly\n  click MetagenomeAssembly href \"../MetagenomeAssembly\"\n    WorkflowExecution <|-- MetagenomeAssembly\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetagenomeAssembly : alternative_identifiers\n\n  MetagenomeAssembly : asm_score\n\n  MetagenomeAssembly : contig_bp\n\n  MetagenomeAssembly : contigs\n\n  MetagenomeAssembly : ctg_l50\n\n  MetagenomeAssembly : ctg_l90\n\n  MetagenomeAssembly : ctg_logsum\n\n  MetagenomeAssembly : ctg_max\n\n  MetagenomeAssembly : ctg_n50\n\n  MetagenomeAssembly : ctg_n90\n\n  MetagenomeAssembly : ctg_powsum\n\n  MetagenomeAssembly : description\n\n  MetagenomeAssembly : end_date\n\n  MetagenomeAssembly : ended_at_time\n\n  MetagenomeAssembly : execution_resource\n\n      MetagenomeAssembly --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetagenomeAssembly : gap_pct\n\n  MetagenomeAssembly : gc_avg\n\n  MetagenomeAssembly : gc_std\n\n  MetagenomeAssembly : git_url\n\n  MetagenomeAssembly : has_failure_categorization\n\n      MetagenomeAssembly --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetagenomeAssembly : has_input\n\n      MetagenomeAssembly --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeAssembly : has_output\n\n      MetagenomeAssembly --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeAssembly : id\n\n  MetagenomeAssembly : insdc_assembly_identifiers\n\n  MetagenomeAssembly : name\n\n  MetagenomeAssembly : num_aligned_reads\n\n  MetagenomeAssembly : num_input_reads\n\n  MetagenomeAssembly : processing_institution\n\n      MetagenomeAssembly --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetagenomeAssembly : protocol_link\n\n      MetagenomeAssembly --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetagenomeAssembly : qc_comment\n\n  MetagenomeAssembly : qc_status\n\n      MetagenomeAssembly --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetagenomeAssembly : scaf_bp\n\n  MetagenomeAssembly : scaf_l50\n\n  MetagenomeAssembly : scaf_l90\n\n  MetagenomeAssembly : scaf_l_gt50k\n\n  MetagenomeAssembly : scaf_logsum\n\n  MetagenomeAssembly : scaf_max\n\n  MetagenomeAssembly : scaf_n50\n\n  MetagenomeAssembly : scaf_n90\n\n  MetagenomeAssembly : scaf_n_gt50k\n\n  MetagenomeAssembly : scaf_pct_gt50k\n\n  MetagenomeAssembly : scaf_powsum\n\n  MetagenomeAssembly : scaffolds\n\n  MetagenomeAssembly : start_date\n\n  MetagenomeAssembly : started_at_time\n\n  MetagenomeAssembly : type\n\n  MetagenomeAssembly : version\n\n  MetagenomeAssembly : was_informed_by\n\n      MetagenomeAssembly --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetagenomeAssembly/#inheritance","title":"Inheritance","text":""},{"location":"MetagenomeAssembly/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance asm_score 0..1 Float A score for comparing metagenomic assembly quality from same sample direct scaffolds 0..1 Float Total sequence count of all scaffolds direct scaf_logsum 0..1 Float The sum of the (length*log(length)) of all scaffolds, times some constant direct scaf_powsum 0..1 Float Powersum of all scaffolds is the same as logsum except that it uses the sum o... direct scaf_max 0..1 Float Maximum scaffold length direct scaf_bp 0..1 Float Total size in bp of all scaffolds direct scaf_n50 0..1 Float Given a set of scaffolds, each with its own length, the N50 count is defined ... direct scaf_n90 0..1 Float Given a set of scaffolds, each with its own length, the N90 count is defined ... direct scaf_l50 0..1 Float Given a set of scaffolds, the L50 is defined as the sequence length of the sh... direct scaf_l90 0..1 Float The L90 statistic is less than or equal to the L50 statistic; it is the lengt... direct scaf_n_gt50k 0..1 Float Total sequence count of scaffolds greater than 50 KB direct scaf_l_gt50k 0..1 Float Total size in bp of all scaffolds greater than 50 KB direct scaf_pct_gt50k 0..1 Float Total sequence size percentage of scaffolds greater than 50 KB direct contigs 0..1 Float The sum of the (length*log(length)) of all contigs, times some constant direct contig_bp 0..1 Float Total size in bp of all contigs direct ctg_n50 0..1 Float Given a set of contigs, each with its own length, the N50 count is defined as... direct ctg_l50 0..1 Float Given a set of contigs, the L50 is defined as the sequence length of the shor... direct ctg_n90 0..1 Float Given a set of contigs, each with its own length, the N90 count is defined as... direct ctg_l90 0..1 Float The L90 statistic is less than or equal to the L50 statistic; it is the lengt... direct ctg_logsum 0..1 Float Maximum contig length direct ctg_powsum 0..1 Float Powersum of all contigs is the same as logsum except that it uses the sum of ... direct ctg_max 0..1 Float Maximum contig length direct gap_pct 0..1 Float The gap size percentage of all scaffolds direct gc_std 0..1 Float Standard deviation of GC content of all contigs direct gc_avg 0..1 Float Average of GC content of all contigs direct num_input_reads 0..1 Float The sequence count number of input reads for assembly direct num_aligned_reads 0..1 Float The sequence count number of input reads aligned to assembled contigs direct insdc_assembly_identifiers 0..1 String direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetagenomeAssembly/#comments","title":"Comments","text":""},{"location":"MetagenomeAssembly/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetagenomeAssembly/#schema-source","title":"Schema Source","text":""},{"location":"MetagenomeAssembly/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetagenomeAssembly native nmdc:MetagenomeAssembly"},{"location":"MetagenomeAssembly/#linkml-source","title":"LinkML Source","text":""},{"location":"MetagenomeAssembly/#direct","title":"Direct","text":"
name: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n  assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n  relevant to NMDC\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetagenomeAssembly\n\n
"},{"location":"MetagenomeAssembly/#induced","title":"Induced","text":"
name: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n  assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n  relevant to NMDC\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  asm_score:\n    name: asm_score\n    description: A score for comparing metagenomic assembly quality from same sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: asm_score\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaffolds:\n    name: scaffolds\n    description: Total sequence count of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaffolds\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_logsum:\n    name: scaf_logsum\n    description: The sum of the (length*log(length)) of all scaffolds, times some\n      constant.  Increase the contiguity, the score will increase\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_logsum\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_powsum:\n    name: scaf_powsum\n    description: Powersum of all scaffolds is the same as logsum except that it uses\n      the sum of (length*(length^P)) for some power P (default P=0.25).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_powsum\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_max:\n    name: scaf_max\n    description: Maximum scaffold length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_max\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_bp:\n    name: scaf_bp\n    description: Total size in bp of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_bp\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n50:\n    name: scaf_n50\n    description: Given a set of scaffolds, each with its own length, the N50 count\n      is defined as the smallest number of scaffolds whose length sum makes up half\n      of genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n50\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n90:\n    name: scaf_n90\n    description: Given a set of scaffolds, each with its own length, the N90 count\n      is defined as the smallest number of scaffolds whose length sum makes up 90%\n      of genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n90\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l50:\n    name: scaf_l50\n    description: Given a set of scaffolds, the L50 is defined as the sequence length\n      of the shortest scaffold at 50% of the total genome length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l50\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l90:\n    name: scaf_l90\n    description: The L90 statistic is less than or equal to the L50 statistic; it\n      is the length for which the collection of all scaffolds of that length or longer\n      contains at least 90% of the sum of the lengths of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l90\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n_gt50k:\n    name: scaf_n_gt50k\n    description: Total sequence count of scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n_gt50k\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l_gt50k:\n    name: scaf_l_gt50k\n    description: Total size in bp of all scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l_gt50k\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_pct_gt50k:\n    name: scaf_pct_gt50k\n    description: Total sequence size percentage of scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_pct_gt50k\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  contigs:\n    name: contigs\n    description: The sum of the (length*log(length)) of all contigs, times some constant.  Increase\n      the contiguity, the score will increase\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: contigs\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  contig_bp:\n    name: contig_bp\n    description: Total size in bp of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: contig_bp\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_n50:\n    name: ctg_n50\n    description: Given a set of contigs, each with its own length, the N50 count is\n      defined as the smallest number_of_contigs whose length sum makes up half of\n      genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_n50\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_l50:\n    name: ctg_l50\n    description: Given a set of contigs, the L50 is defined as the sequence length\n      of the shortest contig at 50% of the total genome length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_l50\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_n90:\n    name: ctg_n90\n    description: Given a set of contigs, each with its own length, the N90 count is\n      defined as the smallest number of contigs whose length sum makes up 90% of genome\n      size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_n90\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_l90:\n    name: ctg_l90\n    description: The L90 statistic is less than or equal to the L50 statistic; it\n      is the length for which the collection of all contigs of that length or longer\n      contains at least 90% of the sum of the lengths of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_l90\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_logsum:\n    name: ctg_logsum\n    description: Maximum contig length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_logsum\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_powsum:\n    name: ctg_powsum\n    description: Powersum of all contigs is the same as logsum except that it uses\n      the sum of (length*(length^P)) for some power P (default P=0.25).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_powsum\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_max:\n    name: ctg_max\n    description: Maximum contig length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_max\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gap_pct:\n    name: gap_pct\n    description: The gap size percentage of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gap_pct\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gc_std:\n    name: gc_std\n    description: Standard deviation of GC content of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gc_std\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gc_avg:\n    name: gc_avg\n    description: Average of GC content of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gc_avg\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  num_input_reads:\n    name: num_input_reads\n    description: The sequence count number of input reads for assembly.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: num_input_reads\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  num_aligned_reads:\n    name: num_aligned_reads\n    description: The sequence count number of input reads aligned to assembled contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: num_aligned_reads\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  insdc_assembly_identifiers:\n    name: insdc_assembly_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: assembly_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_assembly_identifiers\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: string\n    pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetagenomeAssembly\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetagenomeAssembly\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetagenomeAssembly\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetagenomeAssembly\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetagenomeAssembly\n\n
"},{"location":"MetagenomeSequencing/","title":"Class: Metagenome sequencing activity (MetagenomeSequencing)","text":"

Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.

URI: nmdc:MetagenomeSequencing

classDiagram\n  class MetagenomeSequencing\n  click MetagenomeSequencing href \"../MetagenomeSequencing\"\n    WorkflowExecution <|-- MetagenomeSequencing\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetagenomeSequencing : alternative_identifiers\n\n  MetagenomeSequencing : description\n\n  MetagenomeSequencing : end_date\n\n  MetagenomeSequencing : ended_at_time\n\n  MetagenomeSequencing : execution_resource\n\n      MetagenomeSequencing --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetagenomeSequencing : git_url\n\n  MetagenomeSequencing : has_failure_categorization\n\n      MetagenomeSequencing --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetagenomeSequencing : has_input\n\n      MetagenomeSequencing --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeSequencing : has_output\n\n      MetagenomeSequencing --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeSequencing : id\n\n  MetagenomeSequencing : name\n\n  MetagenomeSequencing : processing_institution\n\n      MetagenomeSequencing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetagenomeSequencing : protocol_link\n\n      MetagenomeSequencing --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetagenomeSequencing : qc_comment\n\n  MetagenomeSequencing : qc_status\n\n      MetagenomeSequencing --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetagenomeSequencing : start_date\n\n  MetagenomeSequencing : started_at_time\n\n  MetagenomeSequencing : type\n\n  MetagenomeSequencing : version\n\n  MetagenomeSequencing : was_informed_by\n\n      MetagenomeSequencing --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetagenomeSequencing/#inheritance","title":"Inheritance","text":""},{"location":"MetagenomeSequencing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetagenomeSequencing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetagenomeSequencing/#schema-source","title":"Schema Source","text":""},{"location":"MetagenomeSequencing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetagenomeSequencing native nmdc:MetagenomeSequencing"},{"location":"MetagenomeSequencing/#linkml-source","title":"LinkML Source","text":""},{"location":"MetagenomeSequencing/#direct","title":"Direct","text":"
name: MetagenomeSequencing\ndescription: Initial sequencing activity that precedes any analysis.  This activity\n  has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetagenomeSequencing\n\n
"},{"location":"MetagenomeSequencing/#induced","title":"Induced","text":"
name: MetagenomeSequencing\ndescription: Initial sequencing activity that precedes any analysis.  This activity\n  has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetagenomeSequencing\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetagenomeSequencing\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetagenomeSequencing\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetagenomeSequencing\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetagenomeSequencing\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetagenomeSequencing\n\n
"},{"location":"MetaproteomicsAnalysis/","title":"Class: MetaproteomicsAnalysis","text":"

URI: nmdc:MetaproteomicsAnalysis

classDiagram\n  class MetaproteomicsAnalysis\n  click MetaproteomicsAnalysis href \"../MetaproteomicsAnalysis\"\n    WorkflowExecution <|-- MetaproteomicsAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetaproteomicsAnalysis : alternative_identifiers\n\n  MetaproteomicsAnalysis : description\n\n  MetaproteomicsAnalysis : end_date\n\n  MetaproteomicsAnalysis : ended_at_time\n\n  MetaproteomicsAnalysis : execution_resource\n\n      MetaproteomicsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetaproteomicsAnalysis : git_url\n\n  MetaproteomicsAnalysis : has_failure_categorization\n\n      MetaproteomicsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetaproteomicsAnalysis : has_input\n\n      MetaproteomicsAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetaproteomicsAnalysis : has_output\n\n      MetaproteomicsAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetaproteomicsAnalysis : has_peptide_quantifications\n\n      MetaproteomicsAnalysis --> \"*\" PeptideQuantification : has_peptide_quantifications\n    click PeptideQuantification href \"../PeptideQuantification\"\n\n  MetaproteomicsAnalysis : id\n\n  MetaproteomicsAnalysis : name\n\n  MetaproteomicsAnalysis : processing_institution\n\n      MetaproteomicsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetaproteomicsAnalysis : protocol_link\n\n      MetaproteomicsAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetaproteomicsAnalysis : qc_comment\n\n  MetaproteomicsAnalysis : qc_status\n\n      MetaproteomicsAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetaproteomicsAnalysis : start_date\n\n  MetaproteomicsAnalysis : started_at_time\n\n  MetaproteomicsAnalysis : type\n\n  MetaproteomicsAnalysis : version\n\n  MetaproteomicsAnalysis : was_informed_by\n\n      MetaproteomicsAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetaproteomicsAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"MetaproteomicsAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_peptide_quantifications * PeptideQuantification direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetaproteomicsAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetaproteomicsAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"MetaproteomicsAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetaproteomicsAnalysis native nmdc:MetaproteomicsAnalysis"},{"location":"MetaproteomicsAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"MetaproteomicsAnalysis/#direct","title":"Direct","text":"
name: MetaproteomicsAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- has_peptide_quantifications\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetaproteomicsAnalysis\n\n
"},{"location":"MetaproteomicsAnalysis/#induced","title":"Induced","text":"
name: MetaproteomicsAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_peptide_quantifications:\n    name: has_peptide_quantifications\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_peptide_quantifications\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - MetaproteomicsAnalysis\n    range: PeptideQuantification\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetaproteomicsAnalysis\n\n
"},{"location":"MetatranscriptomeAnnotation/","title":"Class: MetatranscriptomeAnnotation","text":"

URI: nmdc:MetatranscriptomeAnnotation

classDiagram\n  class MetatranscriptomeAnnotation\n  click MetatranscriptomeAnnotation href \"../MetatranscriptomeAnnotation\"\n    WorkflowExecution <|-- MetatranscriptomeAnnotation\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetatranscriptomeAnnotation : alternative_identifiers\n\n  MetatranscriptomeAnnotation : description\n\n  MetatranscriptomeAnnotation : end_date\n\n  MetatranscriptomeAnnotation : ended_at_time\n\n  MetatranscriptomeAnnotation : execution_resource\n\n      MetatranscriptomeAnnotation --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetatranscriptomeAnnotation : git_url\n\n  MetatranscriptomeAnnotation : gold_analysis_project_identifiers\n\n  MetatranscriptomeAnnotation : has_failure_categorization\n\n      MetatranscriptomeAnnotation --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetatranscriptomeAnnotation : has_input\n\n      MetatranscriptomeAnnotation --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeAnnotation : has_output\n\n      MetatranscriptomeAnnotation --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeAnnotation : id\n\n  MetatranscriptomeAnnotation : img_identifiers\n\n  MetatranscriptomeAnnotation : name\n\n  MetatranscriptomeAnnotation : processing_institution\n\n      MetatranscriptomeAnnotation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetatranscriptomeAnnotation : protocol_link\n\n      MetatranscriptomeAnnotation --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetatranscriptomeAnnotation : qc_comment\n\n  MetatranscriptomeAnnotation : qc_status\n\n      MetatranscriptomeAnnotation --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetatranscriptomeAnnotation : start_date\n\n  MetatranscriptomeAnnotation : started_at_time\n\n  MetatranscriptomeAnnotation : type\n\n  MetatranscriptomeAnnotation : version\n\n  MetatranscriptomeAnnotation : was_informed_by\n\n      MetatranscriptomeAnnotation --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetatranscriptomeAnnotation/#inheritance","title":"Inheritance","text":""},{"location":"MetatranscriptomeAnnotation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct gold_analysis_project_identifiers * ExternalIdentifier identifiers for corresponding analysis projects in GOLD direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetatranscriptomeAnnotation/#usages","title":"Usages","text":"used by used in type used FunctionalAnnotationAggMember metagenome_annotation_id any_of[range] MetatranscriptomeAnnotation"},{"location":"MetatranscriptomeAnnotation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetatranscriptomeAnnotation/#schema-source","title":"Schema Source","text":""},{"location":"MetatranscriptomeAnnotation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetatranscriptomeAnnotation native nmdc:MetatranscriptomeAnnotation"},{"location":"MetatranscriptomeAnnotation/#linkml-source","title":"LinkML Source","text":""},{"location":"MetatranscriptomeAnnotation/#direct","title":"Direct","text":"
name: MetatranscriptomeAnnotation\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\n- gold_analysis_project_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\nclass_uri: nmdc:MetatranscriptomeAnnotation\n\n
"},{"location":"MetatranscriptomeAnnotation/#induced","title":"Induced","text":"
name: MetatranscriptomeAnnotation\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\nattributes:\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n    maximum_cardinality: 1\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    description: identifiers for corresponding analysis projects in GOLD\n    examples:\n    - value: https://bioregistry.io/gold:Ga0526289\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: analysis_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_analysis_project_identifiers\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - MetagenomeAnnotation\n    - MetatranscriptomeAnnotation\n    range: external_identifier\n    multivalued: true\n    pattern: ^gold:Ga[0-9]+$\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetatranscriptomeAnnotation\n\n
"},{"location":"MetatranscriptomeAssembly/","title":"Class: MetatranscriptomeAssembly","text":"

URI: nmdc:MetatranscriptomeAssembly

classDiagram\n  class MetatranscriptomeAssembly\n  click MetatranscriptomeAssembly href \"../MetatranscriptomeAssembly\"\n    WorkflowExecution <|-- MetatranscriptomeAssembly\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetatranscriptomeAssembly : alternative_identifiers\n\n  MetatranscriptomeAssembly : asm_score\n\n  MetatranscriptomeAssembly : contig_bp\n\n  MetatranscriptomeAssembly : contigs\n\n  MetatranscriptomeAssembly : ctg_l50\n\n  MetatranscriptomeAssembly : ctg_l90\n\n  MetatranscriptomeAssembly : ctg_logsum\n\n  MetatranscriptomeAssembly : ctg_max\n\n  MetatranscriptomeAssembly : ctg_n50\n\n  MetatranscriptomeAssembly : ctg_n90\n\n  MetatranscriptomeAssembly : ctg_powsum\n\n  MetatranscriptomeAssembly : description\n\n  MetatranscriptomeAssembly : end_date\n\n  MetatranscriptomeAssembly : ended_at_time\n\n  MetatranscriptomeAssembly : execution_resource\n\n      MetatranscriptomeAssembly --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetatranscriptomeAssembly : gap_pct\n\n  MetatranscriptomeAssembly : gc_avg\n\n  MetatranscriptomeAssembly : gc_std\n\n  MetatranscriptomeAssembly : git_url\n\n  MetatranscriptomeAssembly : has_failure_categorization\n\n      MetatranscriptomeAssembly --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetatranscriptomeAssembly : has_input\n\n      MetatranscriptomeAssembly --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeAssembly : has_output\n\n      MetatranscriptomeAssembly --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeAssembly : id\n\n  MetatranscriptomeAssembly : insdc_assembly_identifiers\n\n  MetatranscriptomeAssembly : name\n\n  MetatranscriptomeAssembly : num_aligned_reads\n\n  MetatranscriptomeAssembly : num_input_reads\n\n  MetatranscriptomeAssembly : processing_institution\n\n      MetatranscriptomeAssembly --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetatranscriptomeAssembly : protocol_link\n\n      MetatranscriptomeAssembly --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetatranscriptomeAssembly : qc_comment\n\n  MetatranscriptomeAssembly : qc_status\n\n      MetatranscriptomeAssembly --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetatranscriptomeAssembly : scaf_bp\n\n  MetatranscriptomeAssembly : scaf_l50\n\n  MetatranscriptomeAssembly : scaf_l90\n\n  MetatranscriptomeAssembly : scaf_l_gt50k\n\n  MetatranscriptomeAssembly : scaf_logsum\n\n  MetatranscriptomeAssembly : scaf_max\n\n  MetatranscriptomeAssembly : scaf_n50\n\n  MetatranscriptomeAssembly : scaf_n90\n\n  MetatranscriptomeAssembly : scaf_n_gt50k\n\n  MetatranscriptomeAssembly : scaf_pct_gt50k\n\n  MetatranscriptomeAssembly : scaf_powsum\n\n  MetatranscriptomeAssembly : scaffolds\n\n  MetatranscriptomeAssembly : start_date\n\n  MetatranscriptomeAssembly : started_at_time\n\n  MetatranscriptomeAssembly : type\n\n  MetatranscriptomeAssembly : version\n\n  MetatranscriptomeAssembly : was_informed_by\n\n      MetatranscriptomeAssembly --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetatranscriptomeAssembly/#inheritance","title":"Inheritance","text":""},{"location":"MetatranscriptomeAssembly/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance asm_score 0..1 Float A score for comparing metagenomic assembly quality from same sample direct scaffolds 0..1 Float Total sequence count of all scaffolds direct scaf_logsum 0..1 Float The sum of the (length*log(length)) of all scaffolds, times some constant direct scaf_powsum 0..1 Float Powersum of all scaffolds is the same as logsum except that it uses the sum o... direct scaf_max 0..1 Float Maximum scaffold length direct scaf_bp 0..1 Float Total size in bp of all scaffolds direct scaf_n50 0..1 Float Given a set of scaffolds, each with its own length, the N50 count is defined ... direct scaf_n90 0..1 Float Given a set of scaffolds, each with its own length, the N90 count is defined ... direct scaf_l50 0..1 Float Given a set of scaffolds, the L50 is defined as the sequence length of the sh... direct scaf_l90 0..1 Float The L90 statistic is less than or equal to the L50 statistic; it is the lengt... direct scaf_n_gt50k 0..1 Float Total sequence count of scaffolds greater than 50 KB direct scaf_l_gt50k 0..1 Float Total size in bp of all scaffolds greater than 50 KB direct scaf_pct_gt50k 0..1 Float Total sequence size percentage of scaffolds greater than 50 KB direct contigs 0..1 Float The sum of the (length*log(length)) of all contigs, times some constant direct contig_bp 0..1 Float Total size in bp of all contigs direct ctg_n50 0..1 Float Given a set of contigs, each with its own length, the N50 count is defined as... direct ctg_l50 0..1 Float Given a set of contigs, the L50 is defined as the sequence length of the shor... direct ctg_n90 0..1 Float Given a set of contigs, each with its own length, the N90 count is defined as... direct ctg_l90 0..1 Float The L90 statistic is less than or equal to the L50 statistic; it is the lengt... direct ctg_logsum 0..1 Float Maximum contig length direct ctg_powsum 0..1 Float Powersum of all contigs is the same as logsum except that it uses the sum of ... direct ctg_max 0..1 Float Maximum contig length direct gap_pct 0..1 Float The gap size percentage of all scaffolds direct gc_std 0..1 Float Standard deviation of GC content of all contigs direct gc_avg 0..1 Float Average of GC content of all contigs direct num_input_reads 0..1 Float The sequence count number of input reads for assembly direct num_aligned_reads 0..1 Float The sequence count number of input reads aligned to assembled contigs direct insdc_assembly_identifiers 0..1 String direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetatranscriptomeAssembly/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetatranscriptomeAssembly/#schema-source","title":"Schema Source","text":""},{"location":"MetatranscriptomeAssembly/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetatranscriptomeAssembly native nmdc:MetatranscriptomeAssembly"},{"location":"MetatranscriptomeAssembly/#linkml-source","title":"LinkML Source","text":""},{"location":"MetatranscriptomeAssembly/#direct","title":"Direct","text":"
name: MetatranscriptomeAssembly\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetatranscriptomeAssembly\n\n
"},{"location":"MetatranscriptomeAssembly/#induced","title":"Induced","text":"
name: MetatranscriptomeAssembly\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  asm_score:\n    name: asm_score\n    description: A score for comparing metagenomic assembly quality from same sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: asm_score\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaffolds:\n    name: scaffolds\n    description: Total sequence count of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaffolds\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_logsum:\n    name: scaf_logsum\n    description: The sum of the (length*log(length)) of all scaffolds, times some\n      constant.  Increase the contiguity, the score will increase\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_logsum\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_powsum:\n    name: scaf_powsum\n    description: Powersum of all scaffolds is the same as logsum except that it uses\n      the sum of (length*(length^P)) for some power P (default P=0.25).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_powsum\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_max:\n    name: scaf_max\n    description: Maximum scaffold length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_max\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_bp:\n    name: scaf_bp\n    description: Total size in bp of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_bp\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n50:\n    name: scaf_n50\n    description: Given a set of scaffolds, each with its own length, the N50 count\n      is defined as the smallest number of scaffolds whose length sum makes up half\n      of genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n50\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n90:\n    name: scaf_n90\n    description: Given a set of scaffolds, each with its own length, the N90 count\n      is defined as the smallest number of scaffolds whose length sum makes up 90%\n      of genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n90\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l50:\n    name: scaf_l50\n    description: Given a set of scaffolds, the L50 is defined as the sequence length\n      of the shortest scaffold at 50% of the total genome length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l50\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l90:\n    name: scaf_l90\n    description: The L90 statistic is less than or equal to the L50 statistic; it\n      is the length for which the collection of all scaffolds of that length or longer\n      contains at least 90% of the sum of the lengths of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l90\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n_gt50k:\n    name: scaf_n_gt50k\n    description: Total sequence count of scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n_gt50k\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l_gt50k:\n    name: scaf_l_gt50k\n    description: Total size in bp of all scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l_gt50k\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_pct_gt50k:\n    name: scaf_pct_gt50k\n    description: Total sequence size percentage of scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_pct_gt50k\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  contigs:\n    name: contigs\n    description: The sum of the (length*log(length)) of all contigs, times some constant.  Increase\n      the contiguity, the score will increase\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: contigs\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  contig_bp:\n    name: contig_bp\n    description: Total size in bp of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: contig_bp\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_n50:\n    name: ctg_n50\n    description: Given a set of contigs, each with its own length, the N50 count is\n      defined as the smallest number_of_contigs whose length sum makes up half of\n      genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_n50\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_l50:\n    name: ctg_l50\n    description: Given a set of contigs, the L50 is defined as the sequence length\n      of the shortest contig at 50% of the total genome length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_l50\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_n90:\n    name: ctg_n90\n    description: Given a set of contigs, each with its own length, the N90 count is\n      defined as the smallest number of contigs whose length sum makes up 90% of genome\n      size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_n90\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_l90:\n    name: ctg_l90\n    description: The L90 statistic is less than or equal to the L50 statistic; it\n      is the length for which the collection of all contigs of that length or longer\n      contains at least 90% of the sum of the lengths of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_l90\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_logsum:\n    name: ctg_logsum\n    description: Maximum contig length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_logsum\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_powsum:\n    name: ctg_powsum\n    description: Powersum of all contigs is the same as logsum except that it uses\n      the sum of (length*(length^P)) for some power P (default P=0.25).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_powsum\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_max:\n    name: ctg_max\n    description: Maximum contig length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_max\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gap_pct:\n    name: gap_pct\n    description: The gap size percentage of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gap_pct\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gc_std:\n    name: gc_std\n    description: Standard deviation of GC content of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gc_std\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gc_avg:\n    name: gc_avg\n    description: Average of GC content of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gc_avg\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  num_input_reads:\n    name: num_input_reads\n    description: The sequence count number of input reads for assembly.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: num_input_reads\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  num_aligned_reads:\n    name: num_aligned_reads\n    description: The sequence count number of input reads aligned to assembled contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: num_aligned_reads\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  insdc_assembly_identifiers:\n    name: insdc_assembly_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: assembly_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_assembly_identifiers\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: string\n    pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetatranscriptomeAssembly\n\n
"},{"location":"MetatranscriptomeExpressionAnalysis/","title":"Class: MetatranscriptomeExpressionAnalysis","text":"

A workflow process that provides expression values and read counts for gene features predicted on the contigs.

URI: nmdc:MetatranscriptomeExpressionAnalysis

classDiagram\n  class MetatranscriptomeExpressionAnalysis\n  click MetatranscriptomeExpressionAnalysis href \"../MetatranscriptomeExpressionAnalysis\"\n    WorkflowExecution <|-- MetatranscriptomeExpressionAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetatranscriptomeExpressionAnalysis : alternative_identifiers\n\n  MetatranscriptomeExpressionAnalysis : description\n\n  MetatranscriptomeExpressionAnalysis : end_date\n\n  MetatranscriptomeExpressionAnalysis : ended_at_time\n\n  MetatranscriptomeExpressionAnalysis : execution_resource\n\n      MetatranscriptomeExpressionAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetatranscriptomeExpressionAnalysis : git_url\n\n  MetatranscriptomeExpressionAnalysis : has_failure_categorization\n\n      MetatranscriptomeExpressionAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetatranscriptomeExpressionAnalysis : has_input\n\n      MetatranscriptomeExpressionAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeExpressionAnalysis : has_output\n\n      MetatranscriptomeExpressionAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeExpressionAnalysis : id\n\n  MetatranscriptomeExpressionAnalysis : img_identifiers\n\n  MetatranscriptomeExpressionAnalysis : name\n\n  MetatranscriptomeExpressionAnalysis : processing_institution\n\n      MetatranscriptomeExpressionAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetatranscriptomeExpressionAnalysis : protocol_link\n\n      MetatranscriptomeExpressionAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetatranscriptomeExpressionAnalysis : qc_comment\n\n  MetatranscriptomeExpressionAnalysis : qc_status\n\n      MetatranscriptomeExpressionAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetatranscriptomeExpressionAnalysis : start_date\n\n  MetatranscriptomeExpressionAnalysis : started_at_time\n\n  MetatranscriptomeExpressionAnalysis : type\n\n  MetatranscriptomeExpressionAnalysis : version\n\n  MetatranscriptomeExpressionAnalysis : was_informed_by\n\n      MetatranscriptomeExpressionAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetatranscriptomeExpressionAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"MetatranscriptomeExpressionAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetatranscriptomeExpressionAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetatranscriptomeExpressionAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"MetatranscriptomeExpressionAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetatranscriptomeExpressionAnalysis native nmdc:MetatranscriptomeExpressionAnalysis"},{"location":"MetatranscriptomeExpressionAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"MetatranscriptomeExpressionAnalysis/#direct","title":"Direct","text":"
name: MetatranscriptomeExpressionAnalysis\ndescription: A workflow process that provides expression values and read counts for\n  gene features predicted on the contigs.\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetatranscriptomeExpressionAnalysis\n\n
"},{"location":"MetatranscriptomeExpressionAnalysis/#induced","title":"Induced","text":"
name: MetatranscriptomeExpressionAnalysis\ndescription: A workflow process that provides expression values and read counts for\n  gene features predicted on the contigs.\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n    maximum_cardinality: 1\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetatranscriptomeExpressionAnalysis\n\n
"},{"location":"MixingProcess/","title":"Class: MixingProcess","text":"

The combining of components, particles or layers into a more homogeneous state.

__

URI: nmdc:MixingProcess

classDiagram\n  class MixingProcess\n  click MixingProcess href \"../MixingProcess\"\n    MaterialProcessing <|-- MixingProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  MixingProcess : alternative_identifiers\n\n  MixingProcess : description\n\n  MixingProcess : duration\n\n      MixingProcess --> \"0..1\" QuantityValue : duration\n    click QuantityValue href \"../QuantityValue\"\n\n  MixingProcess : end_date\n\n  MixingProcess : has_failure_categorization\n\n      MixingProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MixingProcess : has_input\n\n      MixingProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MixingProcess : has_output\n\n      MixingProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  MixingProcess : id\n\n  MixingProcess : instrument_used\n\n      MixingProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  MixingProcess : name\n\n  MixingProcess : processing_institution\n\n      MixingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MixingProcess : protocol_link\n\n      MixingProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MixingProcess : qc_comment\n\n  MixingProcess : qc_status\n\n      MixingProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MixingProcess : start_date\n\n  MixingProcess : type\n\n\n\n
"},{"location":"MixingProcess/#inheritance","title":"Inheritance","text":""},{"location":"MixingProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance duration 0..1 QuantityValue The elapsed time of an activity direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample The mixed sample PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MixingProcess/#comments","title":"Comments","text":""},{"location":"MixingProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixingProcess/#schema-source","title":"Schema Source","text":""},{"location":"MixingProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MixingProcess native nmdc:MixingProcess"},{"location":"MixingProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"MixingProcess/#direct","title":"Direct","text":"
name: MixingProcess\ndescription: 'The combining of components, particles or layers into a more homogeneous\n  state.\n\n  '\ncomments:\n- The mixing may be achieved manually or mechanically by shifting the material with\n  stirrers or pumps or by revolving or shaking the container.\n- The process must not permit segregation of particles of different size or properties.\n- Homogeneity may be considered to have been achieved in a practical sense when the\n  sampling error of the processed portion is negligible compared to the total error\n  of the measurement system.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nis_a: MaterialProcessing\nslots:\n- duration\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The mixed sample.\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MixingProcess\n\n
"},{"location":"MixingProcess/#induced","title":"Induced","text":"
name: MixingProcess\ndescription: 'The combining of components, particles or layers into a more homogeneous\n  state.\n\n  '\ncomments:\n- The mixing may be achieved manually or mechanically by shifting the material with\n  stirrers or pumps or by revolving or shaking the container.\n- The process must not permit segregation of particles of different size or properties.\n- Homogeneity may be considered to have been achieved in a practical sense when the\n  sampling error of the processed portion is negligible compared to the total error\n  of the measurement system.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The mixed sample.\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  duration:\n    name: duration\n    description: The elapsed time of an activity.\n    examples:\n    - value: JsonObj(has_numeric_value=2, has_unit='hours')\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: duration\n    owner: MixingProcess\n    domain_of:\n    - MixingProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: MixingProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The mixed sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MixingProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MixingProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MixingProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MixingProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MixingProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MixingProcess\n\n
"},{"location":"MixsEnvironmentalTriad/","title":"Subset: MixsEnvironmentalTriad","text":"

URI: MixsEnvironmentalTriad

"},{"location":"MixsEnvironmentalTriad/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixsEnvironmentalTriad/#schema-source","title":"Schema Source","text":""},{"location":"MixsExtension/","title":"Subset: MixsExtension","text":"

URI: MixsExtension

"},{"location":"MixsExtension/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixsExtension/#schema-source","title":"Schema Source","text":""},{"location":"MixsExtension/#slots-in-subset","title":"Slots in subset","text":"Slot Description env_package MIxS extension for reporting of measurements and observations obtained from o..."},{"location":"MobilePhaseSegment/","title":"Class: MobilePhaseSegment","text":"

A fluid mixture of substances that flow though a chromatographic stationary phase.

URI: nmdc:MobilePhaseSegment

classDiagram\n  class MobilePhaseSegment\n  click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n  MobilePhaseSegment : duration\n\n      MobilePhaseSegment --> \"0..1\" QuantityValue : duration\n    click QuantityValue href \"../QuantityValue\"\n\n  MobilePhaseSegment : substances_used\n\n      MobilePhaseSegment --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  MobilePhaseSegment : type\n\n  MobilePhaseSegment : volume\n\n      MobilePhaseSegment --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"MobilePhaseSegment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance duration 0..1 QuantityValue The elapsed time of an activity direct substances_used * PortionOfSubstance The substances that are combined to enable a ChemicalConversionProcess direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct volume 0..1 QuantityValue The volume of a substance direct"},{"location":"MobilePhaseSegment/#usages","title":"Usages","text":"used by used in type used ChromatographyConfiguration ordered_mobile_phases range MobilePhaseSegment ChromatographicSeparationProcess ordered_mobile_phases range MobilePhaseSegment"},{"location":"MobilePhaseSegment/#comments","title":"Comments","text":""},{"location":"MobilePhaseSegment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MobilePhaseSegment/#schema-source","title":"Schema Source","text":""},{"location":"MobilePhaseSegment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MobilePhaseSegment native nmdc:MobilePhaseSegment"},{"location":"MobilePhaseSegment/#linkml-source","title":"LinkML Source","text":""},{"location":"MobilePhaseSegment/#direct","title":"Direct","text":"
name: MobilePhaseSegment\ndescription: A fluid mixture of substances that flow though a chromatographic stationary\n  phase.\ncomments:\n- Can be assembled into a list to account for a gradient.\n- Works best for separations that can be accounted for by a series of essentially\n  linear changes in the mobile phase composition.\n- For gradients, each segment should declare it's duration.\n- For step-wise separations that might be implemented with a syringe and a cartridge,\n  it will probably be more important to assert volumes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- duration\n- substances_used\n- type\n- volume\nclass_uri: nmdc:MobilePhaseSegment\n\n
"},{"location":"MobilePhaseSegment/#induced","title":"Induced","text":"
name: MobilePhaseSegment\ndescription: A fluid mixture of substances that flow though a chromatographic stationary\n  phase.\ncomments:\n- Can be assembled into a list to account for a gradient.\n- Works best for separations that can be accounted for by a series of essentially\n  linear changes in the mobile phase composition.\n- For gradients, each segment should declare it's duration.\n- For step-wise separations that might be implemented with a syringe and a cartridge,\n  it will probably be more important to assert volumes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  duration:\n    name: duration\n    description: The elapsed time of an activity.\n    examples:\n    - value: JsonObj(has_numeric_value=2, has_unit='hours')\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: duration\n    owner: MobilePhaseSegment\n    domain_of:\n    - MixingProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: QuantityValue\n  substances_used:\n    name: substances_used\n    description: The substances that are combined to enable a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: MobilePhaseSegment\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MobilePhaseSegment\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  volume:\n    name: volume\n    description: The volume of a substance.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: MobilePhaseSegment\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\nclass_uri: nmdc:MobilePhaseSegment\n\n
"},{"location":"NMDC/","title":"NMDC","text":"

Schema for National Microbiome Data Collaborative (NMDC). This schema is organized into multiple modules, such as:

URI: https://w3id.org/nmdc/nmdc

"},{"location":"NamedThing/","title":"Class: NamedThing","text":"

a databased entity or concept/class

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:NamedThing

classDiagram\n  class NamedThing\n  click NamedThing href \"../NamedThing\"\n    NamedThing <|-- GeneProduct\n      click GeneProduct href \"../GeneProduct\"\n    NamedThing <|-- OntologyClass\n      click OntologyClass href \"../OntologyClass\"\n    NamedThing <|-- MaterialEntity\n      click MaterialEntity href \"../MaterialEntity\"\n    NamedThing <|-- PlannedProcess\n      click PlannedProcess href \"../PlannedProcess\"\n    NamedThing <|-- Study\n      click Study href \"../Study\"\n    NamedThing <|-- InformationObject\n      click InformationObject href \"../InformationObject\"\n\n\n\n  NamedThing : alternative_identifiers\n\n  NamedThing : description\n\n  NamedThing : id\n\n  NamedThing : name\n\n  NamedThing : type\n\n\n\n
"},{"location":"NamedThing/#inheritance","title":"Inheritance","text":""},{"location":"NamedThing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing direct name 0..1 String A human readable label for an entity direct description 0..1 String a human-readable description of a thing direct alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"NamedThing/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_input range NamedThing MassSpectrometry has_input range NamedThing Pooling has_input range NamedThing Extraction has_input range NamedThing LibraryPreparation has_input range NamedThing ProtocolExecution has_input range NamedThing ProtocolExecution has_output range NamedThing SubSamplingProcess has_input range NamedThing MixingProcess has_input range NamedThing FiltrationProcess has_input range NamedThing StorageProcess has_input range NamedThing StorageProcess has_output range NamedThing ChromatographicSeparationProcess has_input range NamedThing DissolvingProcess has_input range NamedThing ChemicalConversionProcess has_input range NamedThing MetagenomeAnnotation has_input range NamedThing MetagenomeAnnotation has_output range NamedThing MaterialProcessing has_input range NamedThing PlannedProcess has_input range NamedThing PlannedProcess has_output range NamedThing DataGeneration has_input range NamedThing WorkflowExecution has_input range NamedThing WorkflowExecution has_output range NamedThing MetagenomeAssembly has_input range NamedThing MetagenomeAssembly has_output range NamedThing MetatranscriptomeAssembly has_input range NamedThing MetatranscriptomeAssembly has_output range NamedThing MetatranscriptomeAnnotation has_input range NamedThing MetatranscriptomeAnnotation has_output range NamedThing MetatranscriptomeExpressionAnalysis has_input range NamedThing MetatranscriptomeExpressionAnalysis has_output range NamedThing MagsAnalysis has_input range NamedThing MagsAnalysis has_output range NamedThing MetagenomeSequencing has_input range NamedThing MetagenomeSequencing has_output range NamedThing ReadQcAnalysis has_input range NamedThing ReadQcAnalysis has_output range NamedThing ReadBasedTaxonomyAnalysis has_input range NamedThing ReadBasedTaxonomyAnalysis has_output range NamedThing MetabolomicsAnalysis has_input range NamedThing MetabolomicsAnalysis has_output range NamedThing MetaproteomicsAnalysis has_input range NamedThing MetaproteomicsAnalysis has_output range NamedThing NomAnalysis has_input range NamedThing NomAnalysis has_output range NamedThing"},{"location":"NamedThing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NamedThing/#schema-source","title":"Schema Source","text":""},{"location":"NamedThing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:NamedThing native nmdc:NamedThing"},{"location":"NamedThing/#linkml-source","title":"LinkML Source","text":""},{"location":"NamedThing/#direct","title":"Direct","text":"
name: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- id\n- name\n- description\n- alternative_identifiers\n- type\nclass_uri: nmdc:NamedThing\n\n
"},{"location":"NamedThing/#induced","title":"Induced","text":"
name: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedThing\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: NamedThing\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: NamedThing\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: NamedThing\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: NamedThing\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:NamedThing\n\n
"},{"location":"Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Ncname/#schema-source","title":"Schema Source","text":""},{"location":"Ncname/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:ncname"},{"location":"Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"Nodeidentifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self shex:nonLiteral native nmdc:nodeidentifier"},{"location":"NomAnalysis/","title":"Class: NomAnalysis","text":"

URI: nmdc:NomAnalysis

classDiagram\n  class NomAnalysis\n  click NomAnalysis href \"../NomAnalysis\"\n    WorkflowExecution <|-- NomAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  NomAnalysis : alternative_identifiers\n\n  NomAnalysis : description\n\n  NomAnalysis : end_date\n\n  NomAnalysis : ended_at_time\n\n  NomAnalysis : execution_resource\n\n      NomAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  NomAnalysis : git_url\n\n  NomAnalysis : has_calibration\n\n  NomAnalysis : has_failure_categorization\n\n      NomAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  NomAnalysis : has_input\n\n      NomAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  NomAnalysis : has_output\n\n      NomAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  NomAnalysis : id\n\n  NomAnalysis : name\n\n  NomAnalysis : processing_institution\n\n      NomAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  NomAnalysis : protocol_link\n\n      NomAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  NomAnalysis : qc_comment\n\n  NomAnalysis : qc_status\n\n      NomAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  NomAnalysis : start_date\n\n  NomAnalysis : started_at_time\n\n  NomAnalysis : type\n\n  NomAnalysis : version\n\n  NomAnalysis : was_informed_by\n\n      NomAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"NomAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"NomAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_calibration 0..1 String\u00a0or\u00a0CalibrationInformation\u00a0or\u00a0String a calibration instance associated with a process direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"NomAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NomAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"NomAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:NomAnalysis native nmdc:NomAnalysis"},{"location":"NomAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"NomAnalysis/#direct","title":"Direct","text":"
name: NomAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- has_calibration\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:NomAnalysis\n\n
"},{"location":"NomAnalysis/#induced","title":"Induced","text":"
name: NomAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_calibration:\n    name: has_calibration\n    description: a calibration instance associated with a process\n    notes:\n    - 'has_calibration slot will be removed from all WorkflowExecution classes but\n      remain on the MassSpectrometry class after an ingest of the appropriate set\n      has occurred.  Once this has occurred, this slot''s range can be updated to\n      CalibrationInformation and class/slot definitions can move to nmdc.yaml.   See\n      PR #29 in Berkeley schema.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_calibration\n    owner: NomAnalysis\n    domain_of:\n    - MassSpectrometry\n    - MetabolomicsAnalysis\n    - NomAnalysis\n    range: string\n    any_of:\n    - range: CalibrationInformation\n    - range: string\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NomAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: NomAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: NomAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: NomAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: NomAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:NomAnalysis\n\n
"},{"location":"NucleicAcidSequenceSource/","title":"Subset: NucleicAcidSequenceSource","text":"

URI: NucleicAcidSequenceSource

"},{"location":"NucleicAcidSequenceSource/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NucleicAcidSequenceSource/#schema-source","title":"Schema Source","text":""},{"location":"NucleotideSequencing/","title":"Class: NucleotideSequencing","text":"

A DataGeneration in which the sequence of DNA or RNA molecules is generated.

URI: nmdc:NucleotideSequencing

classDiagram\n  class NucleotideSequencing\n  click NucleotideSequencing href \"../NucleotideSequencing\"\n    DataGeneration <|-- NucleotideSequencing\n      click DataGeneration href \"../DataGeneration\"\n\n\n\n  NucleotideSequencing : add_date\n\n  NucleotideSequencing : alternative_identifiers\n\n  NucleotideSequencing : analyte_category\n\n      NucleotideSequencing --> \"1\" AnalyteCategoryEnum : analyte_category\n    click AnalyteCategoryEnum href \"../AnalyteCategoryEnum\"\n\n  NucleotideSequencing : associated_studies\n\n      NucleotideSequencing --> \"1..*\" Study : associated_studies\n    click Study href \"../Study\"\n\n  NucleotideSequencing : description\n\n  NucleotideSequencing : end_date\n\n  NucleotideSequencing : gold_sequencing_project_identifiers\n\n  NucleotideSequencing : has_failure_categorization\n\n      NucleotideSequencing --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  NucleotideSequencing : has_input\n\n      NucleotideSequencing --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  NucleotideSequencing : has_output\n\n      NucleotideSequencing --> \"*\" DataObject : has_output\n    click DataObject href \"../DataObject\"\n\n  NucleotideSequencing : id\n\n  NucleotideSequencing : insdc_bioproject_identifiers\n\n  NucleotideSequencing : insdc_experiment_identifiers\n\n  NucleotideSequencing : instrument_used\n\n      NucleotideSequencing --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  NucleotideSequencing : mod_date\n\n  NucleotideSequencing : name\n\n  NucleotideSequencing : ncbi_project_name\n\n  NucleotideSequencing : principal_investigator\n\n      NucleotideSequencing --> \"0..1\" PersonValue : principal_investigator\n    click PersonValue href \"../PersonValue\"\n\n  NucleotideSequencing : processing_institution\n\n      NucleotideSequencing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  NucleotideSequencing : protocol_link\n\n      NucleotideSequencing --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  NucleotideSequencing : qc_comment\n\n  NucleotideSequencing : qc_status\n\n      NucleotideSequencing --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  NucleotideSequencing : start_date\n\n  NucleotideSequencing : target_gene\n\n      NucleotideSequencing --> \"0..1\" TextValue : target_gene\n    click TextValue href \"../TextValue\"\n\n  NucleotideSequencing : target_subfragment\n\n      NucleotideSequencing --> \"0..1\" TextValue : target_subfragment\n    click TextValue href \"../TextValue\"\n\n  NucleotideSequencing : type\n\n\n\n
"},{"location":"NucleotideSequencing/#inheritance","title":"Inheritance","text":""},{"location":"NucleotideSequencing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gold_sequencing_project_identifiers * ExternalIdentifier identifiers for corresponding sequencing project in GOLD direct insdc_bioproject_identifiers * ExternalIdentifier identifiers for corresponding project in INSDC Bioproject direct insdc_experiment_identifiers * ExternalIdentifier direct ncbi_project_name 0..1 String direct target_gene 0..1 TextValue Targeted gene or locus name for marker gene studies direct target_subfragment 0..1 TextValue Name of subfragment of a gene or locus direct add_date 0..1 String The date on which the information was added to the database DataGeneration analyte_category 1 AnalyteCategoryEnum The type of analyte(s) that were measured in the data generation process and ... DataGeneration associated_studies 1..* Study The study associated with a resource DataGeneration instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing DataGeneration mod_date 0..1 String The last date on which the database information was modified DataGeneration principal_investigator 0..1 PersonValue Principal Investigator who led the study and/or generated the dataset DataGeneration has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * DataObject An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"NucleotideSequencing/#comments","title":"Comments","text":""},{"location":"NucleotideSequencing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NucleotideSequencing/#schema-source","title":"Schema Source","text":""},{"location":"NucleotideSequencing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:NucleotideSequencing native nmdc:NucleotideSequencing"},{"location":"NucleotideSequencing/#linkml-source","title":"LinkML Source","text":""},{"location":"NucleotideSequencing/#direct","title":"Direct","text":"
name: NucleotideSequencing\ndescription: A DataGeneration in which the sequence of DNA or RNA molecules is generated.\ncomments:\n- For example data generated from an Illumina or Pacific Biosciences instrument.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: DataGeneration\nslots:\n- gold_sequencing_project_identifiers\n- insdc_bioproject_identifiers\n- insdc_experiment_identifiers\n- ncbi_project_name\n- target_gene\n- target_subfragment\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:NucleotideSequencing\n\n
"},{"location":"NucleotideSequencing/#induced","title":"Induced","text":"
name: NucleotideSequencing\ndescription: A DataGeneration in which the sequence of DNA or RNA molecules is generated.\ncomments:\n- For example data generated from an Illumina or Pacific Biosciences instrument.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: DataGeneration\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  gold_sequencing_project_identifiers:\n    name: gold_sequencing_project_identifiers\n    description: identifiers for corresponding sequencing project in GOLD\n    examples:\n    - value: https://bioregistry.io/gold:Gp0108335\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: omics_processing_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_sequencing_project_identifiers\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    range: external_identifier\n    multivalued: true\n    pattern: ^gold:Gp[0-9]+$\n  insdc_bioproject_identifiers:\n    name: insdc_bioproject_identifiers\n    description: identifiers for corresponding project in INSDC Bioproject\n    comments:\n    - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n      one to one\n    examples:\n    - value: https://bioregistry.io/bioproject:PRJNA366857\n      description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2\n        metatranscriptome\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ncbi.nlm.nih.gov/bioproject/\n    - https://www.ddbj.nig.ac.jp/bioproject/index-e.html\n    aliases:\n    - NCBI bioproject identifiers\n    - DDBJ bioproject identifiers\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_bioproject_identifiers\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n  insdc_experiment_identifiers:\n    name: insdc_experiment_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_experiment_identifiers\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    - DataObject\n    range: external_identifier\n    multivalued: true\n    pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n  ncbi_project_name:\n    name: ncbi_project_name\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: ncbi_project_name\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    range: string\n  target_gene:\n    name: target_gene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gene name\n    description: Targeted gene or locus name for marker gene studies\n    title: target gene\n    examples:\n    - value: 16S rRNA, 18S rRNA, nif, amoA, rpo\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - target gene\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000044\n    alias: target_gene\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    range: TextValue\n    multivalued: false\n  target_subfragment:\n    name: target_subfragment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gene fragment name\n    description: Name of subfragment of a gene or locus. Important to e.g. identify\n      special regions on marker genes like V6 on 16S rRNA\n    title: target subfragment\n    examples:\n    - value: V6, V9, ITS\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - target subfragment\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000045\n    alias: target_subfragment\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    range: TextValue\n    multivalued: false\n  add_date:\n    name: add_date\n    description: The date on which the information was added to the database.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: add_date\n    owner: NucleotideSequencing\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  analyte_category:\n    name: analyte_category\n    description: \"The type of analyte(s) that were measured in the data generation\\\n      \\ process and analyzed\\n  in the Workflow Chain\\n\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: analyte_category\n    owner: NucleotideSequencing\n    domain_of:\n    - DataGeneration\n    range: AnalyteCategoryEnum\n    required: true\n  associated_studies:\n    name: associated_studies\n    description: The study associated with a resource.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: associated_studies\n    owner: NucleotideSequencing\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: Study\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: NucleotideSequencing\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  mod_date:\n    name: mod_date\n    description: The last date on which the database information was modified.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mod_date\n    owner: NucleotideSequencing\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  principal_investigator:\n    name: principal_investigator\n    description: Principal Investigator who led the study and/or generated the dataset.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - PI\n    rank: 1000\n    alias: principal_investigator\n    owner: NucleotideSequencing\n    domain_of:\n    - Study\n    - DataGeneration\n    range: PersonValue\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: DataObject\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NucleotideSequencing\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: NucleotideSequencing\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: NucleotideSequencing\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: NucleotideSequencing\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: NucleotideSequencing\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:NucleotideSequencing\n\n
"},{"location":"Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"Objectidentifier/#comments","title":"Comments","text":""},{"location":"Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"Objectidentifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self shex:iri native nmdc:objectidentifier"},{"location":"OccupDocumentEnum/","title":"Enum: OccupDocumentEnum","text":"

URI: OccupDocumentEnum

"},{"location":"OccupDocumentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description automated count None estimate None manual count None videos None"},{"location":"OccupDocumentEnum/#slots","title":"Slots","text":"Name Description occup_document The type of documentation of occupancy"},{"location":"OccupDocumentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OccupDocumentEnum/#schema-source","title":"Schema Source","text":""},{"location":"OccupDocumentEnum/#linkml-source","title":"LinkML Source","text":"
name: occup_document_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  automated count:\n    text: automated count\n  estimate:\n    text: estimate\n  manual count:\n    text: manual count\n  videos:\n    text: videos\n\n
"},{"location":"OntologyClass/","title":"Class: OntologyClass","text":"

URI: nmdc:OntologyClass

classDiagram\n  class OntologyClass\n  click OntologyClass href \"../OntologyClass\"\n    NamedThing <|-- OntologyClass\n      click NamedThing href \"../NamedThing\"\n\n\n    OntologyClass <|-- EnvironmentalMaterialTerm\n      click EnvironmentalMaterialTerm href \"../EnvironmentalMaterialTerm\"\n    OntologyClass <|-- ChemicalEntity\n      click ChemicalEntity href \"../ChemicalEntity\"\n    OntologyClass <|-- FunctionalAnnotationTerm\n      click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n  OntologyClass : alternative_identifiers\n\n  OntologyClass : description\n\n  OntologyClass : id\n\n  OntologyClass : name\n\n  OntologyClass : type\n\n\n\n
"},{"location":"OntologyClass/#inheritance","title":"Inheritance","text":""},{"location":"OntologyClass/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"OntologyClass/#usages","title":"Usages","text":"used by used in type used ControlledTermValue term range OntologyClass ControlledIdentifiedTermValue term range OntologyClass"},{"location":"OntologyClass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OntologyClass/#schema-source","title":"Schema Source","text":""},{"location":"OntologyClass/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:OntologyClass native nmdc:OntologyClass"},{"location":"OntologyClass/#linkml-source","title":"LinkML Source","text":""},{"location":"OntologyClass/#direct","title":"Direct","text":"
name: OntologyClass\nnotes:\n- The identifiers for terms from external ontologies can't have their ids constrained\n  to the nmdc namespace\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n  id:\n    name: id\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nclass_uri: nmdc:OntologyClass\n\n
"},{"location":"OntologyClass/#induced","title":"Induced","text":"
name: OntologyClass\nnotes:\n- The identifiers for terms from external ontologies can't have their ids constrained\n  to the nmdc namespace\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n  id:\n    name: id\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: OntologyClass\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: OntologyClass\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: OntologyClass\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: OntologyClass\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: OntologyClass\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:OntologyClass\n\n
"},{"location":"OrganismCountEnum/","title":"Enum: OrganismCountEnum","text":"

URI: OrganismCountEnum

"},{"location":"OrganismCountEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ATP None MPN None other None"},{"location":"OrganismCountEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OrganismCountEnum/#schema-source","title":"Schema Source","text":""},{"location":"OrganismCountEnum/#linkml-source","title":"LinkML Source","text":"
name: organism_count_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  ATP:\n    text: ATP\n  MPN:\n    text: MPN\n  other:\n    text: other\n\n
"},{"location":"OrthologyGroup/","title":"Class: OrthologyGroup","text":"

A set of genes or gene products in which all members are orthologous

URI: nmdc:OrthologyGroup

classDiagram\n  class OrthologyGroup\n  click OrthologyGroup href \"../OrthologyGroup\"\n    FunctionalAnnotationTerm <|-- OrthologyGroup\n      click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n  OrthologyGroup : alternative_identifiers\n\n  OrthologyGroup : description\n\n  OrthologyGroup : id\n\n  OrthologyGroup : name\n\n  OrthologyGroup : type\n\n\n\n
"},{"location":"OrthologyGroup/#inheritance","title":"Inheritance","text":""},{"location":"OrthologyGroup/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"OrthologyGroup/#todos","title":"TODOs","text":""},{"location":"OrthologyGroup/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OrthologyGroup/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"OrthologyGroup/#schema-source","title":"Schema Source","text":""},{"location":"OrthologyGroup/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:OrthologyGroup native nmdc:OrthologyGroup exact biolink:GeneFamily"},{"location":"OrthologyGroup/#linkml-source","title":"LinkML Source","text":""},{"location":"OrthologyGroup/#direct","title":"Direct","text":"
name: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\ntodos:\n- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable\n  in the Data Portal?\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nclass_uri: nmdc:OrthologyGroup\n\n
"},{"location":"OrthologyGroup/#induced","title":"Induced","text":"
name: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\ntodos:\n- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable\n  in the Data Portal?\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: OrthologyGroup\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: OrthologyGroup\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: OrthologyGroup\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: OrthologyGroup\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: OrthologyGroup\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:OrthologyGroup\n\n
"},{"location":"OxyStatSampEnum/","title":"Enum: OxyStatSampEnum","text":"

URI: OxyStatSampEnum

"},{"location":"OxyStatSampEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aerobic None anaerobic None other None"},{"location":"OxyStatSampEnum/#slots","title":"Slots","text":"Name Description oxy_stat_samp Oxygenation status of sample"},{"location":"OxyStatSampEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OxyStatSampEnum/#schema-source","title":"Schema Source","text":""},{"location":"OxyStatSampEnum/#linkml-source","title":"LinkML Source","text":"
name: oxy_stat_samp_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  aerobic:\n    text: aerobic\n  anaerobic:\n    text: anaerobic\n  other:\n    text: other\n\n
"},{"location":"Package/","title":"Subset: Package","text":"

A MIxS package. These can be combined with checklists

URI: Package

"},{"location":"Package/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Package/#schema-source","title":"Schema Source","text":""},{"location":"Pathway/","title":"Class: Pathway (DEPRECATED)

A pathway is a sequence of steps/reactions carried out by an organism or community of organisms

URI: nmdc:Pathway

classDiagram\n  class Pathway\n  click Pathway href \"../Pathway\"\n    FunctionalAnnotationTerm <|-- Pathway\n      click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n  Pathway : alternative_identifiers\n\n  Pathway : description\n\n  Pathway : id\n\n  Pathway : name\n\n  Pathway : type\n\n\n\n
","text":""},{"location":"Pathway/#inheritance","title":"Inheritance","text":""},{"location":"Pathway/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Pathway/#aliases","title":"Aliases","text":""},{"location":"Pathway/#todos","title":"TODOs","text":""},{"location":"Pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Pathway/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"Pathway/#schema-source","title":"Schema Source","text":""},{"location":"Pathway/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Pathway native nmdc:Pathway exact biolink:Pathway"},{"location":"Pathway/#linkml-source","title":"LinkML Source","text":""},{"location":"Pathway/#direct","title":"Direct","text":"
name: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n  or community of organisms\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\ntodos:\n- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable\n  part_of a Pathway\n- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in\n  the Data Portal?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nclass_uri: nmdc:Pathway\n\n
"},{"location":"Pathway/#induced","title":"Induced","text":"
name: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n  or community of organisms\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\ntodos:\n- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable\n  part_of a Pathway\n- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in\n  the Data Portal?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Pathway\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Pathway\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Pathway\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Pathway\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Pathway\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Pathway\n\n
"},{"location":"PeptideQuantification/","title":"Class: PeptideQuantification","text":"

This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information

URI: nmdc:PeptideQuantification

classDiagram\n  class PeptideQuantification\n  click PeptideQuantification href \"../PeptideQuantification\"\n\n  PeptideQuantification : all_proteins\n\n      PeptideQuantification --> \"*\" GeneProduct : all_proteins\n    click GeneProduct href \"../GeneProduct\"\n\n  PeptideQuantification : best_protein\n\n      PeptideQuantification --> \"0..1\" GeneProduct : best_protein\n    click GeneProduct href \"../GeneProduct\"\n\n  PeptideQuantification : min_q_value\n\n  PeptideQuantification : peptide_sequence\n\n  PeptideQuantification : peptide_spectral_count\n\n  PeptideQuantification : peptide_sum_masic_abundance\n\n  PeptideQuantification : type\n\n\n\n
"},{"location":"PeptideQuantification/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance type 1 Uriorcurie the class_uri of the class that has been instantiated direct all_proteins * GeneProduct the list of protein identifiers that are associated with the peptide sequence direct best_protein 0..1 GeneProduct the specific protein identifier most correctly associated with the peptide se... direct min_q_value 0..1 Float smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... direct peptide_sequence 0..1 String direct peptide_spectral_count 0..1 Integer sum of filter passing MS2 spectra associated with the peptide sequence within... direct peptide_sum_masic_abundance 0..1 Integer combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... direct"},{"location":"PeptideQuantification/#usages","title":"Usages","text":"used by used in type used MetaproteomicsAnalysis has_peptide_quantifications range PeptideQuantification"},{"location":"PeptideQuantification/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PeptideQuantification/#schema-source","title":"Schema Source","text":""},{"location":"PeptideQuantification/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:PeptideQuantification native nmdc:PeptideQuantification"},{"location":"PeptideQuantification/#linkml-source","title":"LinkML Source","text":""},{"location":"PeptideQuantification/#direct","title":"Direct","text":"
name: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n  peptide sequence and related information\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- type\n- all_proteins\n- best_protein\n- min_q_value\n- peptide_sequence\n- peptide_spectral_count\n- peptide_sum_masic_abundance\nclass_uri: nmdc:PeptideQuantification\n\n
"},{"location":"PeptideQuantification/#induced","title":"Induced","text":"
name: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n  peptide sequence and related information\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: PeptideQuantification\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  all_proteins:\n    name: all_proteins\n    description: the list of protein identifiers that are associated with the peptide\n      sequence\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: all_proteins\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    - ProteinQuantification\n    range: GeneProduct\n    multivalued: true\n  best_protein:\n    name: best_protein\n    description: the specific protein identifier most correctly associated with the\n      peptide sequence\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: best_protein\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    - ProteinQuantification\n    range: GeneProduct\n  min_q_value:\n    name: min_q_value\n    description: smallest Q-Value associated with the peptide sequence as provided\n      by MSGFPlus tool\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - OBI:0001442\n    rank: 1000\n    alias: min_q_value\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    range: float\n  peptide_sequence:\n    name: peptide_sequence\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: peptide_sequence\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    range: string\n  peptide_spectral_count:\n    name: peptide_spectral_count\n    description: sum of filter passing MS2 spectra associated with the peptide sequence\n      within a given LC-MS/MS data file\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: peptide_spectral_count\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    range: integer\n  peptide_sum_masic_abundance:\n    name: peptide_sum_masic_abundance\n    description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n      associated with the peptide sequence from a given LC-MS/MS data file using the\n      MASIC tool\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: peptide_sum_masic_abundance\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    range: integer\nclass_uri: nmdc:PeptideQuantification\n\n
"},{"location":"PersonValue/","title":"Class: PersonValue","text":"

An attribute value representing a person

URI: nmdc:PersonValue

classDiagram\n  class PersonValue\n  click PersonValue href \"../PersonValue\"\n    AttributeValue <|-- PersonValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  PersonValue : email\n\n  PersonValue : has_raw_value\n\n  PersonValue : name\n\n  PersonValue : orcid\n\n  PersonValue : profile_image_url\n\n  PersonValue : type\n\n  PersonValue : websites\n\n\n\n
"},{"location":"PersonValue/#inheritance","title":"Inheritance","text":""},{"location":"PersonValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance email 0..1 String An email address for an entity such as a person direct name 0..1 String The full name of the Investigator direct orcid 0..1 String The ORCID of a person direct profile_image_url 0..1 String A url that points to an image of a person direct websites * String A list of websites that are associated with the entity direct has_raw_value 0..1 String The full name of the Investigator in format FIRST LAST AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"PersonValue/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing principal_investigator range PersonValue MassSpectrometry principal_investigator range PersonValue CreditAssociation applies_to_person range PersonValue Study principal_investigator range PersonValue DataGeneration principal_investigator range PersonValue"},{"location":"PersonValue/#todos","title":"TODOs","text":""},{"location":"PersonValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PersonValue/#schema-source","title":"Schema Source","text":""},{"location":"PersonValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:PersonValue native nmdc:PersonValue"},{"location":"PersonValue/#linkml-source","title":"LinkML Source","text":""},{"location":"PersonValue/#direct","title":"Direct","text":"
name: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- email\n- name\n- orcid\n- profile_image_url\n- websites\nslot_usage:\n  orcid:\n    name: orcid\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Open Researcher and Contributor ID for this person. See https://orcid.org\n  email:\n    name: email\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Email address for this person.\n  has_raw_value:\n    name: has_raw_value\n    description: The full name of the Investigator in format FIRST LAST.\n    notes:\n    - May eventually be deprecated in favor of \"name\".\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: First name, middle initial, and last name of this person.\n    description: The full name of the Investigator. It should follow the format FIRST\n      [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\nclass_uri: nmdc:PersonValue\n\n
"},{"location":"PersonValue/#induced","title":"Induced","text":"
name: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslot_usage:\n  orcid:\n    name: orcid\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Open Researcher and Contributor ID for this person. See https://orcid.org\n  email:\n    name: email\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Email address for this person.\n  has_raw_value:\n    name: has_raw_value\n    description: The full name of the Investigator in format FIRST LAST.\n    notes:\n    - May eventually be deprecated in favor of \"name\".\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: First name, middle initial, and last name of this person.\n    description: The full name of the Investigator. It should follow the format FIRST\n      [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\nattributes:\n  email:\n    name: email\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Email address for this person.\n    description: An email address for an entity such as a person. This should be the\n      primary email address used.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: schema:email\n    alias: email\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    range: string\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: First name, middle initial, and last name of this person.\n    description: The full name of the Investigator. It should follow the format FIRST\n      [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  orcid:\n    name: orcid\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Open Researcher and Contributor ID for this person. See https://orcid.org\n    description: The ORCID of a person.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: orcid\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    range: string\n  profile_image_url:\n    name: profile_image_url\n    description: A url that points to an image of a person.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: profile_image_url\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    range: string\n  websites:\n    name: websites\n    description: A list of websites that are associated with the entity.\n    comments:\n    - DOIs should not be included as websites. Instead, use the associated_dois slot.\n    - A consortium's homepage website should be included in the homepage_website slot,\n      not in websites.\n    - consortium is a convenience term for a Study whose study_category value is consortium\n    - the website slot and its subproperties are virtually identical to the url slot,\n      except that they are multivalued and url is single-valued.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:url\n    rank: 1000\n    alias: websites\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    - Study\n    range: string\n    multivalued: true\n    pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n  has_raw_value:\n    name: has_raw_value\n    description: The full name of the Investigator in format FIRST LAST.\n    notes:\n    - May eventually be deprecated in favor of \"name\".\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: PersonValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: PersonValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:PersonValue\n\n
"},{"location":"PlannedProcess/","title":"Class: Planned Process (PlannedProcess)","text":"

Note

This is an abstract class and should not be instantiated directly.

URI: OBI:0000011

classDiagram\n  class PlannedProcess\n  click PlannedProcess href \"../PlannedProcess\"\n    NamedThing <|-- PlannedProcess\n      click NamedThing href \"../NamedThing\"\n\n\n    PlannedProcess <|-- CollectingBiosamplesFromSite\n      click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n    PlannedProcess <|-- ProtocolExecution\n      click ProtocolExecution href \"../ProtocolExecution\"\n    PlannedProcess <|-- StorageProcess\n      click StorageProcess href \"../StorageProcess\"\n    PlannedProcess <|-- MaterialProcessing\n      click MaterialProcessing href \"../MaterialProcessing\"\n    PlannedProcess <|-- DataGeneration\n      click DataGeneration href \"../DataGeneration\"\n    PlannedProcess <|-- WorkflowExecution\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  PlannedProcess : alternative_identifiers\n\n  PlannedProcess : description\n\n  PlannedProcess : end_date\n\n  PlannedProcess : has_failure_categorization\n\n      PlannedProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  PlannedProcess : has_input\n\n      PlannedProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  PlannedProcess : has_output\n\n      PlannedProcess --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  PlannedProcess : id\n\n  PlannedProcess : name\n\n  PlannedProcess : processing_institution\n\n      PlannedProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  PlannedProcess : protocol_link\n\n      PlannedProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  PlannedProcess : qc_comment\n\n  PlannedProcess : qc_status\n\n      PlannedProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  PlannedProcess : start_date\n\n  PlannedProcess : type\n\n\n\n
"},{"location":"PlannedProcess/#inheritance","title":"Inheritance","text":""},{"location":"PlannedProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_input * NamedThing An input to a process direct has_output * NamedThing An output from a process direct processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample direct protocol_link 0..1 Protocol direct start_date 0..1 String The date on which any process or activity was started direct end_date 0..1 String The date on which any process or activity was ended direct qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... direct qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output direct has_failure_categorization * FailureCategorization direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"PlannedProcess/#usages","title":"Usages","text":"used by used in type used ProtocolExecution has_process_parts range PlannedProcess"},{"location":"PlannedProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlannedProcess/#schema-source","title":"Schema Source","text":""},{"location":"PlannedProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self OBI:0000011 native nmdc:PlannedProcess"},{"location":"PlannedProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"PlannedProcess/#direct","title":"Direct","text":"
name: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nslots:\n- has_input\n- has_output\n- processing_institution\n- protocol_link\n- start_date\n- end_date\n- qc_status\n- qc_comment\n- has_failure_categorization\nclass_uri: OBI:0000011\n\n
"},{"location":"PlannedProcess/#induced","title":"Induced","text":"
name: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nattributes:\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: PlannedProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: PlannedProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: PlannedProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: PlannedProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: PlannedProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: OBI:0000011\n\n
"},{"location":"PlantGrowthMedEnum/","title":"Enum: PlantGrowthMedEnum","text":"

URI: PlantGrowthMedEnum

"},{"location":"PlantGrowthMedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description other artificial liquid medium None other artificial solid medium None peat moss None perlite None pumice None sand None soil None vermiculite None water None"},{"location":"PlantGrowthMedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantGrowthMedEnum/#schema-source","title":"Schema Source","text":""},{"location":"PlantGrowthMedEnum/#linkml-source","title":"LinkML Source","text":"
name: plant_growth_med_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  other artificial liquid medium:\n    text: other artificial liquid medium\n  other artificial solid medium:\n    text: other artificial solid medium\n  peat moss:\n    text: peat moss\n  perlite:\n    text: perlite\n  pumice:\n    text: pumice\n  sand:\n    text: sand\n  soil:\n    text: soil\n  vermiculite:\n    text: vermiculite\n  water:\n    text: water\n\n
"},{"location":"PlantSexEnum/","title":"Enum: PlantSexEnum","text":"

URI: PlantSexEnum

"},{"location":"PlantSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Androdioecious None Androecious None Androgynous None Androgynomonoecious None Andromonoecious None Bisexual None Dichogamous None Diclinous None Dioecious None Gynodioecious None Gynoecious None Gynomonoecious None Hermaphroditic None Imperfect None Monoclinous None Monoecious None Perfect None Polygamodioecious None Polygamomonoecious None Polygamous None Protandrous None Protogynous None Subandroecious None Subdioecious None Subgynoecious None Synoecious None Trimonoecious None Trioecious None Unisexual None"},{"location":"PlantSexEnum/#slots","title":"Slots","text":"Name Description plant_sex Sex of the reproductive parts on the whole plant, e"},{"location":"PlantSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantSexEnum/#schema-source","title":"Schema Source","text":""},{"location":"PlantSexEnum/#linkml-source","title":"LinkML Source","text":"
name: plant_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Androdioecious:\n    text: Androdioecious\n  Androecious:\n    text: Androecious\n  Androgynous:\n    text: Androgynous\n  Androgynomonoecious:\n    text: Androgynomonoecious\n  Andromonoecious:\n    text: Andromonoecious\n  Bisexual:\n    text: Bisexual\n  Dichogamous:\n    text: Dichogamous\n  Diclinous:\n    text: Diclinous\n  Dioecious:\n    text: Dioecious\n  Gynodioecious:\n    text: Gynodioecious\n  Gynoecious:\n    text: Gynoecious\n  Gynomonoecious:\n    text: Gynomonoecious\n  Hermaphroditic:\n    text: Hermaphroditic\n  Imperfect:\n    text: Imperfect\n  Monoclinous:\n    text: Monoclinous\n  Monoecious:\n    text: Monoecious\n  Perfect:\n    text: Perfect\n  Polygamodioecious:\n    text: Polygamodioecious\n  Polygamomonoecious:\n    text: Polygamomonoecious\n  Polygamous:\n    text: Polygamous\n  Protandrous:\n    text: Protandrous\n  Protogynous:\n    text: Protogynous\n  Subandroecious:\n    text: Subandroecious\n  Subdioecious:\n    text: Subdioecious\n  Subgynoecious:\n    text: Subgynoecious\n  Synoecious:\n    text: Synoecious\n  Trimonoecious:\n    text: Trimonoecious\n  Trioecious:\n    text: Trioecious\n  Unisexual:\n    text: Unisexual\n\n
"},{"location":"PolarityModeEnum/","title":"Enum: PolarityModeEnum","text":"

URI: PolarityModeEnum

"},{"location":"PolarityModeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description positive None negative None"},{"location":"PolarityModeEnum/#slots","title":"Slots","text":"Name Description polarity_mode the polarity of which ions are generated and detected"},{"location":"PolarityModeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PolarityModeEnum/#schema-source","title":"Schema Source","text":""},{"location":"PolarityModeEnum/#linkml-source","title":"LinkML Source","text":"
name: PolarityModeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  positive:\n    text: positive\n  negative:\n    text: negative\n\n
"},{"location":"Pooling/","title":"Class: Pooling","text":"

physical combination of several instances of like material.

URI: nmdc:Pooling

classDiagram\n  class Pooling\n  click Pooling href \"../Pooling\"\n    MaterialProcessing <|-- Pooling\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  Pooling : alternative_identifiers\n\n  Pooling : description\n\n  Pooling : end_date\n\n  Pooling : has_failure_categorization\n\n      Pooling --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  Pooling : has_input\n\n      Pooling --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  Pooling : has_output\n\n      Pooling --> \"1..*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  Pooling : id\n\n  Pooling : instrument_used\n\n      Pooling --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  Pooling : name\n\n  Pooling : processing_institution\n\n      Pooling --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  Pooling : protocol_link\n\n      Pooling --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  Pooling : qc_comment\n\n  Pooling : qc_status\n\n      Pooling --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  Pooling : start_date\n\n  Pooling : type\n\n\n\n
"},{"location":"Pooling/#inheritance","title":"Inheritance","text":""},{"location":"Pooling/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output 1..* ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Pooling/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Pooling/#schema-source","title":"Schema Source","text":""},{"location":"Pooling/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Pooling native nmdc:Pooling exact OBI:0600016"},{"location":"Pooling/#linkml-source","title":"LinkML Source","text":""},{"location":"Pooling/#direct","title":"Direct","text":"
name: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: MaterialProcessing\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 2\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 1\n    maximum_cardinality: 1\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:Pooling\n\n
"},{"location":"Pooling/#induced","title":"Induced","text":"
name: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: MaterialProcessing\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 2\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 1\n    maximum_cardinality: 1\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: Pooling\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 2\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 1\n    maximum_cardinality: 1\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Pooling\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Pooling\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Pooling\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Pooling\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Pooling\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Pooling\n\n
"},{"location":"PortionOfSubstance/","title":"Class: Portion of a Substance (PortionOfSubstance)","text":"

A portion of any matter of defined composition that has discrete existence, whose origin may be biological, mineral or chemical.

URI: nmdc:PortionOfSubstance

classDiagram\n  class PortionOfSubstance\n  click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  PortionOfSubstance : final_concentration\n\n      PortionOfSubstance --> \"0..1\" QuantityValue : final_concentration\n    click QuantityValue href \"../QuantityValue\"\n\n  PortionOfSubstance : known_as\n\n      PortionOfSubstance --> \"0..1\" ChemicalEntity : known_as\n    click ChemicalEntity href \"../ChemicalEntity\"\n\n  PortionOfSubstance : mass\n\n      PortionOfSubstance --> \"0..1\" QuantityValue : mass\n    click QuantityValue href \"../QuantityValue\"\n\n  PortionOfSubstance : sample_state_information\n\n      PortionOfSubstance --> \"0..1\" SampleStateEnum : sample_state_information\n    click SampleStateEnum href \"../SampleStateEnum\"\n\n  PortionOfSubstance : source_concentration\n\n      PortionOfSubstance --> \"0..1\" QuantityValue : source_concentration\n    click QuantityValue href \"../QuantityValue\"\n\n  PortionOfSubstance : substance_role\n\n      PortionOfSubstance --> \"0..1\" SubstanceRoleEnum : substance_role\n    click SubstanceRoleEnum href \"../SubstanceRoleEnum\"\n\n  PortionOfSubstance : type\n\n  PortionOfSubstance : volume\n\n      PortionOfSubstance --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"PortionOfSubstance/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance final_concentration 0..1 QuantityValue When solutions A (containing substance X) and B are combined together, this s... direct known_as 0..1 ChemicalEntity direct mass 0..1 QuantityValue A physical quality that inheres in a bearer by virtue of the proportion of th... direct sample_state_information 0..1 SampleStateEnum The chemical phase of a pure sample, or the state of a mixed sample direct source_concentration 0..1 QuantityValue When solutions A (containing substance X) and B are combined together, this s... direct substance_role 0..1 SubstanceRoleEnum The role of a substance in a process direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct volume 0..1 QuantityValue The volume of a substance direct"},{"location":"PortionOfSubstance/#usages","title":"Usages","text":"used by used in type used Extraction substances_used range PortionOfSubstance StorageProcess substances_used range PortionOfSubstance DissolvingProcess substances_used range PortionOfSubstance ChemicalConversionProcess substances_used range PortionOfSubstance MobilePhaseSegment substances_used range PortionOfSubstance"},{"location":"PortionOfSubstance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PortionOfSubstance/#schema-source","title":"Schema Source","text":""},{"location":"PortionOfSubstance/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:PortionOfSubstance native nmdc:PortionOfSubstance undefined schema:Substance"},{"location":"PortionOfSubstance/#linkml-source","title":"LinkML Source","text":""},{"location":"PortionOfSubstance/#direct","title":"Direct","text":"
name: PortionOfSubstance\ndescription: A portion of any matter of defined composition that has discrete existence,\n  whose origin may be biological, mineral or chemical.\ntitle: Portion of a Substance\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:Substance\nslots:\n- final_concentration\n- known_as\n- mass\n- sample_state_information\n- source_concentration\n- substance_role\n- type\n- volume\nclass_uri: nmdc:PortionOfSubstance\n\n
"},{"location":"PortionOfSubstance/#induced","title":"Induced","text":"
name: PortionOfSubstance\ndescription: A portion of any matter of defined composition that has discrete existence,\n  whose origin may be biological, mineral or chemical.\ntitle: Portion of a Substance\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:Substance\nattributes:\n  final_concentration:\n    name: final_concentration\n    description: When solutions A (containing substance X) and B are combined together,\n      this slot captures the concentration of X in the combination\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: concentration\n    alias: final_concentration\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: QuantityValue\n  known_as:\n    name: known_as\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: known_as\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: ChemicalEntity\n  mass:\n    name: mass\n    description: A physical quality that inheres in a bearer by virtue of the proportion\n      of the bearer's amount of matter.\n    title: mass\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - PATO:0000125\n    rank: 1000\n    alias: mass\n    owner: PortionOfSubstance\n    domain_of:\n    - SubSamplingProcess\n    - PortionOfSubstance\n    range: QuantityValue\n  sample_state_information:\n    name: sample_state_information\n    description: The chemical phase of a pure sample, or the state of a mixed sample\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: sample_state_information\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: SampleStateEnum\n  source_concentration:\n    name: source_concentration\n    description: When solutions A (containing substance X) and B are combined together,\n      this slot captures the concentration of X in solution A\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: concentration\n    alias: source_concentration\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: QuantityValue\n  substance_role:\n    name: substance_role\n    description: The role of a substance in a process\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substance_role\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: SubstanceRoleEnum\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: PortionOfSubstance\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  volume:\n    name: volume\n    description: The volume of a substance.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: PortionOfSubstance\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\nclass_uri: nmdc:PortionOfSubstance\n\n
"},{"location":"ProcessedSample/","title":"Class: Processed Sample (ProcessedSample)","text":"

URI: nmdc:ProcessedSample

classDiagram\n  class ProcessedSample\n  click ProcessedSample href \"../ProcessedSample\"\n    MaterialEntity <|-- ProcessedSample\n      click MaterialEntity href \"../MaterialEntity\"\n\n\n\n  ProcessedSample : alternative_identifiers\n\n  ProcessedSample : biomaterial_purity\n\n      ProcessedSample --> \"0..1\" QuantityValue : biomaterial_purity\n    click QuantityValue href \"../QuantityValue\"\n\n  ProcessedSample : description\n\n  ProcessedSample : dna_absorb1\n\n  ProcessedSample : dna_concentration\n\n  ProcessedSample : external_database_identifiers\n\n  ProcessedSample : id\n\n  ProcessedSample : name\n\n  ProcessedSample : type\n\n\n\n
"},{"location":"ProcessedSample/#inheritance","title":"Inheritance","text":""},{"location":"ProcessedSample/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance biomaterial_purity 0..1 QuantityValue direct dna_absorb1 0..1 recommended Float 260/280 measurement of DNA sample purity direct dna_concentration 0..1 recommended Float direct external_database_identifiers * ExternalIdentifier Link to corresponding identifier in external database direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ProcessedSample/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_input any_of[range] ProcessedSample MassSpectrometry has_input any_of[range] ProcessedSample Database processed_sample_set range ProcessedSample Pooling has_input any_of[range] ProcessedSample Pooling has_output range ProcessedSample Extraction has_input any_of[range] ProcessedSample Extraction has_output range ProcessedSample LibraryPreparation has_input any_of[range] ProcessedSample LibraryPreparation has_output range ProcessedSample SubSamplingProcess has_input any_of[range] ProcessedSample SubSamplingProcess has_output range ProcessedSample MixingProcess has_input any_of[range] ProcessedSample MixingProcess has_output range ProcessedSample FiltrationProcess has_input any_of[range] ProcessedSample FiltrationProcess has_output range ProcessedSample ChromatographicSeparationProcess has_input any_of[range] ProcessedSample ChromatographicSeparationProcess has_output range ProcessedSample DissolvingProcess has_input any_of[range] ProcessedSample DissolvingProcess has_output range ProcessedSample ChemicalConversionProcess has_input any_of[range] ProcessedSample ChemicalConversionProcess has_output range ProcessedSample MaterialProcessing has_input any_of[range] ProcessedSample MaterialProcessing has_output range ProcessedSample DataGeneration has_input any_of[range] ProcessedSample"},{"location":"ProcessedSample/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProcessedSample/#schema-source","title":"Schema Source","text":""},{"location":"ProcessedSample/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ProcessedSample native nmdc:ProcessedSample"},{"location":"ProcessedSample/#linkml-source","title":"LinkML Source","text":""},{"location":"ProcessedSample/#direct","title":"Direct","text":"
name: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslots:\n- biomaterial_purity\n- dna_absorb1\n- dna_concentration\n- external_database_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ProcessedSample\n\n
"},{"location":"ProcessedSample/#induced","title":"Induced","text":"
name: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  biomaterial_purity:\n    name: biomaterial_purity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: biomaterial_purity\n    owner: ProcessedSample\n    domain_of:\n    - ProcessedSample\n    range: QuantityValue\n  dna_absorb1:\n    name: dna_absorb1\n    description: 260/280 measurement of DNA sample purity\n    title: DNA absorbance 260/280\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 7\n    is_a: biomaterial_purity\n    alias: dna_absorb1\n    owner: ProcessedSample\n    domain_of:\n    - Biosample\n    - ProcessedSample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n  dna_concentration:\n    name: dna_concentration\n    title: DNA concentration in ng/ul\n    comments:\n    - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n      a fluorometric method. Acceptable values are 0-2000.\n    examples:\n    - value: '100'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:nucleic_acid_concentration\n    rank: 5\n    alias: dna_concentration\n    owner: ProcessedSample\n    domain_of:\n    - Biosample\n    - ProcessedSample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 2000\n  external_database_identifiers:\n    name: external_database_identifiers\n    description: Link to corresponding identifier in external database\n    notes:\n    - had tried ranges of external identifier and string\n    comments:\n    - The value of this field is always a registered CURIE\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - skos:closeMatch\n    rank: 1000\n    is_a: alternative_identifiers\n    abstract: true\n    alias: external_database_identifiers\n    owner: ProcessedSample\n    domain_of:\n    - ProcessedSample\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ProcessedSample\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ProcessedSample\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ProcessedSample\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ProcessedSample\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ProcessedSample\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ProcessedSample\n\n
"},{"location":"ProcessingInstitutionEnum/","title":"Enum: ProcessingInstitutionEnum","text":"

URI: ProcessingInstitutionEnum

"},{"location":"ProcessingInstitutionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UCSD https://ror.org/0168r3w48 JGI https://ror.org/04xm1d337 EMSL https://ror.org/04rc0xn13 Battelle https://ror.org/01h5tnr73 ANL https://ror.org/05gvnxz63 UCD_Genome_Center https://genomecenter.ucdavis.edu/ Azenta https://www.azenta.com/"},{"location":"ProcessingInstitutionEnum/#slots","title":"Slots","text":"Name Description processing_institution The organization that processed the sample"},{"location":"ProcessingInstitutionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProcessingInstitutionEnum/#schema-source","title":"Schema Source","text":""},{"location":"ProcessingInstitutionEnum/#linkml-source","title":"LinkML Source","text":"
name: ProcessingInstitutionEnum\nnotes:\n- use ROR meanings like https://ror.org/0168r3w48 for UCSD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  UCSD:\n    text: UCSD\n    meaning: https://ror.org/0168r3w48\n    title: University of California, San Diego\n  JGI:\n    text: JGI\n    meaning: https://ror.org/04xm1d337\n    title: Joint Genome Institute\n  EMSL:\n    text: EMSL\n    meaning: https://ror.org/04rc0xn13\n    title: Environmental Molecular Sciences Laboratory\n    aliases:\n    - Environmental Molecular Science Laboratory\n    - Environmental Molecular Sciences Lab\n  Battelle:\n    text: Battelle\n    meaning: https://ror.org/01h5tnr73\n    title: Battelle Memorial Institute\n  ANL:\n    text: ANL\n    meaning: https://ror.org/05gvnxz63\n    title: Argonne National Laboratory\n  UCD_Genome_Center:\n    text: UCD_Genome_Center\n    meaning: https://genomecenter.ucdavis.edu/\n    title: University of California, Davis Genome Center\n  Azenta:\n    text: Azenta\n    meaning: https://www.azenta.com/\n    title: Azenta Life Sciences\n\n
"},{"location":"ProfilePositionEnum/","title":"Enum: ProfilePositionEnum","text":"

URI: ProfilePositionEnum

"},{"location":"ProfilePositionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description summit None shoulder None backslope None footslope None toeslope None"},{"location":"ProfilePositionEnum/#slots","title":"Slots","text":"Name Description profile_position Cross-sectional position in the hillslope where sample was collected"},{"location":"ProfilePositionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProfilePositionEnum/#schema-source","title":"Schema Source","text":""},{"location":"ProfilePositionEnum/#linkml-source","title":"LinkML Source","text":"
name: profile_position_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  summit:\n    text: summit\n  shoulder:\n    text: shoulder\n  backslope:\n    text: backslope\n  footslope:\n    text: footslope\n  toeslope:\n    text: toeslope\n\n
"},{"location":"Proteases/","title":"Subset: Proteases","text":"

URI: Proteases

"},{"location":"Proteases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Proteases/#schema-source","title":"Schema Source","text":""},{"location":"ProteinQuantification/","title":"Class: ProteinQuantification","text":"

This is used to link a metaproteomics analysis workflow to a specific protein

URI: nmdc:ProteinQuantification

classDiagram\n  class ProteinQuantification\n  click ProteinQuantification href \"../ProteinQuantification\"\n\n  ProteinQuantification : all_proteins\n\n      ProteinQuantification --> \"*\" GeneProduct : all_proteins\n    click GeneProduct href \"../GeneProduct\"\n\n  ProteinQuantification : best_protein\n\n      ProteinQuantification --> \"0..1\" GeneProduct : best_protein\n    click GeneProduct href \"../GeneProduct\"\n\n  ProteinQuantification : peptide_sequence_count\n\n  ProteinQuantification : protein_spectral_count\n\n  ProteinQuantification : protein_sum_masic_abundance\n\n  ProteinQuantification : type\n\n\n\n
"},{"location":"ProteinQuantification/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance all_proteins * GeneProduct the grouped list of protein identifiers associated with the peptide sequences... direct best_protein 0..1 GeneProduct the specific protein identifier most correctly grouped to its associated pept... direct peptide_sequence_count 0..1 Integer count of peptide sequences grouped to the best_protein direct protein_spectral_count 0..1 Integer sum of filter passing MS2 spectra associated with the best protein within a g... direct protein_sum_masic_abundance 0..1 Integer combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"ProteinQuantification/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProteinQuantification/#schema-source","title":"Schema Source","text":""},{"location":"ProteinQuantification/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ProteinQuantification native nmdc:ProteinQuantification"},{"location":"ProteinQuantification/#linkml-source","title":"LinkML Source","text":""},{"location":"ProteinQuantification/#direct","title":"Direct","text":"
name: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n  protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- all_proteins\n- best_protein\n- peptide_sequence_count\n- protein_spectral_count\n- protein_sum_masic_abundance\n- type\nslot_usage:\n  best_protein:\n    name: best_protein\n    description: the specific protein identifier most correctly grouped to its associated\n      peptide sequences\n  all_proteins:\n    name: all_proteins\n    description: the grouped list of protein identifiers associated with the peptide\n      sequences that were grouped to a best protein\nclass_uri: nmdc:ProteinQuantification\n\n
"},{"location":"ProteinQuantification/#induced","title":"Induced","text":"
name: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n  protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n  best_protein:\n    name: best_protein\n    description: the specific protein identifier most correctly grouped to its associated\n      peptide sequences\n  all_proteins:\n    name: all_proteins\n    description: the grouped list of protein identifiers associated with the peptide\n      sequences that were grouped to a best protein\nattributes:\n  all_proteins:\n    name: all_proteins\n    description: the grouped list of protein identifiers associated with the peptide\n      sequences that were grouped to a best protein\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: all_proteins\n    owner: ProteinQuantification\n    domain_of:\n    - PeptideQuantification\n    - ProteinQuantification\n    range: GeneProduct\n    multivalued: true\n  best_protein:\n    name: best_protein\n    description: the specific protein identifier most correctly grouped to its associated\n      peptide sequences\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: best_protein\n    owner: ProteinQuantification\n    domain_of:\n    - PeptideQuantification\n    - ProteinQuantification\n    range: GeneProduct\n  peptide_sequence_count:\n    name: peptide_sequence_count\n    description: count of peptide sequences grouped to the best_protein\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: peptide_sequence_count\n    owner: ProteinQuantification\n    domain_of:\n    - ProteinQuantification\n    range: integer\n  protein_spectral_count:\n    name: protein_spectral_count\n    description: sum of filter passing MS2 spectra associated with the best protein\n      within a given LC-MS/MS data file\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protein_spectral_count\n    owner: ProteinQuantification\n    domain_of:\n    - ProteinQuantification\n    range: integer\n  protein_sum_masic_abundance:\n    name: protein_sum_masic_abundance\n    description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n      associated with the best protein from a given LC-MS/MS data file using the MASIC\n      tool\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protein_sum_masic_abundance\n    owner: ProteinQuantification\n    domain_of:\n    - ProteinQuantification\n    range: integer\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ProteinQuantification\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ProteinQuantification\n\n
"},{"location":"Protocol/","title":"Class: Protocol","text":"

URI: nmdc:Protocol

classDiagram\n  class Protocol\n  click Protocol href \"../Protocol\"\n\n  Protocol : name\n\n  Protocol : type\n\n  Protocol : url\n\n\n\n
"},{"location":"Protocol/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance url 0..1 String direct name 0..1 String A human readable label for an entity direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"Protocol/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing protocol_link range Protocol MassSpectrometry protocol_link range Protocol Pooling protocol_link range Protocol Extraction protocol_link range Protocol LibraryPreparation protocol_link range Protocol CollectingBiosamplesFromSite protocol_link range Protocol ProtocolExecution protocol_link range Protocol SubSamplingProcess protocol_link range Protocol MixingProcess protocol_link range Protocol FiltrationProcess protocol_link range Protocol StorageProcess protocol_link range Protocol ChromatographicSeparationProcess protocol_link range Protocol DissolvingProcess protocol_link range Protocol ChemicalConversionProcess protocol_link range Protocol MetagenomeAnnotation protocol_link range Protocol MaterialProcessing protocol_link range Protocol PlannedProcess protocol_link range Protocol Study protocol_link range Protocol DataGeneration protocol_link range Protocol WorkflowExecution protocol_link range Protocol MetagenomeAssembly protocol_link range Protocol MetatranscriptomeAssembly protocol_link range Protocol MetatranscriptomeAnnotation protocol_link range Protocol MetatranscriptomeExpressionAnalysis protocol_link range Protocol MagsAnalysis protocol_link range Protocol MetagenomeSequencing protocol_link range Protocol ReadQcAnalysis protocol_link range Protocol ReadBasedTaxonomyAnalysis protocol_link range Protocol MetabolomicsAnalysis protocol_link range Protocol MetaproteomicsAnalysis protocol_link range Protocol NomAnalysis protocol_link range Protocol"},{"location":"Protocol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Protocol/#schema-source","title":"Schema Source","text":""},{"location":"Protocol/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Protocol native nmdc:Protocol"},{"location":"Protocol/#linkml-source","title":"LinkML Source","text":""},{"location":"Protocol/#direct","title":"Direct","text":"
name: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- url\n- name\n- type\nclass_uri: nmdc:Protocol\n\n
"},{"location":"Protocol/#induced","title":"Induced","text":"
name: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  url:\n    name: url\n    notes:\n    - See issue 207 - this clashes with the mixs field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: url\n    owner: Protocol\n    domain_of:\n    - ImageValue\n    - Protocol\n    - DataObject\n    range: string\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Protocol\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Protocol\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Protocol\n\n
"},{"location":"ProtocolCategoryEnum/","title":"Enum: ProtocolCategoryEnum","text":"

The possible protocols that may be followed for an assay.

URI: ProtocolCategoryEnum

"},{"location":"ProtocolCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mplex None derivatization None filter_clean_up None organic_matter_extraction None solid_phase_extraction None phosphorus_extraction None ph_measurement None respiration_measurement None texture_measurement None dna_extraction None phenol_chloroform_extraction None"},{"location":"ProtocolCategoryEnum/#slots","title":"Slots","text":"Name Description protocol_execution_category"},{"location":"ProtocolCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProtocolCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ProtocolCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ProtocolCategoryEnum\ndescription: The possible protocols that may be followed for an assay.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  mplex:\n    text: mplex\n  derivatization:\n    text: derivatization\n  filter_clean_up:\n    text: filter_clean_up\n  organic_matter_extraction:\n    text: organic_matter_extraction\n  solid_phase_extraction:\n    text: solid_phase_extraction\n  phosphorus_extraction:\n    text: phosphorus_extraction\n  ph_measurement:\n    text: ph_measurement\n  respiration_measurement:\n    text: respiration_measurement\n  texture_measurement:\n    text: texture_measurement\n  dna_extraction:\n    text: dna_extraction\n  phenol_chloroform_extraction:\n    text: phenol_chloroform_extraction\n\n
"},{"location":"ProtocolExecution/","title":"Class: ProtocolExecution","text":"

A PlannedProces that has PlannedProcess parts. Can be used to represent the case of someone following a Protocol.

URI: nmdc:ProtocolExecution

classDiagram\n  class ProtocolExecution\n  click ProtocolExecution href \"../ProtocolExecution\"\n    PlannedProcess <|-- ProtocolExecution\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n\n  ProtocolExecution : alternative_identifiers\n\n  ProtocolExecution : description\n\n  ProtocolExecution : end_date\n\n  ProtocolExecution : has_failure_categorization\n\n      ProtocolExecution --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ProtocolExecution : has_input\n\n      ProtocolExecution --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ProtocolExecution : has_output\n\n      ProtocolExecution --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  ProtocolExecution : has_process_parts\n\n      ProtocolExecution --> \"1..*\" PlannedProcess : has_process_parts\n    click PlannedProcess href \"../PlannedProcess\"\n\n  ProtocolExecution : id\n\n  ProtocolExecution : name\n\n  ProtocolExecution : processing_institution\n\n      ProtocolExecution --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ProtocolExecution : protocol_execution_category\n\n      ProtocolExecution --> \"1\" ProtocolCategoryEnum : protocol_execution_category\n    click ProtocolCategoryEnum href \"../ProtocolCategoryEnum\"\n\n  ProtocolExecution : protocol_link\n\n      ProtocolExecution --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ProtocolExecution : qc_comment\n\n  ProtocolExecution : qc_status\n\n      ProtocolExecution --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ProtocolExecution : start_date\n\n  ProtocolExecution : type\n\n\n\n
"},{"location":"ProtocolExecution/#inheritance","title":"Inheritance","text":""},{"location":"ProtocolExecution/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_process_parts 1..* PlannedProcess The MaterialProcessing steps that are discrete parts of the ProtocolExecution direct protocol_execution_category 1 ProtocolCategoryEnum direct has_input * NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ProtocolExecution/#usages","title":"Usages","text":"used by used in type used Database protocol_execution_set range ProtocolExecution"},{"location":"ProtocolExecution/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProtocolExecution/#schema-source","title":"Schema Source","text":""},{"location":"ProtocolExecution/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ProtocolExecution native nmdc:ProtocolExecution"},{"location":"ProtocolExecution/#linkml-source","title":"LinkML Source","text":""},{"location":"ProtocolExecution/#direct","title":"Direct","text":"
name: ProtocolExecution\ndescription: A PlannedProces that has PlannedProcess parts. Can be used to represent\n  the case of someone following a Protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: PlannedProcess\nslots:\n- has_process_parts\n- protocol_execution_category\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_process_parts:\n    name: has_process_parts\n    description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ProtocolExecution\n\n
"},{"location":"ProtocolExecution/#induced","title":"Induced","text":"
name: ProtocolExecution\ndescription: A PlannedProces that has PlannedProcess parts. Can be used to represent\n  the case of someone following a Protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: PlannedProcess\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_process_parts:\n    name: has_process_parts\n    description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_process_parts:\n    name: has_process_parts\n    description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    list_elements_ordered: true\n    alias: has_process_parts\n    owner: ProtocolExecution\n    domain_of:\n    - ProtocolExecution\n    range: PlannedProcess\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  protocol_execution_category:\n    name: protocol_execution_category\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_execution_category\n    owner: ProtocolExecution\n    domain_of:\n    - ProtocolExecution\n    range: ProtocolCategoryEnum\n    required: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ProtocolExecution\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ProtocolExecution\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ProtocolExecution\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ProtocolExecution\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ProtocolExecution\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ProtocolExecution\n\n
"},{"location":"QuadPosEnum/","title":"Enum: QuadPosEnum","text":"

URI: QuadPosEnum

"},{"location":"QuadPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description North side None West side None South side None East side None"},{"location":"QuadPosEnum/#slots","title":"Slots","text":"Name Description quad_pos The quadrant position of the sampling room within the building"},{"location":"QuadPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"QuadPosEnum/#schema-source","title":"Schema Source","text":""},{"location":"QuadPosEnum/#linkml-source","title":"LinkML Source","text":"
name: quad_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  North side:\n    text: North side\n  West side:\n    text: West side\n  South side:\n    text: South side\n  East side:\n    text: East side\n\n
"},{"location":"QuantityValue/","title":"Class: QuantityValue","text":"

A simple quantity, e.g. 2cm

URI: nmdc:QuantityValue

classDiagram\n  class QuantityValue\n  click QuantityValue href \"../QuantityValue\"\n    AttributeValue <|-- QuantityValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  QuantityValue : has_maximum_numeric_value\n\n  QuantityValue : has_minimum_numeric_value\n\n  QuantityValue : has_numeric_value\n\n  QuantityValue : has_raw_value\n\n  QuantityValue : has_unit\n\n  QuantityValue : type\n\n\n\n
"},{"location":"QuantityValue/#inheritance","title":"Inheritance","text":""},{"location":"QuantityValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_maximum_numeric_value 0..1 Decimal The maximum value part, expressed as number, of the quantity value when the v... direct has_minimum_numeric_value 0..1 Decimal The minimum value part, expressed as number, of the quantity value when the v... direct has_numeric_value 0..1 Decimal The number part of the quantity direct has_unit 0..1 Unit The unit of the quantity direct has_raw_value 0..1 String Unnormalized atomic string representation, should in syntax {number} {unit} AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"QuantityValue/#usages","title":"Usages","text":"used by used in type used ChromatographyConfiguration temperature range QuantityValue Extraction input_mass range QuantityValue Extraction volume range QuantityValue SubSamplingProcess container_size range QuantityValue SubSamplingProcess temperature range QuantityValue SubSamplingProcess volume range QuantityValue SubSamplingProcess mass range QuantityValue MixingProcess duration range QuantityValue FiltrationProcess container_size range QuantityValue FiltrationProcess filter_pore_size range QuantityValue FiltrationProcess volume range QuantityValue StorageProcess temperature range QuantityValue ChromatographicSeparationProcess temperature range QuantityValue DissolvingProcess duration range QuantityValue DissolvingProcess temperature range QuantityValue ChemicalConversionProcess duration range QuantityValue ChemicalConversionProcess temperature range QuantityValue ChemicalConversionProcess substances_volume range QuantityValue Biosample abs_air_humidity range QuantityValue Biosample air_temp range QuantityValue Biosample al_sat range QuantityValue Biosample alkalinity range QuantityValue Biosample alkyl_diethers range QuantityValue Biosample alt range QuantityValue Biosample aminopept_act range QuantityValue Biosample ammonium range QuantityValue Biosample ammonium_nitrogen range QuantityValue Biosample amount_light range QuantityValue Biosample annual_precpt range QuantityValue Biosample annual_temp range QuantityValue Biosample api range QuantityValue Biosample avg_dew_point range QuantityValue Biosample avg_temp range QuantityValue Biosample bac_prod range QuantityValue Biosample bac_resp range QuantityValue Biosample bacteria_carb_prod range QuantityValue Biosample barometric_press range QuantityValue Biosample benzene range QuantityValue Biosample biochem_oxygen_dem range QuantityValue Biosample bishomohopanol range QuantityValue Biosample blood_press_diast range QuantityValue Biosample blood_press_syst range QuantityValue Biosample bromide range QuantityValue Biosample built_struc_age range QuantityValue Biosample calcium range QuantityValue Biosample carb_dioxide range QuantityValue Biosample carb_monoxide range QuantityValue Biosample carb_nitro_ratio range QuantityValue Biosample ceil_area range QuantityValue Biosample ceil_thermal_mass range QuantityValue Biosample chem_oxygen_dem range QuantityValue Biosample chloride range QuantityValue Biosample chlorophyll range QuantityValue Biosample conduc range QuantityValue Biosample density range QuantityValue Biosample depth range QuantityValue Biosample dew_point range QuantityValue Biosample diss_carb_dioxide range QuantityValue Biosample diss_hydrogen range QuantityValue Biosample diss_inorg_carb range QuantityValue Biosample diss_inorg_nitro range QuantityValue Biosample diss_inorg_phosp range QuantityValue Biosample diss_iron range QuantityValue Biosample diss_org_carb range QuantityValue Biosample diss_org_nitro range QuantityValue Biosample diss_oxygen range QuantityValue Biosample diss_oxygen_fluid range QuantityValue Biosample door_size range QuantityValue Biosample down_par range QuantityValue Biosample efficiency_percent range QuantityValue Biosample ethylbenzene range QuantityValue Biosample exp_duct range QuantityValue Biosample exp_pipe range QuantityValue Biosample floor_age range QuantityValue Biosample floor_area range QuantityValue Biosample floor_thermal_mass range QuantityValue Biosample fluor range QuantityValue Biosample freq_clean range QuantityValue Biosample freq_cook range QuantityValue Biosample glucosidase_act range QuantityValue Biosample hcr_fw_salinity range QuantityValue Biosample height_carper_fiber range QuantityValue Biosample host_age range QuantityValue Biosample host_body_temp range QuantityValue Biosample host_dry_mass range QuantityValue Biosample host_height range QuantityValue Biosample host_length range QuantityValue Biosample host_tot_mass range QuantityValue Biosample host_wet_mass range QuantityValue Biosample humidity range QuantityValue Biosample indust_eff_percent range QuantityValue Biosample inside_lux range QuantityValue Biosample iwf range QuantityValue Biosample lbc_thirty range QuantityValue Biosample lbceq range QuantityValue Biosample light_intensity range QuantityValue Biosample magnesium range QuantityValue Biosample manganese range QuantityValue Biosample max_occup range QuantityValue Biosample mean_frict_vel range QuantityValue Biosample mean_peak_frict_vel range QuantityValue Biosample methane range QuantityValue Biosample microbial_biomass range QuantityValue Biosample nitrate range QuantityValue Biosample nitrate_nitrogen range QuantityValue Biosample nitrite range QuantityValue Biosample nitrite_nitrogen range QuantityValue Biosample nitro range QuantityValue Biosample number_pets range QuantityValue Biosample number_plants range QuantityValue Biosample number_resident range QuantityValue Biosample occup_density_samp range QuantityValue Biosample occup_samp range QuantityValue Biosample org_carb range QuantityValue Biosample org_matter range QuantityValue Biosample org_nitro range QuantityValue Biosample organism_count range QuantityValue Biosample owc_tvdss range QuantityValue Biosample oxygen range QuantityValue Biosample part_org_carb range QuantityValue Biosample part_org_nitro range QuantityValue Biosample petroleum_hydrocarb range QuantityValue Biosample phosphate range QuantityValue Biosample photon_flux range QuantityValue Biosample potassium range QuantityValue Biosample pour_point range QuantityValue Biosample pressure range QuantityValue Biosample primary_prod range QuantityValue Biosample prod_rate range QuantityValue Biosample redox_potential range QuantityValue Biosample rel_air_humidity range QuantityValue Biosample rel_humidity_out range QuantityValue Biosample room_air_exch_rate range QuantityValue Biosample room_occup range QuantityValue Biosample root_med_ph range QuantityValue Biosample salinity range QuantityValue Biosample samp_md range QuantityValue Biosample samp_size range QuantityValue Biosample samp_store_temp range QuantityValue Biosample season_precpt range QuantityValue Biosample season_temp range QuantityValue Biosample silicate range QuantityValue Biosample size_frac_low range QuantityValue Biosample size_frac_up range QuantityValue Biosample slope_aspect range QuantityValue Biosample slope_gradient range QuantityValue Biosample sludge_retent_time range QuantityValue Biosample sodium range QuantityValue Biosample soil_text_measure range QuantityValue Biosample solar_irradiance range QuantityValue Biosample soluble_react_phosp range QuantityValue Biosample specific_humidity range QuantityValue Biosample sulfate range QuantityValue Biosample sulfate_fw range QuantityValue Biosample sulfide range QuantityValue Biosample surf_humidity range QuantityValue Biosample surf_moisture range QuantityValue Biosample surf_temp range QuantityValue Biosample suspend_part_matter range QuantityValue Biosample tan range QuantityValue Biosample temp range QuantityValue Biosample temp_out range QuantityValue Biosample toluene range QuantityValue Biosample tot_carb range QuantityValue Biosample tot_depth_water_col range QuantityValue Biosample tot_diss_nitro range QuantityValue Biosample tot_inorg_nitro range QuantityValue Biosample tot_iron range QuantityValue Biosample tot_nitro range QuantityValue Biosample tot_nitro_content range QuantityValue Biosample tot_org_carb range QuantityValue Biosample tot_part_carb range QuantityValue Biosample tot_phosp range QuantityValue Biosample tot_phosphate range QuantityValue Biosample tot_sulfur range QuantityValue Biosample turbidity range QuantityValue Biosample tvdss_of_hcr_press range QuantityValue Biosample tvdss_of_hcr_temp range QuantityValue Biosample ventilation_rate range QuantityValue Biosample vfa range QuantityValue Biosample vfa_fw range QuantityValue Biosample wall_area range QuantityValue Biosample wall_height range QuantityValue Biosample wall_thermal_mass range QuantityValue Biosample water_current range QuantityValue Biosample water_cut range QuantityValue Biosample water_feat_size range QuantityValue Biosample water_prod_rate range QuantityValue Biosample wind_speed range QuantityValue Biosample xylene range QuantityValue Biosample zinc range QuantityValue Biosample subsurface_depth range QuantityValue Biosample bulk_elect_conductivity range QuantityValue MobilePhaseSegment duration range QuantityValue MobilePhaseSegment volume range QuantityValue PortionOfSubstance final_concentration range QuantityValue PortionOfSubstance mass range QuantityValue PortionOfSubstance source_concentration range QuantityValue PortionOfSubstance volume range QuantityValue ProcessedSample biomaterial_purity range QuantityValue"},{"location":"QuantityValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"QuantityValue/#schema-source","title":"Schema Source","text":""},{"location":"QuantityValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:QuantityValue native nmdc:QuantityValue undefined schema:QuantityValue"},{"location":"QuantityValue/#linkml-source","title":"LinkML Source","text":""},{"location":"QuantityValue/#direct","title":"Direct","text":"
name: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslots:\n- has_maximum_numeric_value\n- has_minimum_numeric_value\n- has_numeric_value\n- has_unit\nslot_usage:\n  has_raw_value:\n    name: has_raw_value\n    description: Unnormalized atomic string representation, should in syntax {number}\n      {unit}\n  has_unit:\n    name: has_unit\n    description: The unit of the quantity\n  has_numeric_value:\n    name: has_numeric_value\n    description: The number part of the quantity\nclass_uri: nmdc:QuantityValue\n\n
"},{"location":"QuantityValue/#induced","title":"Induced","text":"
name: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslot_usage:\n  has_raw_value:\n    name: has_raw_value\n    description: Unnormalized atomic string representation, should in syntax {number}\n      {unit}\n  has_unit:\n    name: has_unit\n    description: The unit of the quantity\n  has_numeric_value:\n    name: has_numeric_value\n    description: The number part of the quantity\nattributes:\n  has_maximum_numeric_value:\n    name: has_maximum_numeric_value\n    description: The maximum value part, expressed as number, of the quantity value\n      when the value covers a range.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: has_numeric_value\n    alias: has_maximum_numeric_value\n    owner: QuantityValue\n    domain_of:\n    - QuantityValue\n    range: decimal\n  has_minimum_numeric_value:\n    name: has_minimum_numeric_value\n    description: The minimum value part, expressed as number, of the quantity value\n      when the value covers a range.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: has_numeric_value\n    alias: has_minimum_numeric_value\n    owner: QuantityValue\n    domain_of:\n    - QuantityValue\n    range: decimal\n  has_numeric_value:\n    name: has_numeric_value\n    description: The number part of the quantity\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - qud:quantityValue\n    - schema:value\n    rank: 1000\n    alias: has_numeric_value\n    owner: QuantityValue\n    domain_of:\n    - QuantityValue\n    range: decimal\n  has_unit:\n    name: has_unit\n    description: The unit of the quantity\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - scale\n    mappings:\n    - qud:unit\n    - schema:unitCode\n    rank: 1000\n    alias: has_unit\n    owner: QuantityValue\n    domain_of:\n    - QuantityValue\n    range: unit\n  has_raw_value:\n    name: has_raw_value\n    description: Unnormalized atomic string representation, should in syntax {number}\n      {unit}\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: QuantityValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: QuantityValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:QuantityValue\n\n
"},{"location":"RNASampleFormatEnum/","title":"Enum: RNASampleFormatEnum","text":"

URI: RNASampleFormatEnum

"},{"location":"RNASampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"RNASampleFormatEnum/#slots","title":"Slots","text":"Name Description rna_sample_format Solution in which the RNA sample has been suspended"},{"location":"RNASampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RNASampleFormatEnum/#schema-source","title":"Schema Source","text":""},{"location":"RNASampleFormatEnum/#linkml-source","title":"LinkML Source","text":"
name: RNASampleFormatEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  10 mM Tris-HCl:\n    text: 10 mM Tris-HCl\n  DNAStable:\n    text: DNAStable\n  Ethanol:\n    text: Ethanol\n  Low EDTA TE:\n    text: Low EDTA TE\n  MDA reaction buffer:\n    text: MDA reaction buffer\n  PBS:\n    text: PBS\n  Pellet:\n    text: Pellet\n  RNAStable:\n    text: RNAStable\n  TE:\n    text: TE\n  Water:\n    text: Water\n  Gentegra-DNA:\n    text: Gentegra-DNA\n  Gentegra-RNA:\n    text: Gentegra-RNA\n\n
"},{"location":"ReadBasedTaxonomyAnalysis/","title":"Class: Read based analysis activity (ReadBasedTaxonomyAnalysis)","text":"

A workflow execution activity that performs taxonomy classification using sequencing reads

URI: nmdc:ReadBasedTaxonomyAnalysis

classDiagram\n  class ReadBasedTaxonomyAnalysis\n  click ReadBasedTaxonomyAnalysis href \"../ReadBasedTaxonomyAnalysis\"\n    WorkflowExecution <|-- ReadBasedTaxonomyAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  ReadBasedTaxonomyAnalysis : alternative_identifiers\n\n  ReadBasedTaxonomyAnalysis : description\n\n  ReadBasedTaxonomyAnalysis : end_date\n\n  ReadBasedTaxonomyAnalysis : ended_at_time\n\n  ReadBasedTaxonomyAnalysis : execution_resource\n\n      ReadBasedTaxonomyAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  ReadBasedTaxonomyAnalysis : git_url\n\n  ReadBasedTaxonomyAnalysis : has_failure_categorization\n\n      ReadBasedTaxonomyAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ReadBasedTaxonomyAnalysis : has_input\n\n      ReadBasedTaxonomyAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ReadBasedTaxonomyAnalysis : has_output\n\n      ReadBasedTaxonomyAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  ReadBasedTaxonomyAnalysis : id\n\n  ReadBasedTaxonomyAnalysis : name\n\n  ReadBasedTaxonomyAnalysis : processing_institution\n\n      ReadBasedTaxonomyAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ReadBasedTaxonomyAnalysis : protocol_link\n\n      ReadBasedTaxonomyAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ReadBasedTaxonomyAnalysis : qc_comment\n\n  ReadBasedTaxonomyAnalysis : qc_status\n\n      ReadBasedTaxonomyAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ReadBasedTaxonomyAnalysis : start_date\n\n  ReadBasedTaxonomyAnalysis : started_at_time\n\n  ReadBasedTaxonomyAnalysis : type\n\n  ReadBasedTaxonomyAnalysis : version\n\n  ReadBasedTaxonomyAnalysis : was_informed_by\n\n      ReadBasedTaxonomyAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"ReadBasedTaxonomyAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"ReadBasedTaxonomyAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ReadBasedTaxonomyAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ReadBasedTaxonomyAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"ReadBasedTaxonomyAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ReadBasedTaxonomyAnalysis native nmdc:ReadBasedTaxonomyAnalysis"},{"location":"ReadBasedTaxonomyAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"ReadBasedTaxonomyAnalysis/#direct","title":"Direct","text":"
name: ReadBasedTaxonomyAnalysis\ndescription: A workflow execution activity that performs taxonomy classification using\n  sequencing reads\ntitle: Read based analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ReadBasedTaxonomyAnalysis\n\n
"},{"location":"ReadBasedTaxonomyAnalysis/#induced","title":"Induced","text":"
name: ReadBasedTaxonomyAnalysis\ndescription: A workflow execution activity that performs taxonomy classification using\n  sequencing reads\ntitle: Read based analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ReadBasedTaxonomyAnalysis\n\n
"},{"location":"ReadQcAnalysis/","title":"Class: Read quality control analysis activity (ReadQcAnalysis)","text":"

A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal

URI: nmdc:ReadQcAnalysis

classDiagram\n  class ReadQcAnalysis\n  click ReadQcAnalysis href \"../ReadQcAnalysis\"\n    WorkflowExecution <|-- ReadQcAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  ReadQcAnalysis : alternative_identifiers\n\n  ReadQcAnalysis : description\n\n  ReadQcAnalysis : end_date\n\n  ReadQcAnalysis : ended_at_time\n\n  ReadQcAnalysis : execution_resource\n\n      ReadQcAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  ReadQcAnalysis : git_url\n\n  ReadQcAnalysis : has_failure_categorization\n\n      ReadQcAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ReadQcAnalysis : has_input\n\n      ReadQcAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ReadQcAnalysis : has_output\n\n      ReadQcAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  ReadQcAnalysis : id\n\n  ReadQcAnalysis : input_base_count\n\n  ReadQcAnalysis : input_read_bases\n\n  ReadQcAnalysis : input_read_count\n\n  ReadQcAnalysis : name\n\n  ReadQcAnalysis : output_base_count\n\n  ReadQcAnalysis : output_read_bases\n\n  ReadQcAnalysis : output_read_count\n\n  ReadQcAnalysis : processing_institution\n\n      ReadQcAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ReadQcAnalysis : protocol_link\n\n      ReadQcAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ReadQcAnalysis : qc_comment\n\n  ReadQcAnalysis : qc_status\n\n      ReadQcAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ReadQcAnalysis : start_date\n\n  ReadQcAnalysis : started_at_time\n\n  ReadQcAnalysis : type\n\n  ReadQcAnalysis : version\n\n  ReadQcAnalysis : was_informed_by\n\n      ReadQcAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"ReadQcAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"ReadQcAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_base_count 0..1 Float The nucleotide base count number of input reads for QC analysis direct input_read_bases 0..1 Float TODO direct input_read_count 0..1 Float The sequence count number of input reads for QC analysis direct output_base_count 0..1 Float After QC analysis nucleotide base count number direct output_read_bases 0..1 Float TODO direct output_read_count 0..1 Float After QC analysis sequence count number direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ReadQcAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ReadQcAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"ReadQcAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ReadQcAnalysis native nmdc:ReadQcAnalysis"},{"location":"ReadQcAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"ReadQcAnalysis/#direct","title":"Direct","text":"
name: ReadQcAnalysis\ndescription: A workflow execution activity that performs quality control on raw Illumina\n  reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n  spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- input_base_count\n- input_read_bases\n- input_read_count\n- output_base_count\n- output_read_bases\n- output_read_count\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ReadQcAnalysis\n\n
"},{"location":"ReadQcAnalysis/#induced","title":"Induced","text":"
name: ReadQcAnalysis\ndescription: A workflow execution activity that performs quality control on raw Illumina\n  reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n  spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  input_base_count:\n    name: input_base_count\n    description: The nucleotide base count number of input reads for QC analysis.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: read_qc_analysis_statistic\n    alias: input_base_count\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  input_read_bases:\n    name: input_read_bases\n    description: 'TODO      '\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: input_read_bases\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  input_read_count:\n    name: input_read_count\n    description: The sequence count number of input reads for QC analysis.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: read_qc_analysis_statistic\n    alias: input_read_count\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  output_base_count:\n    name: output_base_count\n    description: After QC analysis nucleotide base count number.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: read_qc_analysis_statistic\n    alias: output_base_count\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  output_read_bases:\n    name: output_read_bases\n    description: TODO\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: output_read_bases\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  output_read_count:\n    name: output_read_count\n    description: After QC analysis sequence count number.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: read_qc_analysis_statistic\n    alias: output_read_count\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ReadQcAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ReadQcAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ReadQcAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ReadQcAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ReadQcAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ReadQcAnalysis\n\n
"},{"location":"RelSampLocEnum/","title":"Enum: RelSampLocEnum","text":"

URI: RelSampLocEnum

"},{"location":"RelSampLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description edge of car None center of car None under a seat None"},{"location":"RelSampLocEnum/#slots","title":"Slots","text":"Name Description rel_samp_loc The sampling location within the train car"},{"location":"RelSampLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RelSampLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"RelSampLocEnum/#linkml-source","title":"LinkML Source","text":"
name: rel_samp_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  edge of car:\n    text: edge of car\n  center of car:\n    text: center of car\n  under a seat:\n    text: under a seat\n\n
"},{"location":"ResolutionCategoryEnum/","title":"Enum: ResolutionCategoryEnum","text":"

URI: ResolutionCategoryEnum

"},{"location":"ResolutionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description high None higher than unit resolution low None at unit resolution"},{"location":"ResolutionCategoryEnum/#slots","title":"Slots","text":"Name Description resolution_categories The relative resolution at which spectra were collected"},{"location":"ResolutionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ResolutionCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ResolutionCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ResolutionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  high:\n    text: high\n    description: higher than unit resolution\n  low:\n    text: low\n    description: at unit resolution\n\n
"},{"location":"RoomCondtEnum/","title":"Enum: RoomCondtEnum","text":"

URI: RoomCondtEnum

"},{"location":"RoomCondtEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None visible signs of mold/mildew None"},{"location":"RoomCondtEnum/#slots","title":"Slots","text":"Name Description room_condt The condition of the room at the time of sampling"},{"location":"RoomCondtEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomCondtEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomCondtEnum/#linkml-source","title":"LinkML Source","text":"
name: room_condt_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  new:\n    text: new\n  visible wear:\n    text: visible wear\n  needs repair:\n    text: needs repair\n  damaged:\n    text: damaged\n  rupture:\n    text: rupture\n  visible signs of mold/mildew:\n    text: visible signs of mold/mildew\n\n
"},{"location":"RoomConnectedEnum/","title":"Enum: RoomConnectedEnum","text":"

URI: RoomConnectedEnum

"},{"location":"RoomConnectedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None office None stairwell None"},{"location":"RoomConnectedEnum/#slots","title":"Slots","text":"Name Description room_connected List of rooms connected to the sampling room by a doorway"},{"location":"RoomConnectedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomConnectedEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomConnectedEnum/#linkml-source","title":"LinkML Source","text":"
name: room_connected_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  attic:\n    text: attic\n  bathroom:\n    text: bathroom\n  closet:\n    text: closet\n  conference room:\n    text: conference room\n  elevator:\n    text: elevator\n  examining room:\n    text: examining room\n  hallway:\n    text: hallway\n  kitchen:\n    text: kitchen\n  mail room:\n    text: mail room\n  office:\n    text: office\n  stairwell:\n    text: stairwell\n\n
"},{"location":"RoomLocEnum/","title":"Enum: RoomLocEnum","text":"

URI: RoomLocEnum

"},{"location":"RoomLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description corner room None interior room None exterior wall None"},{"location":"RoomLocEnum/#slots","title":"Slots","text":"Name Description room_loc The position of the room within the building"},{"location":"RoomLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomLocEnum/#linkml-source","title":"LinkML Source","text":"
name: room_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  corner room:\n    text: corner room\n  interior room:\n    text: interior room\n  exterior wall:\n    text: exterior wall\n\n
"},{"location":"RoomSampPosEnum/","title":"Enum: RoomSampPosEnum","text":"

URI: RoomSampPosEnum

"},{"location":"RoomSampPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north corner None south corner None west corner None east corner None northeast corner None northwest corner None southeast corner None southwest corner None center None"},{"location":"RoomSampPosEnum/#slots","title":"Slots","text":"Name Description room_samp_pos The horizontal sampling position in the room relative to architectural elemen..."},{"location":"RoomSampPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomSampPosEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomSampPosEnum/#linkml-source","title":"LinkML Source","text":"
name: room_samp_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north corner:\n    text: north corner\n  south corner:\n    text: south corner\n  west corner:\n    text: west corner\n  east corner:\n    text: east corner\n  northeast corner:\n    text: northeast corner\n  northwest corner:\n    text: northwest corner\n  southeast corner:\n    text: southeast corner\n  southwest corner:\n    text: southwest corner\n  center:\n    text: center\n\n
"},{"location":"RoomTypeEnum/","title":"Enum: RoomTypeEnum","text":"

URI: RoomTypeEnum

"},{"location":"RoomTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None private office None open office None stairwell None ,restroom None lobby None vestibule None mechanical or electrical room None data center None laboratory_wet None laboratory_dry None gymnasium None natatorium None auditorium None lockers None cafe None warehouse None"},{"location":"RoomTypeEnum/#slots","title":"Slots","text":"Name Description room_type The main purpose or activity of the sampling room"},{"location":"RoomTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: room_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  attic:\n    text: attic\n  bathroom:\n    text: bathroom\n  closet:\n    text: closet\n  conference room:\n    text: conference room\n  elevator:\n    text: elevator\n  examining room:\n    text: examining room\n  hallway:\n    text: hallway\n  kitchen:\n    text: kitchen\n  mail room:\n    text: mail room\n  private office:\n    text: private office\n  open office:\n    text: open office\n  stairwell:\n    text: stairwell\n  ',restroom':\n    text: ',restroom'\n  lobby:\n    text: lobby\n  vestibule:\n    text: vestibule\n  mechanical or electrical room:\n    text: mechanical or electrical room\n  data center:\n    text: data center\n  laboratory_wet:\n    text: laboratory_wet\n  laboratory_dry:\n    text: laboratory_dry\n  gymnasium:\n    text: gymnasium\n  natatorium:\n    text: natatorium\n  auditorium:\n    text: auditorium\n  lockers:\n    text: lockers\n  cafe:\n    text: cafe\n  warehouse:\n    text: warehouse\n\n
"},{"location":"SampCaptStatusEnum/","title":"Enum: SampCaptStatusEnum","text":"

URI: SampCaptStatusEnum

"},{"location":"SampCaptStatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description active surveillance in response to an outbreak None active surveillance not initiated by an outbreak None farm sample None market sample None other None"},{"location":"SampCaptStatusEnum/#slots","title":"Slots","text":"Name Description samp_capt_status Reason for the sample"},{"location":"SampCaptStatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCaptStatusEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampCaptStatusEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_capt_status_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  active surveillance in response to an outbreak:\n    text: active surveillance in response to an outbreak\n  active surveillance not initiated by an outbreak:\n    text: active surveillance not initiated by an outbreak\n  farm sample:\n    text: farm sample\n  market sample:\n    text: market sample\n  other:\n    text: other\n\n
"},{"location":"SampCollectPointEnum/","title":"Enum: SampCollectPointEnum","text":"

URI: SampCollectPointEnum

"},{"location":"SampCollectPointEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description well None test well None drilling rig None wellhead None separator None storage tank None other None"},{"location":"SampCollectPointEnum/#slots","title":"Slots","text":"Name Description samp_collect_point Sampling point on the asset were sample was collected (e"},{"location":"SampCollectPointEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCollectPointEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampCollectPointEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_collect_point_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  well:\n    text: well\n  test well:\n    text: test well\n  drilling rig:\n    text: drilling rig\n  wellhead:\n    text: wellhead\n  separator:\n    text: separator\n  storage tank:\n    text: storage tank\n  other:\n    text: other\n\n
"},{"location":"SampDisStageEnum/","title":"Enum: SampDisStageEnum","text":"

URI: SampDisStageEnum

"},{"location":"SampDisStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dissemination None growth and reproduction None infection None inoculation None penetration None other None"},{"location":"SampDisStageEnum/#slots","title":"Slots","text":"Name Description samp_dis_stage Stage of the disease at the time of sample collection, e"},{"location":"SampDisStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampDisStageEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampDisStageEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_dis_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  dissemination:\n    text: dissemination\n  growth and reproduction:\n    text: growth and reproduction\n  infection:\n    text: infection\n  inoculation:\n    text: inoculation\n  penetration:\n    text: penetration\n  other:\n    text: other\n\n
"},{"location":"SampFloorEnum/","title":"Enum: SampFloorEnum","text":"

URI: SampFloorEnum

"},{"location":"SampFloorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 1st floor None 2nd floor None basement None lobby None"},{"location":"SampFloorEnum/#slots","title":"Slots","text":"Name Description samp_floor The floor of the building, where the sampling room is located"},{"location":"SampFloorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampFloorEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampFloorEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_floor_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  1st floor:\n    text: 1st floor\n  2nd floor:\n    text: 2nd floor\n  basement:\n    text: basement\n  lobby:\n    text: lobby\n\n
"},{"location":"SampMdEnum/","title":"Enum: SampMdEnum","text":"

URI: SampMdEnum

"},{"location":"SampMdEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DF None RT None KB None MSL None other None"},{"location":"SampMdEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampMdEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampMdEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_md_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  DF:\n    text: DF\n  RT:\n    text: RT\n  KB:\n    text: KB\n  MSL:\n    text: MSL\n  other:\n    text: other\n\n
"},{"location":"SampSubtypeEnum/","title":"Enum: SampSubtypeEnum","text":"

URI: SampSubtypeEnum

"},{"location":"SampSubtypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description oil phase None water phase None biofilm None not applicable None other None"},{"location":"SampSubtypeEnum/#slots","title":"Slots","text":"Name Description samp_subtype Name of sample sub-type"},{"location":"SampSubtypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampSubtypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampSubtypeEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_subtype_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  oil phase:\n    text: oil phase\n  water phase:\n    text: water phase\n  biofilm:\n    text: biofilm\n  not applicable:\n    text: not applicable\n  other:\n    text: other\n\n
"},{"location":"SampWeatherEnum/","title":"Enum: SampWeatherEnum","text":"

URI: SampWeatherEnum

"},{"location":"SampWeatherEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clear sky None cloudy None foggy None hail None rain None snow None sleet None sunny None windy None"},{"location":"SampWeatherEnum/#slots","title":"Slots","text":"Name Description samp_weather The weather on the sampling day"},{"location":"SampWeatherEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampWeatherEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampWeatherEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_weather_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  clear sky:\n    text: clear sky\n  cloudy:\n    text: cloudy\n  foggy:\n    text: foggy\n  hail:\n    text: hail\n  rain:\n    text: rain\n  snow:\n    text: snow\n  sleet:\n    text: sleet\n  sunny:\n    text: sunny\n  windy:\n    text: windy\n\n
"},{"location":"SamplePortionEnum/","title":"Enum: SamplePortionEnum","text":"

URI: SamplePortionEnum

"},{"location":"SamplePortionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description supernatant None pellet None organic_layer None aqueous_layer None non_polar_layer None"},{"location":"SamplePortionEnum/#slots","title":"Slots","text":"Name Description sampled_portion The portion of the sample that is taken for downstream activity"},{"location":"SamplePortionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SamplePortionEnum/#schema-source","title":"Schema Source","text":""},{"location":"SamplePortionEnum/#linkml-source","title":"LinkML Source","text":"
name: SamplePortionEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  supernatant:\n    text: supernatant\n    aliases:\n    - top_layer\n  pellet:\n    text: pellet\n    aliases:\n    - bottom_layer\n  organic_layer:\n    text: organic_layer\n  aqueous_layer:\n    text: aqueous_layer\n  non_polar_layer:\n    text: non_polar_layer\n\n
"},{"location":"SampleStateEnum/","title":"Enum: SampleStateEnum","text":"

URI: SampleStateEnum

"},{"location":"SampleStateEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description solid None liquid None gas None"},{"location":"SampleStateEnum/#slots","title":"Slots","text":"Name Description sample_state_information The chemical phase of a pure sample, or the state of a mixed sample"},{"location":"SampleStateEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleStateEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampleStateEnum/#linkml-source","title":"LinkML Source","text":"
name: SampleStateEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  solid:\n    text: solid\n  liquid:\n    text: liquid\n  gas:\n    text: gas\n\n
"},{"location":"SampleSubset/","title":"Subset: SampleSubset","text":"

Subset consisting of entities linked to the processing of samples. Currently, this subset consists of study, omics process, and biosample.

URI: SampleSubset

"},{"location":"SampleSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleSubset/#schema-source","title":"Schema Source","text":""},{"location":"SampleSubset/#classes-in-subset","title":"Classes in subset","text":"Class Description Biosample Biological source material which can be characterized by an experiment DataGeneration The methods and processes used to generate omics data from a biosample or org... Study A study summarizes the overall goal of a research initiative and outlines the..."},{"location":"SampleTypeEnum/","title":"Enum: SampleTypeEnum","text":"

URI: SampleTypeEnum

"},{"location":"SampleTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description soil None soil - water extract None plant associated None sediment None water None"},{"location":"SampleTypeEnum/#slots","title":"Slots","text":"Name Description sample_type Type of sample being submitted"},{"location":"SampleTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampleTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: SampleTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  soil:\n    text: soil\n  soil - water extract:\n    text: soil - water extract\n  plant associated:\n    text: plant associated\n  sediment:\n    text: sediment\n  water:\n    text: water\n\n
"},{"location":"SeasonUseEnum/","title":"Enum: SeasonUseEnum","text":"

URI: SeasonUseEnum

"},{"location":"SeasonUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Spring None Summer None Fall None Winter None"},{"location":"SeasonUseEnum/#slots","title":"Slots","text":"Name Description season_use The seasons the space is occupied"},{"location":"SeasonUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeasonUseEnum/#schema-source","title":"Schema Source","text":""},{"location":"SeasonUseEnum/#linkml-source","title":"LinkML Source","text":"
name: season_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Spring:\n    text: Spring\n  Summer:\n    text: Summer\n  Fall:\n    text: Fall\n  Winter:\n    text: Winter\n\n
"},{"location":"SedimentTypeEnum/","title":"Enum: SedimentTypeEnum","text":"

URI: SedimentTypeEnum

"},{"location":"SedimentTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description biogenous None cosmogenous None hydrogenous None lithogenous None"},{"location":"SedimentTypeEnum/#slots","title":"Slots","text":"Name Description sediment_type Information about the sediment type based on major constituents"},{"location":"SedimentTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SedimentTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SedimentTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: sediment_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  biogenous:\n    text: biogenous\n  cosmogenous:\n    text: cosmogenous\n  hydrogenous:\n    text: hydrogenous\n  lithogenous:\n    text: lithogenous\n\n
"},{"location":"SeparationMethodEnum/","title":"Enum: SeparationMethodEnum","text":"

The tool/substance used to separate or filter a solution or mixture.

URI: SeparationMethodEnum

"},{"location":"SeparationMethodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ptfe_96_well_filter_plate None syringe None"},{"location":"SeparationMethodEnum/#slots","title":"Slots","text":"Name Description separation_method The method that was used to separate a substance from a solution or mixture"},{"location":"SeparationMethodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeparationMethodEnum/#schema-source","title":"Schema Source","text":""},{"location":"SeparationMethodEnum/#linkml-source","title":"LinkML Source","text":"
name: SeparationMethodEnum\ndescription: The tool/substance used to separate or filter a solution or mixture.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\npermissible_values:\n  ptfe_96_well_filter_plate:\n    text: ptfe_96_well_filter_plate\n  syringe:\n    text: syringe\n\n
"},{"location":"Sequencing/","title":"Subset: Sequencing","text":"

URI: Sequencing

"},{"location":"Sequencing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Sequencing/#schema-source","title":"Schema Source","text":""},{"location":"ShadingDeviceCondEnum/","title":"Enum: ShadingDeviceCondEnum","text":"

URI: ShadingDeviceCondEnum

"},{"location":"ShadingDeviceCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"ShadingDeviceCondEnum/#slots","title":"Slots","text":"Name Description shading_device_cond The physical condition of the shading device at the time of sampling"},{"location":"ShadingDeviceCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"ShadingDeviceCondEnum/#linkml-source","title":"LinkML Source","text":"
name: shading_device_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  damaged:\n    text: damaged\n  needs repair:\n    text: needs repair\n  new:\n    text: new\n  rupture:\n    text: rupture\n  visible wear:\n    text: visible wear\n\n
"},{"location":"ShadingDeviceTypeEnum/","title":"Enum: ShadingDeviceTypeEnum","text":"

URI: ShadingDeviceTypeEnum

"},{"location":"ShadingDeviceTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bahama shutters None exterior roll blind None gambrel awning None hood awning None porchroller awning None sarasota shutters None slatted aluminum None solid aluminum awning None sun screen None tree None trellis None venetian awning None"},{"location":"ShadingDeviceTypeEnum/#slots","title":"Slots","text":"Name Description shading_device_type The type of shading device"},{"location":"ShadingDeviceTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"ShadingDeviceTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: shading_device_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  bahama shutters:\n    text: bahama shutters\n  exterior roll blind:\n    text: exterior roll blind\n  gambrel awning:\n    text: gambrel awning\n  hood awning:\n    text: hood awning\n  porchroller awning:\n    text: porchroller awning\n  sarasota shutters:\n    text: sarasota shutters\n  slatted aluminum:\n    text: slatted aluminum\n  solid aluminum awning:\n    text: solid aluminum awning\n  sun screen:\n    text: sun screen\n  tree:\n    text: tree\n  trellis:\n    text: trellis\n  venetian awning:\n    text: venetian awning\n\n
"},{"location":"Site/","title":"Class: Site (Site)","text":"

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:Site

classDiagram\n  class Site\n  click Site href \"../Site\"\n    MaterialEntity <|-- Site\n      click MaterialEntity href \"../MaterialEntity\"\n\n\n    Site <|-- FieldResearchSite\n      click FieldResearchSite href \"../FieldResearchSite\"\n\n\n\n  Site : alternative_identifiers\n\n  Site : description\n\n  Site : id\n\n  Site : name\n\n  Site : type\n\n\n\n
"},{"location":"Site/#inheritance","title":"Inheritance","text":""},{"location":"Site/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Site/#usages","title":"Usages","text":"used by used in type used CollectingBiosamplesFromSite has_input range Site"},{"location":"Site/#comments","title":"Comments","text":""},{"location":"Site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Site/#schema-source","title":"Schema Source","text":""},{"location":"Site/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Site native nmdc:Site"},{"location":"Site/#linkml-source","title":"LinkML Source","text":""},{"location":"Site/#direct","title":"Direct","text":"
name: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nclass_uri: nmdc:Site\n\n
"},{"location":"Site/#induced","title":"Induced","text":"
name: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Site\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Site\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Site\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Site\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Site\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Site\n\n
"},{"location":"SoilHorizonEnum/","title":"Enum: SoilHorizonEnum","text":"

URI: SoilHorizonEnum

"},{"location":"SoilHorizonEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description O horizon None A horizon None E horizon None B horizon None C horizon None R layer None Permafrost None M horizon None"},{"location":"SoilHorizonEnum/#slots","title":"Slots","text":"Name Description soil_horizon Specific layer in the land area which measures parallel to the soil surface a..."},{"location":"SoilHorizonEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SoilHorizonEnum/#schema-source","title":"Schema Source","text":""},{"location":"SoilHorizonEnum/#linkml-source","title":"LinkML Source","text":"
name: soil_horizon_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  O horizon:\n    text: O horizon\n  A horizon:\n    text: A horizon\n  E horizon:\n    text: E horizon\n  B horizon:\n    text: B horizon\n  C horizon:\n    text: C horizon\n  R layer:\n    text: R layer\n  Permafrost:\n    text: Permafrost\n  M horizon:\n    text: M horizon\n\n
"},{"location":"Sparqlpath/","title":"Type: Sparqlpath","text":"

A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.

URI: xsd:string

"},{"location":"Sparqlpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Sparqlpath/#schema-source","title":"Schema Source","text":""},{"location":"Sparqlpath/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:sparqlpath"},{"location":"SpecificEnum/","title":"Enum: SpecificEnum","text":"

URI: SpecificEnum

"},{"location":"SpecificEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None photos None"},{"location":"SpecificEnum/#slots","title":"Slots","text":"Name Description specific The building specifications"},{"location":"SpecificEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SpecificEnum/#schema-source","title":"Schema Source","text":""},{"location":"SpecificEnum/#linkml-source","title":"LinkML Source","text":"
name: specific_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  operation:\n    text: operation\n  as built:\n    text: as built\n  construction:\n    text: construction\n  bid:\n    text: bid\n  design:\n    text: design\n  photos:\n    text: photos\n\n
"},{"location":"SrDepEnvEnum/","title":"Enum: SrDepEnvEnum","text":"

URI: SrDepEnvEnum

"},{"location":"SrDepEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Lacustine None Fluvioldeltaic None Fluviomarine None Marine None other None"},{"location":"SrDepEnvEnum/#slots","title":"Slots","text":"Name Description sr_dep_env Source rock depositional environment (https://en"},{"location":"SrDepEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrDepEnvEnum/#schema-source","title":"Schema Source","text":""},{"location":"SrDepEnvEnum/#linkml-source","title":"LinkML Source","text":"
name: sr_dep_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Lacustine:\n    text: Lacustine\n  Fluvioldeltaic:\n    text: Fluvioldeltaic\n  Fluviomarine:\n    text: Fluviomarine\n  Marine:\n    text: Marine\n  other:\n    text: other\n\n
"},{"location":"SrGeolAgeEnum/","title":"Enum: SrGeolAgeEnum","text":"

URI: SrGeolAgeEnum

"},{"location":"SrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"SrGeolAgeEnum/#slots","title":"Slots","text":"Name Description sr_geol_age Geological age of source rock (Additional info: https://en"},{"location":"SrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrGeolAgeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SrGeolAgeEnum/#linkml-source","title":"LinkML Source","text":"
name: sr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Archean:\n    text: Archean\n  Cambrian:\n    text: Cambrian\n  Carboniferous:\n    text: Carboniferous\n  Cenozoic:\n    text: Cenozoic\n  Cretaceous:\n    text: Cretaceous\n  Devonian:\n    text: Devonian\n  Jurassic:\n    text: Jurassic\n  Mesozoic:\n    text: Mesozoic\n  Neogene:\n    text: Neogene\n  Ordovician:\n    text: Ordovician\n  Paleogene:\n    text: Paleogene\n  Paleozoic:\n    text: Paleozoic\n  Permian:\n    text: Permian\n  Precambrian:\n    text: Precambrian\n  Proterozoic:\n    text: Proterozoic\n  Silurian:\n    text: Silurian\n  Triassic:\n    text: Triassic\n  other:\n    text: other\n\n
"},{"location":"SrKerogTypeEnum/","title":"Enum: SrKerogTypeEnum","text":"

URI: SrKerogTypeEnum

"},{"location":"SrKerogTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Type I None Type II None Type III None Type IV None other None"},{"location":"SrKerogTypeEnum/#slots","title":"Slots","text":"Name Description sr_kerog_type Origin of kerogen"},{"location":"SrKerogTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrKerogTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SrKerogTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: sr_kerog_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Type I:\n    text: Type I\n  Type II:\n    text: Type II\n  Type III:\n    text: Type III\n  Type IV:\n    text: Type IV\n  other:\n    text: other\n\n
"},{"location":"SrLithologyEnum/","title":"Enum: SrLithologyEnum","text":"

URI: SrLithologyEnum

"},{"location":"SrLithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Clastic None Carbonate None Coal None Biosilicieous None other None"},{"location":"SrLithologyEnum/#slots","title":"Slots","text":"Name Description sr_lithology Lithology of source rock (https://en"},{"location":"SrLithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrLithologyEnum/#schema-source","title":"Schema Source","text":""},{"location":"SrLithologyEnum/#linkml-source","title":"LinkML Source","text":"
name: sr_lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Clastic:\n    text: Clastic\n  Carbonate:\n    text: Carbonate\n  Coal:\n    text: Coal\n  Biosilicieous:\n    text: Biosilicieous\n  other:\n    text: other\n\n
"},{"location":"StationaryPhaseEnum/","title":"Enum: StationaryPhaseEnum","text":"

The type of stationary phase used in a chromatography process.

URI: StationaryPhaseEnum

"},{"location":"StationaryPhaseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description BEH-HILIC None C18 None C8 None C4 None C2 None C1 None C30 None C60 None CNT None CN None Diol None HILIC None NH2 None Phenyl None Polysiloxane None PS-DVB None SAX None SCX None Silica None WCX None WAX None ZIC-HILIC None ZIC-pHILIC None ZIC-cHILIC None"},{"location":"StationaryPhaseEnum/#slots","title":"Slots","text":"Name Description stationary_phase The material the stationary phase is comprised of used in chromatography"},{"location":"StationaryPhaseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StationaryPhaseEnum/#schema-source","title":"Schema Source","text":""},{"location":"StationaryPhaseEnum/#linkml-source","title":"LinkML Source","text":"
name: StationaryPhaseEnum\ndescription: The type of stationary phase used in a chromatography process.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-4504-1039\nrank: 1000\npermissible_values:\n  BEH-HILIC:\n    text: BEH-HILIC\n  C18:\n    text: C18\n  C8:\n    text: C8\n  C4:\n    text: C4\n  C2:\n    text: C2\n  C1:\n    text: C1\n  C30:\n    text: C30\n  C60:\n    text: C60\n  CNT:\n    text: CNT\n  CN:\n    text: CN\n  Diol:\n    text: Diol\n  HILIC:\n    text: HILIC\n  NH2:\n    text: NH2\n  Phenyl:\n    text: Phenyl\n  Polysiloxane:\n    text: Polysiloxane\n  PS-DVB:\n    text: PS-DVB\n  SAX:\n    text: SAX\n  SCX:\n    text: SCX\n  Silica:\n    text: Silica\n  WCX:\n    text: WCX\n  WAX:\n    text: WAX\n  ZIC-HILIC:\n    text: ZIC-HILIC\n  ZIC-pHILIC:\n    text: ZIC-pHILIC\n  ZIC-cHILIC:\n    text: ZIC-cHILIC\n\n
"},{"location":"StatusEnum/","title":"Enum: StatusEnum","text":"

URI: StatusEnum

"},{"location":"StatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description pass None fail None"},{"location":"StatusEnum/#slots","title":"Slots","text":"Name Description qc_status Stores information about the result of a process (ie the process of sequencin..."},{"location":"StatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StatusEnum/#schema-source","title":"Schema Source","text":""},{"location":"StatusEnum/#linkml-source","title":"LinkML Source","text":"
name: StatusEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  pass:\n    text: pass\n  fail:\n    text: fail\n\n
"},{"location":"StorageProcess/","title":"Class: StorageProcess","text":"

A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment.

URI: nmdc:StorageProcess

classDiagram\n  class StorageProcess\n  click StorageProcess href \"../StorageProcess\"\n    PlannedProcess <|-- StorageProcess\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n\n  StorageProcess : alternative_identifiers\n\n  StorageProcess : contained_in\n\n      StorageProcess --> \"0..1\" ContainerCategoryEnum : contained_in\n    click ContainerCategoryEnum href \"../ContainerCategoryEnum\"\n\n  StorageProcess : description\n\n  StorageProcess : end_date\n\n  StorageProcess : has_failure_categorization\n\n      StorageProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  StorageProcess : has_input\n\n      StorageProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  StorageProcess : has_output\n\n      StorageProcess --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  StorageProcess : id\n\n  StorageProcess : name\n\n  StorageProcess : processing_institution\n\n      StorageProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  StorageProcess : protocol_link\n\n      StorageProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  StorageProcess : qc_comment\n\n  StorageProcess : qc_status\n\n      StorageProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  StorageProcess : start_date\n\n  StorageProcess : substances_used\n\n      StorageProcess --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  StorageProcess : temperature\n\n      StorageProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  StorageProcess : type\n\n\n\n
"},{"location":"StorageProcess/#inheritance","title":"Inheritance","text":""},{"location":"StorageProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance substances_used * PortionOfSubstance The substance(s) that a processed sample is stored in direct contained_in 0..1 ContainerCategoryEnum A type of container direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct has_input * NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"StorageProcess/#usages","title":"Usages","text":"used by used in type used Database storage_process_set range StorageProcess"},{"location":"StorageProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StorageProcess/#schema-source","title":"Schema Source","text":""},{"location":"StorageProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:StorageProcess native nmdc:StorageProcess related OBI:0302893"},{"location":"StorageProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"StorageProcess/#direct","title":"Direct","text":"
name: StorageProcess\ndescription: A planned process with the objective to preserve and protect material\n  entities by placing them in an identified  location which may have a controlled\n  environment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0302893\nis_a: PlannedProcess\nslots:\n- substances_used\n- contained_in\n- temperature\nslot_usage:\n  substances_used:\n    name: substances_used\n    description: The substance(s) that a processed sample is stored in.\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:StorageProcess\n\n
"},{"location":"StorageProcess/#induced","title":"Induced","text":"
name: StorageProcess\ndescription: A planned process with the objective to preserve and protect material\n  entities by placing them in an identified  location which may have a controlled\n  environment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0302893\nis_a: PlannedProcess\nslot_usage:\n  substances_used:\n    name: substances_used\n    description: The substance(s) that a processed sample is stored in.\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  substances_used:\n    name: substances_used\n    description: The substance(s) that a processed sample is stored in.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: StorageProcess\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  contained_in:\n    name: contained_in\n    description: A type of container.\n    examples:\n    - value: test tube\n    - value: falcon tube\n    - value: whirlpak\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: contained_in\n    owner: StorageProcess\n    domain_of:\n    - SubSamplingProcess\n    - StorageProcess\n    range: ContainerCategoryEnum\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: StorageProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: StorageProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: StorageProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: StorageProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: StorageProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: StorageProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:StorageProcess\n\n
"},{"location":"StrandedOrientationEnum/","title":"Enum: StrandedOrientationEnum","text":"

This enumeration specifies information about stranded RNA library preparations.

URI: StrandedOrientationEnum

"},{"location":"StrandedOrientationEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description antisense orientation None Orientation that is complementary (non-coding) to a sequence of messenger RNA sense orientation None Orientation that corresponds to the coding sequence of messenger RNA"},{"location":"StrandedOrientationEnum/#slots","title":"Slots","text":"Name Description stranded_orientation Lists the strand orientiation for a stranded RNA library preparation"},{"location":"StrandedOrientationEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StrandedOrientationEnum/#schema-source","title":"Schema Source","text":""},{"location":"StrandedOrientationEnum/#linkml-source","title":"LinkML Source","text":"
name: StrandedOrientationEnum\ndescription: This enumeration specifies information about stranded RNA library preparations.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  antisense orientation:\n    text: antisense orientation\n    description: Orientation that is complementary (non-coding) to a sequence of messenger\n      RNA.\n    comments:\n    - See https://www.genome.gov/genetics-glossary/antisense\n    exact_mappings:\n    - SO:0000077\n  sense orientation:\n    text: sense orientation\n    description: Orientation that corresponds to the coding sequence of messenger\n      RNA.\n\n
"},{"location":"String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"String/#schema-source","title":"Schema Source","text":""},{"location":"String/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:string exact schema:Text"},{"location":"Study/","title":"Class: Study","text":"

A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.

URI: nmdc:Study

classDiagram\n  class Study\n  click Study href \"../Study\"\n    NamedThing <|-- Study\n      click NamedThing href \"../NamedThing\"\n\n\n\n  Study : alternative_descriptions\n\n  Study : alternative_identifiers\n\n  Study : alternative_names\n\n  Study : alternative_titles\n\n  Study : associated_dois\n\n      Study --> \"*\" Doi : associated_dois\n    click Doi href \"../Doi\"\n\n  Study : description\n\n  Study : ecosystem\n\n  Study : ecosystem_category\n\n  Study : ecosystem_subtype\n\n  Study : ecosystem_type\n\n  Study : emsl_project_identifiers\n\n  Study : funding_sources\n\n  Study : gnps_task_identifiers\n\n  Study : gold_study_identifiers\n\n  Study : has_credit_associations\n\n      Study --> \"*\" CreditAssociation : has_credit_associations\n    click CreditAssociation href \"../CreditAssociation\"\n\n  Study : homepage_website\n\n  Study : id\n\n  Study : insdc_bioproject_identifiers\n\n  Study : jgi_portal_study_identifiers\n\n  Study : mgnify_project_identifiers\n\n  Study : name\n\n  Study : neon_study_identifiers\n\n  Study : notes\n\n  Study : objective\n\n  Study : part_of\n\n      Study --> \"*\" Study : part_of\n    click Study href \"../Study\"\n\n  Study : principal_investigator\n\n      Study --> \"0..1\" PersonValue : principal_investigator\n    click PersonValue href \"../PersonValue\"\n\n  Study : protocol_link\n\n      Study --> \"*\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  Study : related_identifiers\n\n  Study : specific_ecosystem\n\n  Study : study_category\n\n      Study --> \"1\" StudyCategoryEnum : study_category\n    click StudyCategoryEnum href \"../StudyCategoryEnum\"\n\n  Study : study_image\n\n      Study --> \"*\" ImageValue : study_image\n    click ImageValue href \"../ImageValue\"\n\n  Study : title\n\n  Study : type\n\n  Study : websites\n\n\n\n
"},{"location":"Study/#inheritance","title":"Inheritance","text":""},{"location":"Study/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance emsl_project_identifiers * ExternalIdentifier Identifiers that link a NMDC study to the EMSL user facility website hosting ... direct gnps_task_identifiers * ExternalIdentifier identifiers that link a NMDC study to a web-based report about metabolomics a... direct gold_study_identifiers * ExternalIdentifier identifiers for corresponding project(s) in GOLD direct insdc_bioproject_identifiers * ExternalIdentifier Unique identifier for a bioproject submitted to INSDC that relates to the NMD... direct jgi_portal_study_identifiers * ExternalIdentifier Identifiers that link a NMDC study to a website hosting raw and analyzed data... direct mgnify_project_identifiers * ExternalIdentifier identifiers for corresponding project in MGnify direct neon_study_identifiers * ExternalIdentifier direct related_identifiers 0..1 String Unique identifier for a study submitted to additional resources direct alternative_descriptions * String A list of alternative descriptions for the entity direct alternative_names * String A list of alternative names used to refer to the entity direct alternative_titles * String A list of alternative titles for the entity direct ecosystem 0..1 String An ecosystem is a combination of a physical environment (abiotic factors) and... direct ecosystem_category 0..1 String Ecosystem categories represent divisions within the ecosystem based on specif... direct ecosystem_subtype 0..1 String Ecosystem subtypes represent further subdivision of Ecosystem types into more... direct ecosystem_type 0..1 String Ecosystem types represent things having common characteristics within the Eco... direct specific_ecosystem 0..1 String Specific ecosystems represent specific features of the environment like aphot... direct associated_dois * Doi A list of DOIs associated with a resource, such as a list of DOIS associated ... direct funding_sources * String A list of organizations, along with the award numbers, that underwrite financ... direct has_credit_associations * CreditAssociation This slot links a study to a credit association direct homepage_website * String The website address (URL) of an entity's homepage direct notes 0..1 String direct objective 0..1 String The scientific objectives associated with the entity direct part_of * Study Links a study or consortium to a parent (or umbrella) study or consortium direct principal_investigator 0..1 PersonValue Principal Investigator who led the study and/or generated the dataset direct protocol_link * Protocol direct study_category 1 StudyCategoryEnum The type of research initiative direct study_image * ImageValue Links a study to one or more images direct title 0..1 String A name given to the entity that differs from the name/label programmatically ... direct websites * String A list of websites that are associated with the entity direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String A brief, link-free summary of a Study NamedThing alternative_identifiers * Uriorcurie Unique identifier for a study submitted to additional resources NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Study/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing associated_studies range Study MassSpectrometry associated_studies range Study Database study_set range Study Biosample associated_studies range Study Study part_of range Study DataGeneration associated_studies range Study"},{"location":"Study/#aliases","title":"Aliases","text":""},{"location":"Study/#comments","title":"Comments","text":""},{"location":"Study/#todos","title":"TODOs","text":""},{"location":"Study/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Study/#schema-source","title":"Schema Source","text":""},{"location":"Study/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Study native nmdc:Study exact OBI:0000066, SIO:000747, NCIT:C41198, ISA:Investigation broad prov:Activity"},{"location":"Study/#linkml-source","title":"LinkML Source","text":""},{"location":"Study/#direct","title":"Direct","text":"
name: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n  the key objective of its underlying projects.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: A study (project) groups together data submitted to the archive and\n      controls its release date. A study accession is typically used when citing data\n      submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n  but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research initiative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslots:\n- emsl_project_identifiers\n- gnps_task_identifiers\n- gold_study_identifiers\n- insdc_bioproject_identifiers\n- jgi_portal_study_identifiers\n- mgnify_project_identifiers\n- neon_study_identifiers\n- related_identifiers\n- alternative_descriptions\n- alternative_names\n- alternative_titles\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- specific_ecosystem\n- associated_dois\n- funding_sources\n- has_credit_associations\n- homepage_website\n- notes\n- objective\n- part_of\n- principal_investigator\n- protocol_link\n- study_category\n- study_image\n- title\n- websites\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a name for the study your samples will belong with.\n  websites:\n    name: websites\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the Principal Investigator's research lab webpage or the study\n          webpage associated with this collection of samples. Multiple links can be\n          provided.\n  homepage_website:\n    name: homepage_website\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the consortium's homepage if the study_category is a consortium.\n  description:\n    name: description\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a brief description of your study.\n    description: A brief, link-free summary of a Study\n    comments:\n    - Include links in other Study slots, such as websites or dois.\n  notes:\n    name: notes\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Add any additional notes or comments about this study.\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Matches that which has been submitted to NMDC\n  alternative_names:\n    name: alternative_names\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Project, study, or sample set names the are also associated with this\n          submission or other names / identifiers for this study.\n  related_identifiers:\n    name: related_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Similar, but not necessarily identical to that which has been submitted to NMDC\n  insdc_bioproject_identifiers:\n    name: insdc_bioproject_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the NCBI BioProject Accession Number associated with the listed\n          NCBI BioProject Title.\n    description: Unique identifier for a bioproject submitted to INSDC that relates\n      to the NMDC submitted study.\n  part_of:\n    name: part_of\n    description: Links a study or consortium to a parent (or umbrella) study or consortium.\n    comments:\n    - Value is the id of the umbrella study or consortium.\n    range: Study\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  protocol_link:\n    name: protocol_link\n    multivalued: true\n    inlined_as_list: true\nclass_uri: nmdc:Study\n\n
"},{"location":"Study/#induced","title":"Induced","text":"
name: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n  the key objective of its underlying projects.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: A study (project) groups together data submitted to the archive and\n      controls its release date. A study accession is typically used when citing data\n      submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n  but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research initiative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a name for the study your samples will belong with.\n  websites:\n    name: websites\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the Principal Investigator's research lab webpage or the study\n          webpage associated with this collection of samples. Multiple links can be\n          provided.\n  homepage_website:\n    name: homepage_website\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the consortium's homepage if the study_category is a consortium.\n  description:\n    name: description\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a brief description of your study.\n    description: A brief, link-free summary of a Study\n    comments:\n    - Include links in other Study slots, such as websites or dois.\n  notes:\n    name: notes\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Add any additional notes or comments about this study.\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Matches that which has been submitted to NMDC\n  alternative_names:\n    name: alternative_names\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Project, study, or sample set names the are also associated with this\n          submission or other names / identifiers for this study.\n  related_identifiers:\n    name: related_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Similar, but not necessarily identical to that which has been submitted to NMDC\n  insdc_bioproject_identifiers:\n    name: insdc_bioproject_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the NCBI BioProject Accession Number associated with the listed\n          NCBI BioProject Title.\n    description: Unique identifier for a bioproject submitted to INSDC that relates\n      to the NMDC submitted study.\n  part_of:\n    name: part_of\n    description: Links a study or consortium to a parent (or umbrella) study or consortium.\n    comments:\n    - Value is the id of the umbrella study or consortium.\n    range: Study\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  protocol_link:\n    name: protocol_link\n    multivalued: true\n    inlined_as_list: true\nattributes:\n  emsl_project_identifiers:\n    name: emsl_project_identifiers\n    description: Identifiers that link a NMDC study to the EMSL user facility website\n      hosting the project description of an EMSL user project\n    title: EMSL Project Identifiers\n    todos:\n    - elaborate on description\n    notes:\n    - these identifiers are all currently 5 digits long but that could change in the\n      future\n    examples:\n    - value: emsl.project:60141\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/927#issuecomment-1802136437\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - emsl_identifiers\n    alias: emsl_project_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^emsl\\.project:[0-9]{5}$\n  gnps_task_identifiers:\n    name: gnps_task_identifiers\n    description: identifiers that link a NMDC study to a web-based report about metabolomics\n      analysis progress and results\n    title: GNPS task identifiers\n    comments:\n    - this could be considered a related identifier, as the metabolomics progress\n      and results aren't a study per se\n    - this identifier was registered with bioregistry but not identifiers.org\n    examples:\n    - value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysis/\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - gnps_identifiers\n    alias: gnps_task_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^gnps\\.task:[a-f0-9]+$\n  gold_study_identifiers:\n    name: gold_study_identifiers\n    description: identifiers for corresponding project(s) in GOLD\n    title: GOLD Study Identifiers\n    comments:\n    - uses the prefix GS (but possibly in a different case)\n    examples:\n    - value: https://bioregistry.io/gold:Gs0110115\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/studies\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_study_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^gold:Gs[0-9]+$\n  insdc_bioproject_identifiers:\n    name: insdc_bioproject_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the NCBI BioProject Accession Number associated with the listed\n          NCBI BioProject Title.\n    description: Unique identifier for a bioproject submitted to INSDC that relates\n      to the NMDC submitted study.\n    comments:\n    - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n      one to one\n    examples:\n    - value: https://bioregistry.io/bioproject:PRJNA366857\n      description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2\n        metatranscriptome\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ncbi.nlm.nih.gov/bioproject/\n    - https://www.ddbj.nig.ac.jp/bioproject/index-e.html\n    aliases:\n    - NCBI bioproject identifiers\n    - DDBJ bioproject identifiers\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_bioproject_identifiers\n    owner: Study\n    domain_of:\n    - NucleotideSequencing\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n  jgi_portal_study_identifiers:\n    name: jgi_portal_study_identifiers\n    id_prefixes:\n    - jgi.proposal\n    description: Identifiers that link a NMDC study to a website hosting raw and analyzed\n      data for a JGI proposal.  The suffix of the curie can used to query the GOLD\n      API and is interoperable with an award DOI from OSTI and a GOLD study identifier.\n    title: JGI Portal Study identifiers\n    comments:\n    - Could this could be considered a related identifier?\n    - Curie suffix is the Site Award Number from an OSTI award page\n    - Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD\n      study identifier gold:Gs0154044\n    - bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\n    examples:\n    - value: jgi.proposal:507130\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - jgi_portal_identifiers\n    alias: jgi_portal_study_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^jgi.proposal:\\d+$\n  mgnify_project_identifiers:\n    name: mgnify_project_identifiers\n    description: identifiers for corresponding project in MGnify\n    examples:\n    - value: https://bioregistry.io/mgnify.proj:MGYS00005757\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - mgnify_identifiers\n    alias: mgnify_project_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^mgnify.proj:[A-Z]+[0-9]+$\n  neon_study_identifiers:\n    name: neon_study_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - neon_identifiers\n    alias: neon_study_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  related_identifiers:\n    name: related_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Similar, but not necessarily identical to that which has been submitted to NMDC\n    title: Related Identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: related_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n  alternative_descriptions:\n    name: alternative_descriptions\n    description: A list of alternative descriptions for the entity. The distinction\n      between description and alternative descriptions is application-specific.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_descriptions\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n    multivalued: true\n  alternative_names:\n    name: alternative_names\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Project, study, or sample set names the are also associated with this\n          submission or other names / identifiers for this study.\n    description: A list of alternative names used to refer to the entity. The distinction\n      between name and alternative names is application-specific.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - dcterms:alternative\n    - skos:altLabel\n    rank: 1000\n    alias: alternative_names\n    owner: Study\n    domain_of:\n    - ChemicalEntity\n    - Study\n    range: string\n    multivalued: true\n  alternative_titles:\n    name: alternative_titles\n    description: A list of alternative titles for the entity. The distinction between\n      title and alternative titles is application-specific.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - dcterms:alternative\n    rank: 1000\n    alias: alternative_titles\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n    multivalued: true\n  ecosystem:\n    name: ecosystem\n    description: An ecosystem is a combination of a physical environment (abiotic\n      factors) and all the organisms (biotic factors) that interact with this environment.\n      Ecosystem is in position 1/5 in a GOLD path.\n    comments:\n    - The abiotic factors play a profound role on the type and composition of organisms\n      in a given environment. The GOLD Ecosystem at the top of the five-level classification\n      system is aimed at capturing the broader environment from which an organism\n      or environmental sample is collected. The three broad groups under Ecosystem\n      are Environmental, Host-associated, and Engineered. They represent samples collected\n      from a natural environment or from another organism or from engineered environments\n      like bioreactors respectively.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_category:\n    name: ecosystem_category\n    description: Ecosystem categories represent divisions within the ecosystem based\n      on specific characteristics of the environment from where an organism or sample\n      is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n    comments:\n    - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n      Ecosystem categories for Host-associated samples can be individual hosts or\n      phyla and for engineered samples it may be manipulated environments like bioreactors,\n      solid waste etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_category\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_subtype:\n    name: ecosystem_subtype\n    description: Ecosystem subtypes represent further subdivision of Ecosystem types\n      into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n      path.\n    comments:\n    - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n      (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n      the Ecosystem subtype category.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_subtype\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_type:\n    name: ecosystem_type\n    description: Ecosystem types represent things having common characteristics within\n      the Ecosystem Category. These common characteristics based grouping is still\n      broad but specific to the characteristics of a given environment. Ecosystem\n      type is in position 3/5 in a GOLD path.\n    comments:\n    - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n      or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n      air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n      type can represent Respiratory system, Digestive system, Roots etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_type\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  specific_ecosystem:\n    name: specific_ecosystem\n    description: Specific ecosystems represent specific features of the environment\n      like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n      Specific ecosystem is in position 5/5 in a GOLD path.\n    comments:\n    - Specific ecosystems help to define samples based on very specific characteristics\n      of an environment under the five-level classification system.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: specific_ecosystem\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  associated_dois:\n    name: associated_dois\n    description: A list of DOIs associated with a resource, such as a list of DOIS\n      associated with a Study.\n    examples:\n    - value: '[{''doi'': ''doi:10.46936/intm.proj.2021.60141/60000423'', ''doi_provider'':\n        ''emsl'', ''doi_category'': ''award_doi''}, {''doi'': ''doi:10.1101/2022.12.12.520098'',\n        ''doi_category'': ''publication_doi''}, {''doi'': ''doi:10.48321/D1Z60Q'',\n        ''doi_category'': ''data_management_plan_doi'', ''doi_provider'': ''gsc''}]'\n      description: Provides a list of two DOIs; specifically, an EMSL award DOI and\n        a publication DOI.\n    in_subset:\n    - data_portal_subset\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Associated DOIs\n    - Associated digital object identifiers\n    rank: 1000\n    alias: associated_dois\n    owner: Study\n    domain_of:\n    - Study\n    range: Doi\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  funding_sources:\n    name: funding_sources\n    description: A list of organizations, along with the award numbers, that underwrite\n      financial support for projects of a particular type. Typically, they process\n      applications and award funds to the chosen qualified applicants.\n    comments:\n    - Include only the name of the funding organization and the award or contract\n      number.\n    examples:\n    - value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n    - value: U.S. Department of Energy, Office of Science, Office of Biological and\n        Environmental Research (BER) under contract DE-AC05-00OR2275\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - NCIT:C39409\n    rank: 1000\n    alias: funding_sources\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n    multivalued: true\n  has_credit_associations:\n    name: has_credit_associations\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Other researchers associated with this study.\n    description: 'This slot links a study to a credit association.  The credit association\n      will be linked to a person value and to a CRediT Contributor Roles term. Overall\n      semantics: person should get credit X for their participation in the study'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: prov:qualifiedAssociation\n    alias: has_credit_associations\n    owner: Study\n    domain_of:\n    - Study\n    range: CreditAssociation\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  homepage_website:\n    name: homepage_website\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the consortium's homepage if the study_category is a consortium.\n    description: The website address (URL) of an entity's homepage.\n    examples:\n    - value: https://www.neonscience.org/\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: websites\n    alias: homepage_website\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n    multivalued: true\n    pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n    maximum_cardinality: 1\n  notes:\n    name: notes\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Add any additional notes or comments about this study.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: notes\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n  objective:\n    name: objective\n    description: The scientific objectives associated with the entity. It SHOULD correspond\n      to scientific norms for objectives field in a structured abstract.\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - SIO:000337\n    rank: 1000\n    alias: objective\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n  part_of:\n    name: part_of\n    description: Links a study or consortium to a parent (or umbrella) study or consortium.\n    comments:\n    - Value is the id of the umbrella study or consortium.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - is part of\n    rank: 1000\n    slot_uri: dcterms:isPartOf\n    alias: part_of\n    owner: Study\n    domain_of:\n    - FieldResearchSite\n    - Study\n    range: Study\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  principal_investigator:\n    name: principal_investigator\n    description: Principal Investigator who led the study and/or generated the dataset.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - PI\n    rank: 1000\n    alias: principal_investigator\n    owner: Study\n    domain_of:\n    - Study\n    - DataGeneration\n    range: PersonValue\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: Study\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n    multivalued: true\n    inlined_as_list: true\n  study_category:\n    name: study_category\n    description: The type of research initiative\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: study_category\n    owner: Study\n    domain_of:\n    - Study\n    range: StudyCategoryEnum\n    required: true\n  study_image:\n    name: study_image\n    description: Links a study to one or more images.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: study_image\n    owner: Study\n    domain_of:\n    - Study\n    range: ImageValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  title:\n    name: title\n    description: A name given to the entity that differs from the name/label programmatically\n      assigned to it. For example, when extracting study information for GOLD, the\n      GOLD system has assigned a name/label. However, for display purposes, we may\n      also wish the capture the title of the proposal that was used to fund the study.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - dcterms:title\n    rank: 1000\n    alias: title\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n  websites:\n    name: websites\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the Principal Investigator's research lab webpage or the study\n          webpage associated with this collection of samples. Multiple links can be\n          provided.\n    description: A list of websites that are associated with the entity.\n    comments:\n    - DOIs should not be included as websites. Instead, use the associated_dois slot.\n    - A consortium's homepage website should be included in the homepage_website slot,\n      not in websites.\n    - consortium is a convenience term for a Study whose study_category value is consortium\n    - the website slot and its subproperties are virtually identical to the url slot,\n      except that they are multivalued and url is single-valued.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:url\n    rank: 1000\n    alias: websites\n    owner: Study\n    domain_of:\n    - PersonValue\n    - Study\n    range: string\n    multivalued: true\n    pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Study\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a name for the study your samples will belong with.\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Study\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a brief description of your study.\n    description: A brief, link-free summary of a Study\n    comments:\n    - Include links in other Study slots, such as websites or dois.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Study\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Matches that which has been submitted to NMDC\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Study\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Study\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Study\n\n
"},{"location":"StudyCategoryEnum/","title":"Enum: StudyCategoryEnum","text":"

URI: StudyCategoryEnum

"},{"location":"StudyCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description research_study None A detailed examination, analysis, or critical inspection of a hypothesis-driv... consortium None A group formed to undertake a venture that is beyond the capabilities of the ..."},{"location":"StudyCategoryEnum/#slots","title":"Slots","text":"Name Description study_category The type of research initiative"},{"location":"StudyCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StudyCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"StudyCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: StudyCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  research_study:\n    text: research_study\n    description: A detailed examination, analysis, or critical inspection of a hypothesis-driven\n      experiment.\n    exact_mappings:\n    - SIO:001066\n    - NCIT:C63536\n    - ISA:Study\n    close_mappings:\n    - OBI:0000355\n  consortium:\n    text: consortium\n    description: A group formed to undertake a venture that is beyond the capabilities\n      of the individual members. Each member of the consortium brings a high level\n      of expertise in a specific area to ensure the successful completion of the project.\n    comments:\n    - A consortium has collections of data, those data do not come from a hypothesis-driven\n      experiment.\n    exact_mappings:\n    - NCIT:C61538\n\n
"},{"location":"SubSamplingProcess/","title":"Class: SubSamplingProcess","text":"

Separating a sample aliquot from the starting material for downstream activity.

__

URI: nmdc:SubSamplingProcess

classDiagram\n  class SubSamplingProcess\n  click SubSamplingProcess href \"../SubSamplingProcess\"\n    MaterialProcessing <|-- SubSamplingProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  SubSamplingProcess : alternative_identifiers\n\n  SubSamplingProcess : contained_in\n\n      SubSamplingProcess --> \"0..1\" ContainerCategoryEnum : contained_in\n    click ContainerCategoryEnum href \"../ContainerCategoryEnum\"\n\n  SubSamplingProcess : container_size\n\n      SubSamplingProcess --> \"0..1\" QuantityValue : container_size\n    click QuantityValue href \"../QuantityValue\"\n\n  SubSamplingProcess : description\n\n  SubSamplingProcess : end_date\n\n  SubSamplingProcess : has_failure_categorization\n\n      SubSamplingProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  SubSamplingProcess : has_input\n\n      SubSamplingProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  SubSamplingProcess : has_output\n\n      SubSamplingProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  SubSamplingProcess : id\n\n  SubSamplingProcess : instrument_used\n\n      SubSamplingProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  SubSamplingProcess : mass\n\n      SubSamplingProcess --> \"0..1\" QuantityValue : mass\n    click QuantityValue href \"../QuantityValue\"\n\n  SubSamplingProcess : name\n\n  SubSamplingProcess : processing_institution\n\n      SubSamplingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  SubSamplingProcess : protocol_link\n\n      SubSamplingProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  SubSamplingProcess : qc_comment\n\n  SubSamplingProcess : qc_status\n\n      SubSamplingProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  SubSamplingProcess : sampled_portion\n\n      SubSamplingProcess --> \"*\" SamplePortionEnum : sampled_portion\n    click SamplePortionEnum href \"../SamplePortionEnum\"\n\n  SubSamplingProcess : start_date\n\n  SubSamplingProcess : temperature\n\n      SubSamplingProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  SubSamplingProcess : type\n\n  SubSamplingProcess : volume\n\n      SubSamplingProcess --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"SubSamplingProcess/#inheritance","title":"Inheritance","text":""},{"location":"SubSamplingProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance container_size 0..1 QuantityValue The volume of the container an analyte is stored in or an activity takes plac... direct contained_in 0..1 ContainerCategoryEnum A type of container direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct volume 0..1 QuantityValue The output volume of the SubSampling Process direct mass 0..1 QuantityValue The output mass of the SubSampling Process direct sampled_portion * SamplePortionEnum The portion of the sample that is taken for downstream activity direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample The subsample PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"SubSamplingProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubSamplingProcess/#schema-source","title":"Schema Source","text":""},{"location":"SubSamplingProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:SubSamplingProcess native nmdc:SubSamplingProcess related OBI:0000744"},{"location":"SubSamplingProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"SubSamplingProcess/#direct","title":"Direct","text":"
name: SubSamplingProcess\ndescription: 'Separating a sample aliquot from the starting material for downstream\n  activity.\n\n  '\nnotes:\n- A subsample may be (a) a portion of the sample obtained by selection or division;\n  (b) an individual unit of the lot taken as part of the sample; (c) the final unit\n  of multistage sampling. The term 'subsample' is used either in the sense of a 'sample\n  of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent\n  from the context or is defined.\n- TODO - Montana to visit slot descriptions\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0000744\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslots:\n- container_size\n- contained_in\n- temperature\n- volume\n- mass\n- sampled_portion\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The output volume of the SubSampling Process.\n  mass:\n    name: mass\n    description: The output mass of the SubSampling Process.\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The subsample.\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:SubSamplingProcess\n\n
"},{"location":"SubSamplingProcess/#induced","title":"Induced","text":"
name: SubSamplingProcess\ndescription: 'Separating a sample aliquot from the starting material for downstream\n  activity.\n\n  '\nnotes:\n- A subsample may be (a) a portion of the sample obtained by selection or division;\n  (b) an individual unit of the lot taken as part of the sample; (c) the final unit\n  of multistage sampling. The term 'subsample' is used either in the sense of a 'sample\n  of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent\n  from the context or is defined.\n- TODO - Montana to visit slot descriptions\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0000744\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The output volume of the SubSampling Process.\n  mass:\n    name: mass\n    description: The output mass of the SubSampling Process.\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The subsample.\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  container_size:\n    name: container_size\n    description: The volume of the container an analyte is stored in or an activity\n      takes place in\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: container_size\n    owner: SubSamplingProcess\n    domain_of:\n    - SubSamplingProcess\n    - FiltrationProcess\n    range: QuantityValue\n  contained_in:\n    name: contained_in\n    description: A type of container.\n    examples:\n    - value: test tube\n    - value: falcon tube\n    - value: whirlpak\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: contained_in\n    owner: SubSamplingProcess\n    domain_of:\n    - SubSamplingProcess\n    - StorageProcess\n    range: ContainerCategoryEnum\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: SubSamplingProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  volume:\n    name: volume\n    description: The output volume of the SubSampling Process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: SubSamplingProcess\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\n  mass:\n    name: mass\n    description: The output mass of the SubSampling Process.\n    title: mass\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - PATO:0000125\n    rank: 1000\n    alias: mass\n    owner: SubSamplingProcess\n    domain_of:\n    - SubSamplingProcess\n    - PortionOfSubstance\n    range: QuantityValue\n  sampled_portion:\n    name: sampled_portion\n    description: The portion of the sample that is taken for downstream activity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: sampled_portion\n    owner: SubSamplingProcess\n    domain_of:\n    - SubSamplingProcess\n    range: SamplePortionEnum\n    multivalued: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: SubSamplingProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The subsample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: SubSamplingProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: SubSamplingProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: SubSamplingProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: SubSamplingProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: SubSamplingProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:SubSamplingProcess\n\n
"},{"location":"SubstanceRoleEnum/","title":"Enum: SubstanceRoleEnum","text":"

URI: SubstanceRoleEnum

"},{"location":"SubstanceRoleEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description buffer CHEBI:35225 Maintains the pH of the solution within a specific range to stabilize analyte... acid CHEBI:37527 Donates a proton or accepts an electron pair in a chemical reaction base CHEBI:22695 Accepts a proton or donates an electron pair in a chemical reaction ms_proteolytic_enzyme MS:1002986 Enzyme that catalyzes the hydrolysis of proteins and is used in mass spectrom... solvent CHEBI:46787 Dissolves the sample or reagents to facilitate reactions or extraction surfactant CHEBI:35195 Reduces surface tension and aids in the solubilization of substances derivatizing_agent None Chemically modifies analytes to improve detection or separation solubilizing_agent None"},{"location":"SubstanceRoleEnum/#slots","title":"Slots","text":"Name Description substance_role The role of a substance in a process"},{"location":"SubstanceRoleEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstanceRoleEnum/#schema-source","title":"Schema Source","text":""},{"location":"SubstanceRoleEnum/#linkml-source","title":"LinkML Source","text":"
name: SubstanceRoleEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  buffer:\n    text: buffer\n    description: Maintains the pH of the solution within a specific range to stabilize\n      analytes or reactions.\n    meaning: CHEBI:35225\n  acid:\n    text: acid\n    description: Donates a proton or accepts an electron pair in a chemical reaction.\n    meaning: CHEBI:37527\n  base:\n    text: base\n    description: Accepts a proton or donates an electron pair in a chemical reaction.\n    meaning: CHEBI:22695\n  ms_proteolytic_enzyme:\n    text: ms_proteolytic_enzyme\n    description: Enzyme that catalyzes the hydrolysis of proteins and is used in mass\n      spectrometry based proteomics\n    meaning: MS:1002986\n  solvent:\n    text: solvent\n    description: Dissolves the sample or reagents to facilitate reactions or extraction.\n    meaning: CHEBI:46787\n  surfactant:\n    text: surfactant\n    description: Reduces surface tension and aids in the solubilization of substances.\n    meaning: CHEBI:35195\n  derivatizing_agent:\n    text: derivatizing_agent\n    description: Chemically modifies analytes to improve detection or separation.\n  solubilizing_agent:\n    text: solubilizing_agent\n\n
"},{"location":"SubstructureTypeEnum/","title":"Enum: SubstructureTypeEnum","text":"

URI: SubstructureTypeEnum

"},{"location":"SubstructureTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crawlspace None slab on grade None basement None"},{"location":"SubstructureTypeEnum/#slots","title":"Slots","text":"Name Description substructure_type The substructure or under building is that largely hidden section of the buil..."},{"location":"SubstructureTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstructureTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SubstructureTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: substructure_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  crawlspace:\n    text: crawlspace\n  slab on grade:\n    text: slab on grade\n  basement:\n    text: basement\n\n
"},{"location":"SurfAirContEnum/","title":"Enum: SurfAirContEnum","text":"

URI: SurfAirContEnum

"},{"location":"SurfAirContEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dust None organic matter None particulate matter None volatile organic compounds None biological contaminants None radon None nutrients None biocides None"},{"location":"SurfAirContEnum/#slots","title":"Slots","text":"Name Description surf_air_cont Contaminant identified on surface"},{"location":"SurfAirContEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfAirContEnum/#schema-source","title":"Schema Source","text":""},{"location":"SurfAirContEnum/#linkml-source","title":"LinkML Source","text":"
name: surf_air_cont_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  dust:\n    text: dust\n  organic matter:\n    text: organic matter\n  particulate matter:\n    text: particulate matter\n  volatile organic compounds:\n    text: volatile organic compounds\n  biological contaminants:\n    text: biological contaminants\n  radon:\n    text: radon\n  nutrients:\n    text: nutrients\n  biocides:\n    text: biocides\n\n
"},{"location":"SurfMaterialEnum/","title":"Enum: SurfMaterialEnum","text":"

URI: SurfMaterialEnum

"},{"location":"SurfMaterialEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description adobe None carpet None cinder blocks None concrete None hay bales None glass None metal None paint None plastic None stainless steel None stone None stucco None tile None vinyl None wood None"},{"location":"SurfMaterialEnum/#slots","title":"Slots","text":"Name Description surf_material Surface materials at the point of sampling"},{"location":"SurfMaterialEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfMaterialEnum/#schema-source","title":"Schema Source","text":""},{"location":"SurfMaterialEnum/#linkml-source","title":"LinkML Source","text":"
name: surf_material_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  adobe:\n    text: adobe\n  carpet:\n    text: carpet\n  cinder blocks:\n    text: cinder blocks\n  concrete:\n    text: concrete\n  hay bales:\n    text: hay bales\n  glass:\n    text: glass\n  metal:\n    text: metal\n  paint:\n    text: paint\n  plastic:\n    text: plastic\n  stainless steel:\n    text: stainless steel\n  stone:\n    text: stone\n  stucco:\n    text: stucco\n  tile:\n    text: tile\n  vinyl:\n    text: vinyl\n  wood:\n    text: wood\n\n
"},{"location":"TextValue/","title":"Class: TextValue","text":"

A basic string value

URI: nmdc:TextValue

classDiagram\n  class TextValue\n  click TextValue href \"../TextValue\"\n    AttributeValue <|-- TextValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  TextValue : has_raw_value\n\n  TextValue : language\n\n  TextValue : type\n\n\n\n
"},{"location":"TextValue/#inheritance","title":"Inheritance","text":""},{"location":"TextValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance language 0..1 LanguageCode Should use ISO 639-1 code e direct has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"TextValue/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing target_gene range TextValue NucleotideSequencing target_subfragment range TextValue LibraryPreparation nucl_acid_amp range TextValue LibraryPreparation pcr_cond range TextValue LibraryPreparation pcr_primers range TextValue FieldResearchSite cur_vegetation range TextValue FieldResearchSite geo_loc_name range TextValue FieldResearchSite local_class range TextValue FieldResearchSite soil_type range TextValue Biosample host_disease_stat range TextValue Biosample add_recov_method range TextValue Biosample additional_info range TextValue Biosample address range TextValue Biosample adj_room range TextValue Biosample aero_struc range TextValue Biosample agrochem_addition range TextValue Biosample air_PM_concen range TextValue Biosample air_temp_regm range TextValue Biosample al_sat_meth range TextValue Biosample alkalinity_method range TextValue Biosample ances_data range TextValue Biosample antibiotic_regm range TextValue Biosample aromatics_pc range TextValue Biosample asphaltenes_pc range TextValue Biosample atmospheric_data range TextValue Biosample avg_occup range TextValue Biosample basin range TextValue Biosample bathroom_count range TextValue Biosample bedroom_count range TextValue Biosample biocide range TextValue Biosample biocide_admin_method range TextValue Biosample biomass range TextValue Biosample biotic_regm range TextValue Biosample built_struc_set range TextValue Biosample built_struc_type range TextValue Biosample ceil_struc range TextValue Biosample ceil_water_mold range TextValue Biosample chem_mutagen range TextValue Biosample chem_treatment range TextValue Biosample climate_environment range TextValue Biosample cool_syst_id range TextValue Biosample crop_rotation range TextValue Biosample cult_root_med range TextValue Biosample cur_vegetation range TextValue Biosample cur_vegetation_meth range TextValue Biosample diether_lipids range TextValue Biosample door_water_mold range TextValue Biosample elevator range TextValue Biosample emulsions range TextValue Biosample env_package range TextValue Biosample escalator range TextValue Biosample ext_door range TextValue Biosample fertilizer_regm range TextValue Biosample field range TextValue Biosample fireplace_type range TextValue Biosample floor_count range TextValue Biosample fungicide_regm range TextValue Biosample gaseous_environment range TextValue Biosample gaseous_substances range TextValue Biosample genetic_mod range TextValue Biosample geo_loc_name range TextValue Biosample gravidity range TextValue Biosample gravity range TextValue Biosample growth_hormone_regm range TextValue Biosample hall_count range TextValue Biosample hcr_pressure range TextValue Biosample hcr_temp range TextValue Biosample heat_system_id range TextValue Biosample heavy_metals range TextValue Biosample heavy_metals_meth range TextValue Biosample herbicide_regm range TextValue Biosample horizon_meth range TextValue Biosample host_body_habitat range TextValue Biosample host_color range TextValue Biosample host_common_name range TextValue Biosample host_diet range TextValue Biosample host_genotype range TextValue Biosample host_growth_cond range TextValue Biosample host_last_meal range TextValue Biosample host_life_stage range TextValue Biosample host_shape range TextValue Biosample host_subject_id range TextValue Biosample host_substrate range TextValue Biosample humidity_regm range TextValue Biosample inorg_particles range TextValue Biosample light_regm range TextValue Biosample link_addit_analys range TextValue Biosample link_class_info range TextValue Biosample link_climate_info range TextValue Biosample local_class range TextValue Biosample local_class_meth range TextValue Biosample mechanical_damage range TextValue Biosample mineral_nutr_regm range TextValue Biosample misc_param range TextValue Biosample n_alkanes range TextValue Biosample org_particles range TextValue Biosample particle_class range TextValue Biosample permeability range TextValue Biosample perturbation range TextValue Biosample pesticide_regm range TextValue Biosample ph_meth range TextValue Biosample ph_regm range TextValue Biosample phaeopigments range TextValue Biosample phosplipid_fatt_acid range TextValue Biosample plant_product range TextValue Biosample pollutants range TextValue Biosample porosity range TextValue Biosample pre_treatment range TextValue Biosample previous_land_use range TextValue Biosample primary_treatment range TextValue Biosample radiation_regm range TextValue Biosample rainfall_regm range TextValue Biosample reactor_type range TextValue Biosample reservoir range TextValue Biosample resins_pc range TextValue Biosample room_count range TextValue Biosample room_dim range TextValue Biosample room_door_dist range TextValue Biosample room_door_share range TextValue Biosample room_hallway range TextValue Biosample room_net_area range TextValue Biosample room_vol range TextValue Biosample room_wall_share range TextValue Biosample root_cond range TextValue Biosample root_med_carbon range TextValue Biosample root_med_macronutr range TextValue Biosample root_med_micronutr range TextValue Biosample root_med_regl range TextValue Biosample root_med_solid range TextValue Biosample root_med_suppl range TextValue Biosample salinity_meth range TextValue Biosample salt_regm range TextValue Biosample samp_loc_corr_rate range TextValue Biosample samp_preserv range TextValue Biosample samp_room_id range TextValue Biosample samp_sort_meth range TextValue Biosample samp_store_dur range TextValue Biosample samp_store_loc range TextValue Biosample samp_time_out range TextValue Biosample samp_transport_cond range TextValue Biosample samp_tvdss range TextValue Biosample samp_type range TextValue Biosample samp_well_name range TextValue Biosample saturates_pc range TextValue Biosample season range TextValue Biosample season_environment range TextValue Biosample secondary_treatment range TextValue Biosample sewage_type range TextValue Biosample shading_device_loc range TextValue Biosample shading_device_mat range TextValue Biosample sieving range TextValue Biosample size_frac range TextValue Biosample soil_type range TextValue Biosample soil_type_meth range TextValue Biosample soluble_inorg_mat range TextValue Biosample soluble_org_mat range TextValue Biosample source_mat_id range TextValue Biosample space_typ_state range TextValue Biosample standing_water_regm range TextValue Biosample store_cond range TextValue Biosample suspend_solids range TextValue Biosample tertiary_treatment range TextValue Biosample tiss_cult_growth_med range TextValue Biosample tot_org_c_meth range TextValue Biosample ventilation_type range TextValue Biosample viscosity range TextValue Biosample volatile_org_comp range TextValue Biosample wall_water_mold range TextValue Biosample wastewater_type range TextValue Biosample water_temp_regm range TextValue Biosample watering_regm range TextValue Biosample win range TextValue Biosample wind_direction range TextValue Biosample window_open_freq range TextValue Biosample window_size range TextValue Biosample window_status range TextValue Biosample window_water_mold range TextValue"},{"location":"TextValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TextValue/#schema-source","title":"Schema Source","text":""},{"location":"TextValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:TextValue native nmdc:TextValue"},{"location":"TextValue/#linkml-source","title":"LinkML Source","text":""},{"location":"TextValue/#direct","title":"Direct","text":"
name: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- language\nclass_uri: nmdc:TextValue\n\n
"},{"location":"TextValue/#induced","title":"Induced","text":"
name: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n  language:\n    name: language\n    description: Should use ISO 639-1 code e.g. \"en\", \"fr\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: language\n    owner: TextValue\n    domain_of:\n    - TextValue\n    range: language code\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: TextValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: TextValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:TextValue\n\n
"},{"location":"TidalStageEnum/","title":"Enum: TidalStageEnum","text":"

URI: TidalStageEnum

"},{"location":"TidalStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low tide None ebb tide None flood tide None high tide None"},{"location":"TidalStageEnum/#slots","title":"Slots","text":"Name Description tidal_stage Stage of tide"},{"location":"TidalStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TidalStageEnum/#schema-source","title":"Schema Source","text":""},{"location":"TidalStageEnum/#linkml-source","title":"LinkML Source","text":"
name: tidal_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  low tide:\n    text: low tide\n  ebb tide:\n    text: ebb tide\n  flood tide:\n    text: flood tide\n  high tide:\n    text: high tide\n\n
"},{"location":"TillageEnum/","title":"Enum: TillageEnum","text":"

URI: TillageEnum

"},{"location":"TillageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drill None cutting disc None ridge till None strip tillage None zonal tillage None chisel None tined None mouldboard None disc plough None"},{"location":"TillageEnum/#slots","title":"Slots","text":"Name Description tillage Note method(s) used for tilling"},{"location":"TillageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TillageEnum/#schema-source","title":"Schema Source","text":""},{"location":"TillageEnum/#linkml-source","title":"LinkML Source","text":"
name: tillage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  drill:\n    text: drill\n  cutting disc:\n    text: cutting disc\n  ridge till:\n    text: ridge till\n  strip tillage:\n    text: strip tillage\n  zonal tillage:\n    text: zonal tillage\n  chisel:\n    text: chisel\n  tined:\n    text: tined\n  mouldboard:\n    text: mouldboard\n  disc plough:\n    text: disc plough\n\n
"},{"location":"Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:time

"},{"location":"Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Time/#schema-source","title":"Schema Source","text":""},{"location":"Time/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:time native nmdc:time exact schema:Time"},{"location":"TimestampValue/","title":"Class: TimestampValue","text":"

A value that is a timestamp. The range should be ISO-8601

URI: nmdc:TimestampValue

classDiagram\n  class TimestampValue\n  click TimestampValue href \"../TimestampValue\"\n    AttributeValue <|-- TimestampValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  TimestampValue : has_raw_value\n\n  TimestampValue : type\n\n\n\n
"},{"location":"TimestampValue/#inheritance","title":"Inheritance","text":""},{"location":"TimestampValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"TimestampValue/#usages","title":"Usages","text":"used by used in type used Biosample collection_date range TimestampValue Biosample date_last_rain range TimestampValue Biosample iw_bt_date_well range TimestampValue Biosample last_clean range TimestampValue Biosample prod_start_date range TimestampValue"},{"location":"TimestampValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TimestampValue/#schema-source","title":"Schema Source","text":""},{"location":"TimestampValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:TimestampValue native nmdc:TimestampValue"},{"location":"TimestampValue/#linkml-source","title":"LinkML Source","text":""},{"location":"TimestampValue/#direct","title":"Direct","text":"
name: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nclass_uri: nmdc:TimestampValue\n\n
"},{"location":"TimestampValue/#induced","title":"Induced","text":"
name: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: TimestampValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: TimestampValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:TimestampValue\n\n
"},{"location":"TrainLineEnum/","title":"Enum: TrainLineEnum","text":"

URI: TrainLineEnum

"},{"location":"TrainLineEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description red None green None orange None"},{"location":"TrainLineEnum/#slots","title":"Slots","text":"Name Description train_line The subway line name"},{"location":"TrainLineEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainLineEnum/#schema-source","title":"Schema Source","text":""},{"location":"TrainLineEnum/#linkml-source","title":"LinkML Source","text":"
name: train_line_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  red:\n    text: red\n  green:\n    text: green\n  orange:\n    text: orange\n\n
"},{"location":"TrainStatLocEnum/","title":"Enum: TrainStatLocEnum","text":"

URI: TrainStatLocEnum

"},{"location":"TrainStatLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description south station above ground None south station underground None south station amtrak None forest hills None riverside None"},{"location":"TrainStatLocEnum/#slots","title":"Slots","text":"Name Description train_stat_loc The train station collection location"},{"location":"TrainStatLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStatLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"TrainStatLocEnum/#linkml-source","title":"LinkML Source","text":"
name: train_stat_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  south station above ground:\n    text: south station above ground\n  south station underground:\n    text: south station underground\n  south station amtrak:\n    text: south station amtrak\n  forest hills:\n    text: forest hills\n  riverside:\n    text: riverside\n\n
"},{"location":"TrainStopLocEnum/","title":"Enum: TrainStopLocEnum","text":"

URI: TrainStopLocEnum

"},{"location":"TrainStopLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description end None mid None downtown None"},{"location":"TrainStopLocEnum/#slots","title":"Slots","text":"Name Description train_stop_loc The train stop collection location"},{"location":"TrainStopLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStopLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"TrainStopLocEnum/#linkml-source","title":"LinkML Source","text":"
name: train_stop_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  end:\n    text: end\n  mid:\n    text: mid\n  downtown:\n    text: downtown\n\n
"},{"location":"Unit/","title":"Type: Unit","text":"

URI: xsd:string

"},{"location":"Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Unit/#schema-source","title":"Schema Source","text":""},{"location":"Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:unit undefined qud:Unit, UO:0000000"},{"location":"Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"Uri/#comments","title":"Comments","text":""},{"location":"Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Uri/#schema-source","title":"Schema Source","text":""},{"location":"Uri/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:anyURI native nmdc:uri close schema:URL"},{"location":"Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"Uriorcurie/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:anyURI native nmdc:uriorcurie"},{"location":"VisMediaEnum/","title":"Enum: VisMediaEnum","text":"

URI: VisMediaEnum

"},{"location":"VisMediaEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description photos None videos None commonly of the building None site context (adjacent buildings, vegetation, terrain, streets) None interiors None equipment None 3D scans None"},{"location":"VisMediaEnum/#slots","title":"Slots","text":"Name Description vis_media The building visual media"},{"location":"VisMediaEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"VisMediaEnum/#schema-source","title":"Schema Source","text":""},{"location":"VisMediaEnum/#linkml-source","title":"LinkML Source","text":"
name: vis_media_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  photos:\n    text: photos\n  videos:\n    text: videos\n  commonly of the building:\n    text: commonly of the building\n  site context (adjacent buildings, vegetation, terrain, streets):\n    text: site context (adjacent buildings, vegetation, terrain, streets)\n  interiors:\n    text: interiors\n  equipment:\n    text: equipment\n  3D scans:\n    text: 3D scans\n\n
"},{"location":"WallConstTypeEnum/","title":"Enum: WallConstTypeEnum","text":"

URI: WallConstTypeEnum

"},{"location":"WallConstTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description frame construction None joisted masonry None light noncombustible None masonry noncombustible None modified fire resistive None fire resistive None"},{"location":"WallConstTypeEnum/#slots","title":"Slots","text":"Name Description wall_const_type The building class of the wall defined by the composition of the building ele..."},{"location":"WallConstTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallConstTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallConstTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_const_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  frame construction:\n    text: frame construction\n  joisted masonry:\n    text: joisted masonry\n  light noncombustible:\n    text: light noncombustible\n  masonry noncombustible:\n    text: masonry noncombustible\n  modified fire resistive:\n    text: modified fire resistive\n  fire resistive:\n    text: fire resistive\n\n
"},{"location":"WallFinishMatEnum/","title":"Enum: WallFinishMatEnum","text":"

URI: WallFinishMatEnum

"},{"location":"WallFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plaster None gypsum plaster None veneer plaster None gypsum board None tile None terrazzo None stone facing None acoustical treatment None wood None metal None masonry None"},{"location":"WallFinishMatEnum/#slots","title":"Slots","text":"Name Description wall_finish_mat The material utilized to finish the outer most layer of the wall"},{"location":"WallFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallFinishMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallFinishMatEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  plaster:\n    text: plaster\n  gypsum plaster:\n    text: gypsum plaster\n  veneer plaster:\n    text: veneer plaster\n  gypsum board:\n    text: gypsum board\n  tile:\n    text: tile\n  terrazzo:\n    text: terrazzo\n  stone facing:\n    text: stone facing\n  acoustical treatment:\n    text: acoustical treatment\n  wood:\n    text: wood\n  metal:\n    text: metal\n  masonry:\n    text: masonry\n\n
"},{"location":"WallLocEnum/","title":"Enum: WallLocEnum","text":"

URI: WallLocEnum

"},{"location":"WallLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WallLocEnum/#slots","title":"Slots","text":"Name Description wall_loc The relative location of the wall within the room"},{"location":"WallLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallLocEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n\n
"},{"location":"WallSurfTreatmentEnum/","title":"Enum: WallSurfTreatmentEnum","text":"

URI: WallSurfTreatmentEnum

"},{"location":"WallSurfTreatmentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description painted None wall paper None no treatment None paneling None stucco None fabric None"},{"location":"WallSurfTreatmentEnum/#slots","title":"Slots","text":"Name Description wall_surf_treatment The surface treatment of interior wall"},{"location":"WallSurfTreatmentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallSurfTreatmentEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallSurfTreatmentEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_surf_treatment_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  painted:\n    text: painted\n  wall paper:\n    text: wall paper\n  no treatment:\n    text: no treatment\n  paneling:\n    text: paneling\n  stucco:\n    text: stucco\n  fabric:\n    text: fabric\n\n
"},{"location":"WallTextureEnum/","title":"Enum: WallTextureEnum","text":"

URI: WallTextureEnum

"},{"location":"WallTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"WallTextureEnum/#slots","title":"Slots","text":"Name Description wall_texture The feel, appearance, or consistency of a wall surface"},{"location":"WallTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallTextureEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallTextureEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  crows feet:\n    text: crows feet\n  crows-foot stomp:\n    text: crows-foot stomp\n  ? ''\n  : text: ''\n  double skip:\n    text: double skip\n  hawk and trowel:\n    text: hawk and trowel\n  knockdown:\n    text: knockdown\n  popcorn:\n    text: popcorn\n  orange peel:\n    text: orange peel\n  rosebud stomp:\n    text: rosebud stomp\n  Santa-Fe texture:\n    text: Santa-Fe texture\n  skip trowel:\n    text: skip trowel\n  smooth:\n    text: smooth\n  stomp knockdown:\n    text: stomp knockdown\n  swirl:\n    text: swirl\n\n
"},{"location":"WaterFeatTypeEnum/","title":"Enum: WaterFeatTypeEnum","text":"

URI: WaterFeatTypeEnum

"},{"location":"WaterFeatTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fountain None pool None standing feature None stream None waterfall None"},{"location":"WaterFeatTypeEnum/#slots","title":"Slots","text":"Name Description water_feat_type The type of water feature present within the building being sampled"},{"location":"WaterFeatTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WaterFeatTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"WaterFeatTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: water_feat_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  fountain:\n    text: fountain\n  pool:\n    text: pool\n  standing feature:\n    text: standing feature\n  stream:\n    text: stream\n  waterfall:\n    text: waterfall\n\n
"},{"location":"WeekdayEnum/","title":"Enum: WeekdayEnum","text":"

URI: WeekdayEnum

"},{"location":"WeekdayEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Monday None Tuesday None Wednesday None Thursday None Friday None Saturday None Sunday None"},{"location":"WeekdayEnum/#slots","title":"Slots","text":"Name Description weekday The day of the week when sampling occurred"},{"location":"WeekdayEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WeekdayEnum/#schema-source","title":"Schema Source","text":""},{"location":"WeekdayEnum/#linkml-source","title":"LinkML Source","text":"
name: weekday_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Monday:\n    text: Monday\n  Tuesday:\n    text: Tuesday\n  Wednesday:\n    text: Wednesday\n  Thursday:\n    text: Thursday\n  Friday:\n    text: Friday\n  Saturday:\n    text: Saturday\n  Sunday:\n    text: Sunday\n\n
"},{"location":"WindowCondEnum/","title":"Enum: WindowCondEnum","text":"

URI: WindowCondEnum

"},{"location":"WindowCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"WindowCondEnum/#slots","title":"Slots","text":"Name Description window_cond The physical condition of the window at the time of sampling"},{"location":"WindowCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowCondEnum/#linkml-source","title":"LinkML Source","text":"
name: window_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  damaged:\n    text: damaged\n  needs repair:\n    text: needs repair\n  new:\n    text: new\n  rupture:\n    text: rupture\n  visible wear:\n    text: visible wear\n\n
"},{"location":"WindowCoverEnum/","title":"Enum: WindowCoverEnum","text":"

URI: WindowCoverEnum

"},{"location":"WindowCoverEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description blinds None curtains None none None"},{"location":"WindowCoverEnum/#slots","title":"Slots","text":"Name Description window_cover The type of window covering"},{"location":"WindowCoverEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCoverEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowCoverEnum/#linkml-source","title":"LinkML Source","text":"
name: window_cover_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  blinds:\n    text: blinds\n  curtains:\n    text: curtains\n  none:\n    text: none\n\n
"},{"location":"WindowHorizPosEnum/","title":"Enum: WindowHorizPosEnum","text":"

URI: WindowHorizPosEnum

"},{"location":"WindowHorizPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description left None middle None right None"},{"location":"WindowHorizPosEnum/#slots","title":"Slots","text":"Name Description window_horiz_pos The horizontal position of the window on the wall"},{"location":"WindowHorizPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowHorizPosEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowHorizPosEnum/#linkml-source","title":"LinkML Source","text":"
name: window_horiz_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  left:\n    text: left\n  middle:\n    text: middle\n  right:\n    text: right\n\n
"},{"location":"WindowLocEnum/","title":"Enum: WindowLocEnum","text":"

URI: WindowLocEnum

"},{"location":"WindowLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WindowLocEnum/#slots","title":"Slots","text":"Name Description window_loc The relative location of the window within the room"},{"location":"WindowLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowLocEnum/#linkml-source","title":"LinkML Source","text":"
name: window_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n\n
"},{"location":"WindowMatEnum/","title":"Enum: WindowMatEnum","text":"

URI: WindowMatEnum

"},{"location":"WindowMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clad None fiberglass None metal None vinyl None wood None"},{"location":"WindowMatEnum/#slots","title":"Slots","text":"Name Description window_mat The type of material used to finish a window"},{"location":"WindowMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowMatEnum/#linkml-source","title":"LinkML Source","text":"
name: window_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  clad:\n    text: clad\n  fiberglass:\n    text: fiberglass\n  metal:\n    text: metal\n  vinyl:\n    text: vinyl\n  wood:\n    text: wood\n\n
"},{"location":"WindowTypeEnum/","title":"Enum: WindowTypeEnum","text":"

URI: WindowTypeEnum

"},{"location":"WindowTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description single-hung sash window None horizontal sash window None fixed window None"},{"location":"WindowTypeEnum/#slots","title":"Slots","text":"Name Description window_type The type of windows"},{"location":"WindowTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: window_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  single-hung sash window:\n    text: single-hung sash window\n  horizontal sash window:\n    text: horizontal sash window\n  fixed window:\n    text: fixed window\n\n
"},{"location":"WindowVertPosEnum/","title":"Enum: WindowVertPosEnum","text":"

URI: WindowVertPosEnum

"},{"location":"WindowVertPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bottom None middle None top None low None high None"},{"location":"WindowVertPosEnum/#slots","title":"Slots","text":"Name Description window_vert_pos The vertical position of the window on the wall"},{"location":"WindowVertPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowVertPosEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowVertPosEnum/#linkml-source","title":"LinkML Source","text":"
name: window_vert_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  bottom:\n    text: bottom\n  middle:\n    text: middle\n  top:\n    text: top\n  low:\n    text: low\n  high:\n    text: high\n\n
"},{"location":"WorkflowExecution/","title":"Class: WorkflowExecution","text":"

Represents an instance of an execution of a particular workflow

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:WorkflowExecution

Note

Mermaid class diagram too large to render.

"},{"location":"WorkflowExecution/#inheritance","title":"Inheritance","text":""},{"location":"WorkflowExecution/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance ended_at_time 0..1 String direct execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed direct git_url 1 String The url that points to the exact github location of a workflow direct started_at_time 1 String direct version 0..1 String direct was_informed_by 1 DataGeneration direct has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"WorkflowExecution/#usages","title":"Usages","text":"used by used in type used FunctionalAnnotationAggMember metagenome_annotation_id range WorkflowExecution Database workflow_execution_set range WorkflowExecution FunctionalAnnotation was_generated_by any_of[range] WorkflowExecution DataObject was_generated_by range WorkflowExecution DataObject was_generated_by any_of[range] WorkflowExecution"},{"location":"WorkflowExecution/#aliases","title":"Aliases","text":""},{"location":"WorkflowExecution/#comments","title":"Comments","text":""},{"location":"WorkflowExecution/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WorkflowExecution/#schema-source","title":"Schema Source","text":""},{"location":"WorkflowExecution/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:WorkflowExecution native nmdc:WorkflowExecution"},{"location":"WorkflowExecution/#linkml-source","title":"LinkML Source","text":""},{"location":"WorkflowExecution/#direct","title":"Direct","text":"
name: WorkflowExecution\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: An analysis contains secondary analysis results derived from sequence\n      reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) subclasses of WorkflowExecution is a distinct\n  run with start and stop times, potentially with different inputs and outputs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: PlannedProcess\nabstract: true\nslots:\n- ended_at_time\n- execution_resource\n- git_url\n- started_at_time\n- version\n- was_informed_by\nslot_usage:\n  started_at_time:\n    name: started_at_time\n    required: true\n  git_url:\n    name: git_url\n    required: true\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  execution_resource:\n    name: execution_resource\n    required: true\n  was_informed_by:\n    name: was_informed_by\n    required: true\nclass_uri: nmdc:WorkflowExecution\nrules:\n- preconditions:\n    slot_conditions:\n      qc_status:\n        name: qc_status\n        equals_string: pass\n  postconditions:\n    slot_conditions:\n      has_output:\n        name: has_output\n        required: true\n  description: If qc_status has a value of pass, then the has_output slot is required.\n  title: qc_status_pass_has_output_required\n- preconditions:\n    slot_conditions:\n      qc_status:\n        name: qc_status\n        value_presence: ABSENT\n  postconditions:\n    slot_conditions:\n      has_output:\n        name: has_output\n        required: true\n  description: If qc_status is not specified, then the has_output slot is required.\n  title: qc_status_pass_null_has_output_required\n\n
"},{"location":"WorkflowExecution/#induced","title":"Induced","text":"
name: WorkflowExecution\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: An analysis contains secondary analysis results derived from sequence\n      reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) subclasses of WorkflowExecution is a distinct\n  run with start and stop times, potentially with different inputs and outputs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n  started_at_time:\n    name: started_at_time\n    required: true\n  git_url:\n    name: git_url\n    required: true\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  execution_resource:\n    name: execution_resource\n    required: true\n  was_informed_by:\n    name: was_informed_by\n    required: true\nattributes:\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: WorkflowExecution\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: WorkflowExecution\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: WorkflowExecution\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: WorkflowExecution\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: WorkflowExecution\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:WorkflowExecution\nrules:\n- preconditions:\n    slot_conditions:\n      qc_status:\n        name: qc_status\n        equals_string: pass\n  postconditions:\n    slot_conditions:\n      has_output:\n        name: has_output\n        required: true\n  description: If qc_status has a value of pass, then the has_output slot is required.\n  title: qc_status_pass_has_output_required\n- preconditions:\n    slot_conditions:\n      qc_status:\n        name: qc_status\n        value_presence: ABSENT\n  postconditions:\n    slot_conditions:\n      has_output:\n        name: has_output\n        required: true\n  description: If qc_status is not specified, then the has_output slot is required.\n  title: qc_status_pass_null_has_output_required\n\n
"},{"location":"WorkflowSubset/","title":"Subset: WorkflowSubset","text":"

Subset consisting of just the workflow execution activities

URI: WorkflowSubset

"},{"location":"WorkflowSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WorkflowSubset/#schema-source","title":"Schema Source","text":""},{"location":"WorkflowSubset/#classes-in-subset","title":"Classes in subset","text":"Class Description MagsAnalysis A workflow execution activity that uses computational binning tools to group ... MetabolomicsAnalysis MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... MetagenomeSequencing Initial sequencing activity that precedes any analysis MetaproteomicsAnalysis MetatranscriptomeAnnotation MetatranscriptomeAssembly MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... NomAnalysis ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... WorkflowExecution Represents an instance of an execution of a particular workflow"},{"location":"YesNoEnum/","title":"Enum: YesNoEnum","text":"

replaces DnaDnaseEnum and DnaseRnaEnum

URI: YesNoEnum

"},{"location":"YesNoEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description no None yes None"},{"location":"YesNoEnum/#slots","title":"Slots","text":"Name Description dna_dnase dnase_rna"},{"location":"YesNoEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"YesNoEnum/#schema-source","title":"Schema Source","text":""},{"location":"YesNoEnum/#linkml-source","title":"LinkML Source","text":"
name: YesNoEnum\ndescription: replaces DnaDnaseEnum and DnaseRnaEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  'no':\n    text: 'no'\n  'yes':\n    text: 'yes'\n\n
"},{"location":"about/","title":"About","text":""},{"location":"about/#nmdc-schema","title":"NMDC Schema","text":"

Schema resources for the National Microbiome Data Collaborative (NMDC)

The purpose of the NMDC Schema is to define metadata for the National Microbiome Data Collaborative (NMDC). The NMDC is a multi-organizational effort to enable integrated microbiome data across diverse areas in medicine, agriculture, bioenergy, and the environment. This integrated platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science.

The NMDC schema is used during the translation process to specify how metadata elements are related.

"},{"location":"about/#credits","title":"Credits","text":"

this project was made using the LinkML framework

"},{"location":"abs_air_humidity/","title":"Slot: absolute air humidity (abs_air_humidity)","text":"

Actual mass of water vapor - mh20 - present in the air water vapor mixture

URI: MIXS:0000122

"},{"location":"abs_air_humidity/#inheritance","title":"Inheritance","text":""},{"location":"abs_air_humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"abs_air_humidity/#properties","title":"Properties","text":""},{"location":"abs_air_humidity/#aliases","title":"Aliases","text":""},{"location":"abs_air_humidity/#examples","title":"Examples","text":"Value 9 gram per gram"},{"location":"abs_air_humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"abs_air_humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"abs_air_humidity/#schema-source","title":"Schema Source","text":""},{"location":"abs_air_humidity/#linkml-source","title":"LinkML Source","text":"
name: abs_air_humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per gram, kilogram per kilogram, kilogram, pound\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Actual mass of water vapor - mh20 - present in the air water vapor mixture\ntitle: absolute air humidity\nexamples:\n- value: 9 gram per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- absolute air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000122\nalias: abs_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"add_date/","title":"Slot: add_date","text":"

The date on which the information was added to the database.

URI: nmdc:add_date

"},{"location":"add_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no Biosample Biological source material which can be characterized by an experiment no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"add_date/#properties","title":"Properties","text":""},{"location":"add_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"add_date/#schema-source","title":"Schema Source","text":""},{"location":"add_date/#linkml-source","title":"LinkML Source","text":"
name: add_date\ndescription: The date on which the information was added to the database.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: add_date\ndomain_of:\n- Biosample\n- DataGeneration\nrange: string\n\n
"},{"location":"add_recov_method/","title":"Slot: secondary and tertiary recovery methods and start date (add_recov_method)","text":"

Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0001009

"},{"location":"add_recov_method/#inheritance","title":"Inheritance","text":""},{"location":"add_recov_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"add_recov_method/#properties","title":"Properties","text":""},{"location":"add_recov_method/#aliases","title":"Aliases","text":""},{"location":"add_recov_method/#examples","title":"Examples","text":"Value Polymer Addition;2018-06-21T14:30Z"},{"location":"add_recov_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"add_recov_method/#annotations","title":"Annotations","text":"property value expected_value enumeration;timestamp"},{"location":"add_recov_method/#schema-source","title":"Schema Source","text":""},{"location":"add_recov_method/#linkml-source","title":"LinkML Source","text":"
name: add_recov_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration;timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n  for increase of hydrocarbon recovery from resource and start date for each one of\n  them. If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: secondary and tertiary recovery methods and start date\nexamples:\n- value: Polymer Addition;2018-06-21T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary and tertiary recovery methods and start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001009\nalias: add_recov_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"additional_info/","title":"Slot: additional info (additional_info)","text":"

Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary

URI: MIXS:0000300

"},{"location":"additional_info/#inheritance","title":"Inheritance","text":""},{"location":"additional_info/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"additional_info/#properties","title":"Properties","text":""},{"location":"additional_info/#aliases","title":"Aliases","text":""},{"location":"additional_info/#examples","title":"Examples","text":"Value"},{"location":"additional_info/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"additional_info/#annotations","title":"Annotations","text":"property value expected_value text"},{"location":"additional_info/#schema-source","title":"Schema Source","text":""},{"location":"additional_info/#linkml-source","title":"LinkML Source","text":"
name: additional_info\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information that doesn't fit anywhere else. Can also be used to propose\n  new entries for fields with controlled vocabulary\ntitle: additional info\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- additional info\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000300\nalias: additional_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"address/","title":"Slot: address (address)","text":"

The street name and building number where the sampling occurred.

URI: MIXS:0000218

"},{"location":"address/#inheritance","title":"Inheritance","text":""},{"location":"address/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"address/#properties","title":"Properties","text":""},{"location":"address/#aliases","title":"Aliases","text":""},{"location":"address/#examples","title":"Examples","text":"Value"},{"location":"address/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"address/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"address/#schema-source","title":"Schema Source","text":""},{"location":"address/#linkml-source","title":"LinkML Source","text":"
name: address\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The street name and building number where the sampling occurred.\ntitle: address\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- address\nrank: 1000\nis_a: core field\nstring_serialization: '{integer}{text}'\nslot_uri: MIXS:0000218\nalias: address\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"adj_room/","title":"Slot: adjacent rooms (adj_room)","text":"

List of rooms (room number, room name) immediately adjacent to the sampling room

URI: MIXS:0000219

"},{"location":"adj_room/#inheritance","title":"Inheritance","text":""},{"location":"adj_room/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"adj_room/#properties","title":"Properties","text":""},{"location":"adj_room/#aliases","title":"Aliases","text":""},{"location":"adj_room/#examples","title":"Examples","text":"Value"},{"location":"adj_room/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"adj_room/#annotations","title":"Annotations","text":"property value expected_value room name;room number"},{"location":"adj_room/#schema-source","title":"Schema Source","text":""},{"location":"adj_room/#linkml-source","title":"LinkML Source","text":"
name: adj_room\nannotations:\n  expected_value:\n    tag: expected_value\n    value: room name;room number\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of rooms (room number, room name) immediately adjacent to the sampling\n  room\ntitle: adjacent rooms\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- adjacent rooms\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000219\nalias: adj_room\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"aero_struc/","title":"Slot: aerospace structure (aero_struc)","text":"

Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together

URI: MIXS:0000773

"},{"location":"aero_struc/#inheritance","title":"Inheritance","text":""},{"location":"aero_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"aero_struc/#properties","title":"Properties","text":""},{"location":"aero_struc/#aliases","title":"Aliases","text":""},{"location":"aero_struc/#examples","title":"Examples","text":"Value plane"},{"location":"aero_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"aero_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"aero_struc/#schema-source","title":"Schema Source","text":""},{"location":"aero_struc/#linkml-source","title":"LinkML Source","text":"
name: aero_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Aerospace structures typically consist of thin plates with stiffeners\n  for the external surfaces, bulkheads and frames to support the shape and fasteners\n  such as welds, rivets, screws and bolts to hold the components together\ntitle: aerospace structure\nexamples:\n- value: plane\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aerospace structure\nrank: 1000\nis_a: core field\nstring_serialization: '[plane|glider]'\nslot_uri: MIXS:0000773\nalias: aero_struc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"agrochem_addition/","title":"Slot: history/agrochemical additions (agrochem_addition)","text":"

Addition of fertilizers, pesticides, etc. - amount and time of applications

URI: MIXS:0000639

"},{"location":"agrochem_addition/#inheritance","title":"Inheritance","text":""},{"location":"agrochem_addition/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"agrochem_addition/#properties","title":"Properties","text":""},{"location":"agrochem_addition/#aliases","title":"Aliases","text":""},{"location":"agrochem_addition/#examples","title":"Examples","text":"Value roundup;5 milligram per liter;2018-06-21"},{"location":"agrochem_addition/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"agrochem_addition/#annotations","title":"Annotations","text":"property value expected_value agrochemical name;agrochemical amount;timestamp"},{"location":"agrochem_addition/#schema-source","title":"Schema Source","text":""},{"location":"agrochem_addition/#linkml-source","title":"LinkML Source","text":"
name: agrochem_addition\nannotations:\n  expected_value:\n    tag: expected_value\n    value: agrochemical name;agrochemical amount;timestamp\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Addition of fertilizers, pesticides, etc. - amount and time of applications\ntitle: history/agrochemical additions\nexamples:\n- value: roundup;5 milligram per liter;2018-06-21\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/agrochemical additions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{timestamp}'\nslot_uri: MIXS:0000639\nalias: agrochem_addition\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"air_PM_concen/","title":"Slot: air particulate matter concentration (air_PM_concen)","text":"

Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM

URI: MIXS:0000108

"},{"location":"air_PM_concen/#inheritance","title":"Inheritance","text":""},{"location":"air_PM_concen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"air_PM_concen/#properties","title":"Properties","text":""},{"location":"air_PM_concen/#aliases","title":"Aliases","text":""},{"location":"air_PM_concen/#examples","title":"Examples","text":"Value PM2.5;10 microgram per cubic meter"},{"location":"air_PM_concen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"air_PM_concen/#annotations","title":"Annotations","text":"property value expected_value particulate matter name;measurement value"},{"location":"air_PM_concen/#schema-source","title":"Schema Source","text":""},{"location":"air_PM_concen/#linkml-source","title":"LinkML Source","text":"
name: air_PM_concen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: particulate matter name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micrograms per cubic meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of substances that remain suspended in the air, and comprise\n  mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple\n  PM's by entering numeric values preceded by name of PM\ntitle: air particulate matter concentration\nexamples:\n- value: PM2.5;10 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air particulate matter concentration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000108\nalias: air_PM_concen\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"air_temp/","title":"Slot: air temperature (air_temp)","text":"

Temperature of the air at the time of sampling

URI: MIXS:0000124

"},{"location":"air_temp/#inheritance","title":"Inheritance","text":""},{"location":"air_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"air_temp/#properties","title":"Properties","text":""},{"location":"air_temp/#aliases","title":"Aliases","text":""},{"location":"air_temp/#examples","title":"Examples","text":"Value 20 degree Celsius"},{"location":"air_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"air_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"air_temp/#schema-source","title":"Schema Source","text":""},{"location":"air_temp/#linkml-source","title":"LinkML Source","text":"
name: air_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Temperature of the air at the time of sampling\ntitle: air temperature\nexamples:\n- value: 20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000124\nalias: air_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"air_temp_regm/","title":"Slot: air temperature regimen (air_temp_regm)","text":"

Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens

URI: MIXS:0000551

"},{"location":"air_temp_regm/#inheritance","title":"Inheritance","text":""},{"location":"air_temp_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"air_temp_regm/#properties","title":"Properties","text":""},{"location":"air_temp_regm/#aliases","title":"Aliases","text":""},{"location":"air_temp_regm/#examples","title":"Examples","text":"Value 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"air_temp_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"air_temp_regm/#annotations","title":"Annotations","text":"property value expected_value temperature value;treatment interval and duration"},{"location":"air_temp_regm/#schema-source","title":"Schema Source","text":""},{"location":"air_temp_regm/#linkml-source","title":"LinkML Source","text":"
name: air_temp_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: temperature value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to varying temperatures;\n  should include the temperature, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include different temperature regimens\ntitle: air temperature regimen\nexamples:\n- value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000551\nalias: air_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"al_sat/","title":"Slot: extreme_unusual_properties/Al saturation (al_sat)","text":"

Aluminum saturation (esp. For tropical soils)

URI: MIXS:0000607

"},{"location":"al_sat/#inheritance","title":"Inheritance","text":""},{"location":"al_sat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"al_sat/#properties","title":"Properties","text":""},{"location":"al_sat/#aliases","title":"Aliases","text":""},{"location":"al_sat/#examples","title":"Examples","text":"Value"},{"location":"al_sat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"al_sat/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"al_sat/#schema-source","title":"Schema Source","text":""},{"location":"al_sat/#linkml-source","title":"LinkML Source","text":"
name: al_sat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Aluminum saturation (esp. For tropical soils)\ntitle: extreme_unusual_properties/Al saturation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000607\nalias: al_sat\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"al_sat_meth/","title":"Slot: extreme_unusual_properties/Al saturation method (al_sat_meth)","text":"

Reference or method used in determining Al saturation

URI: MIXS:0000324

"},{"location":"al_sat_meth/#inheritance","title":"Inheritance","text":""},{"location":"al_sat_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"al_sat_meth/#properties","title":"Properties","text":""},{"location":"al_sat_meth/#aliases","title":"Aliases","text":""},{"location":"al_sat_meth/#examples","title":"Examples","text":"Value"},{"location":"al_sat_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"al_sat_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or URL"},{"location":"al_sat_meth/#schema-source","title":"Schema Source","text":""},{"location":"al_sat_meth/#linkml-source","title":"LinkML Source","text":"
name: al_sat_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or URL\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining Al saturation\ntitle: extreme_unusual_properties/Al saturation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000324\nalias: al_sat_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"alkalinity/","title":"Slot: alkalinity (alkalinity)","text":"

Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate

URI: MIXS:0000421

"},{"location":"alkalinity/#inheritance","title":"Inheritance","text":""},{"location":"alkalinity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"alkalinity/#properties","title":"Properties","text":""},{"location":"alkalinity/#aliases","title":"Aliases","text":""},{"location":"alkalinity/#examples","title":"Examples","text":"Value 50 milligram per liter"},{"location":"alkalinity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alkalinity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"alkalinity/#schema-source","title":"Schema Source","text":""},{"location":"alkalinity/#linkml-source","title":"LinkML Source","text":"
name: alkalinity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milliequivalent per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Alkalinity, the ability of a solution to neutralize acids to the equivalence\n  point of carbonate or bicarbonate\ntitle: alkalinity\nexamples:\n- value: 50 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000421\nalias: alkalinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"alkalinity_method/","title":"Slot: alkalinity method (alkalinity_method)","text":"

Method used for alkalinity measurement

URI: MIXS:0000298

"},{"location":"alkalinity_method/#inheritance","title":"Inheritance","text":""},{"location":"alkalinity_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"alkalinity_method/#properties","title":"Properties","text":""},{"location":"alkalinity_method/#aliases","title":"Aliases","text":""},{"location":"alkalinity_method/#examples","title":"Examples","text":"Value titration"},{"location":"alkalinity_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alkalinity_method/#annotations","title":"Annotations","text":"property value expected_value description of method"},{"location":"alkalinity_method/#schema-source","title":"Schema Source","text":""},{"location":"alkalinity_method/#linkml-source","title":"LinkML Source","text":"
name: alkalinity_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: description of method\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Method used for alkalinity measurement\ntitle: alkalinity method\nexamples:\n- value: titration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000298\nalias: alkalinity_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"alkyl_diethers/","title":"Slot: alkyl diethers (alkyl_diethers)","text":"

Concentration of alkyl diethers

URI: MIXS:0000490

"},{"location":"alkyl_diethers/#inheritance","title":"Inheritance","text":""},{"location":"alkyl_diethers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"alkyl_diethers/#properties","title":"Properties","text":""},{"location":"alkyl_diethers/#aliases","title":"Aliases","text":""},{"location":"alkyl_diethers/#examples","title":"Examples","text":"Value 0.005 mole per liter"},{"location":"alkyl_diethers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alkyl_diethers/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"alkyl_diethers/#schema-source","title":"Schema Source","text":""},{"location":"alkyl_diethers/#linkml-source","title":"LinkML Source","text":"
name: alkyl_diethers\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of alkyl diethers\ntitle: alkyl diethers\nexamples:\n- value: 0.005 mole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkyl diethers\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000490\nalias: alkyl_diethers\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"all_proteins/","title":"Slot: all_proteins","text":"

the list of protein identifiers that are associated with the peptide sequence

URI: nmdc:all_proteins

"},{"location":"all_proteins/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes"},{"location":"all_proteins/#properties","title":"Properties","text":""},{"location":"all_proteins/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"all_proteins/#schema-source","title":"Schema Source","text":""},{"location":"all_proteins/#linkml-source","title":"LinkML Source","text":"
name: all_proteins\ndescription: the list of protein identifiers that are associated with the peptide\n  sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: all_proteins\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\nmultivalued: true\n\n
"},{"location":"alt/","title":"Slot: altitude (alt)","text":"

Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air

URI: MIXS:0000094

"},{"location":"alt/#inheritance","title":"Inheritance","text":""},{"location":"alt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"alt/#properties","title":"Properties","text":""},{"location":"alt/#aliases","title":"Aliases","text":""},{"location":"alt/#examples","title":"Examples","text":"Value 100 meter"},{"location":"alt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alt/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"alt/#schema-source","title":"Schema Source","text":""},{"location":"alt/#linkml-source","title":"LinkML Source","text":"
name: alt\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\ndescription: Altitude is a term used to identify heights of objects such as airplanes,\n  space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric\n  layers and clouds. It is used to measure the height of an object which is above\n  the earth's surface. In this context, the altitude measurement is the vertical distance\n  between the earth's surface above sea level and the sampled position in the air\ntitle: altitude\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- altitude\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000094\nalias: alt\ndomain_of:\n- agriculture\n- air\n- built environment\n- core\n- food-animal and animal feed\n- food-farm environment\n- food-food production facility\n- food-human foods\n- host-associated\n- human-associated\n- human-gut\n- human-oral\n- human-skin\n- human-vaginal\n- hydrocarbon resources-cores\n- hydrocarbon resources-fluids_swabs\n- microbial mat_biofilm\n- miscellaneous natural or artificial environment\n- plant-associated\n- sediment\n- soil\n- symbiont-associated\n- wastewater_sludge\n- water\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"alternative_descriptions/","title":"Slot: alternative_descriptions","text":"

A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.

URI: nmdc:alternative_descriptions

"},{"location":"alternative_descriptions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_descriptions/#properties","title":"Properties","text":""},{"location":"alternative_descriptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alternative_descriptions/#schema-source","title":"Schema Source","text":""},{"location":"alternative_descriptions/#linkml-source","title":"LinkML Source","text":"
name: alternative_descriptions\ndescription: A list of alternative descriptions for the entity. The distinction between\n  description and alternative descriptions is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternative_descriptions\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\n
"},{"location":"alternative_identifiers/","title":"Slot: alternative_identifiers","text":"

A list of alternative identifiers for the entity.

URI: nmdc:alternative_identifiers

"},{"location":"alternative_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"alternative_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no NamedThing a databased entity or concept/class no Extraction A material separation in which a desired component of an input material is se... no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no WorkflowExecution Represents an instance of an execution of a particular workflow no Biosample Biological source material which can be characterized by an experiment yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no Configuration A set of parameters that define the actions of a process and is shared among ... no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no Site no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no MetabolomicsAnalysis no ProcessedSample no OntologyClass no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DataObject An object that primarily consists of symbols that represent information no GeneProduct A molecule encoded by a gene that has an evolved function no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no Instrument A material entity that is designed to perform a function in a scientific inve... no MetatranscriptomeAssembly no ChemicalEntity An atom or molecule that can be represented with a chemical formula no FiltrationProcess The process of segregation of phases; e no MetagenomeSequencing Initial sequencing activity that precedes any analysis no EnvironmentalMaterialTerm no LibraryPreparation no Pooling physical combination of several instances of like material no MaterialEntity no CalibrationInformation A calibration object that is associated with a process no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no DataGeneration The methods and processes used to generate omics data from a biosample or org... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no OrthologyGroup A set of genes or gene products in which all members are orthologous no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no Study A study summarizes the overall goal of a research initiative and outlines the... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no Manifest no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"alternative_identifiers/#properties","title":"Properties","text":""},{"location":"alternative_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alternative_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"alternative_identifiers/#linkml-source","title":"LinkML Source","text":"
name: alternative_identifiers\ndescription: A list of alternative identifiers for the entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternative_identifiers\ndomain_of:\n- MetaboliteIdentification\n- NamedThing\nrange: uriorcurie\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"alternative_names/","title":"Slot: alternative_names","text":"

A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.

URI: nmdc:alternative_names

"},{"location":"alternative_names/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"alternative_names/#properties","title":"Properties","text":""},{"location":"alternative_names/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alternative_names/#schema-source","title":"Schema Source","text":""},{"location":"alternative_names/#linkml-source","title":"LinkML Source","text":"
name: alternative_names\ndescription: A list of alternative names used to refer to the entity. The distinction\n  between name and alternative names is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\n- skos:altLabel\nrank: 1000\nalias: alternative_names\ndomain_of:\n- ChemicalEntity\n- Study\nrange: string\nmultivalued: true\n\n
"},{"location":"alternative_titles/","title":"Slot: alternative_titles","text":"

A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.

URI: nmdc:alternative_titles

"},{"location":"alternative_titles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_titles/#properties","title":"Properties","text":""},{"location":"alternative_titles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alternative_titles/#schema-source","title":"Schema Source","text":""},{"location":"alternative_titles/#linkml-source","title":"LinkML Source","text":"
name: alternative_titles\ndescription: A list of alternative titles for the entity. The distinction between\n  title and alternative titles is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\nrank: 1000\nalias: alternative_titles\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\n
"},{"location":"aminopept_act/","title":"Slot: aminopeptidase activity (aminopept_act)","text":"

Measurement of aminopeptidase activity

URI: MIXS:0000172

"},{"location":"aminopept_act/#inheritance","title":"Inheritance","text":""},{"location":"aminopept_act/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"aminopept_act/#properties","title":"Properties","text":""},{"location":"aminopept_act/#aliases","title":"Aliases","text":""},{"location":"aminopept_act/#examples","title":"Examples","text":"Value 0.269 mole per liter per hour"},{"location":"aminopept_act/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"aminopept_act/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"aminopept_act/#schema-source","title":"Schema Source","text":""},{"location":"aminopept_act/#linkml-source","title":"LinkML Source","text":"
name: aminopept_act\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per liter per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of aminopeptidase activity\ntitle: aminopeptidase activity\nexamples:\n- value: 0.269 mole per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aminopeptidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000172\nalias: aminopept_act\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ammonium/","title":"Slot: ammonium (ammonium)","text":"

Concentration of ammonium in the sample

URI: MIXS:0000427

"},{"location":"ammonium/#inheritance","title":"Inheritance","text":""},{"location":"ammonium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ammonium/#properties","title":"Properties","text":""},{"location":"ammonium/#aliases","title":"Aliases","text":""},{"location":"ammonium/#examples","title":"Examples","text":"Value 1.5 milligram per liter"},{"location":"ammonium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ammonium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ammonium/#schema-source","title":"Schema Source","text":""},{"location":"ammonium/#linkml-source","title":"LinkML Source","text":"
name: ammonium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of ammonium in the sample\ntitle: ammonium\nexamples:\n- value: 1.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ammonium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000427\nalias: ammonium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ammonium_nitrogen/","title":"Slot: ammonium nitrogen (ammonium_nitrogen)","text":"

Concentration of ammonium nitrogen in the sample

URI: nmdc:ammonium_nitrogen

"},{"location":"ammonium_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ammonium_nitrogen/#properties","title":"Properties","text":""},{"location":"ammonium_nitrogen/#aliases","title":"Aliases","text":""},{"location":"ammonium_nitrogen/#examples","title":"Examples","text":"Value 2.3 mg/kg"},{"location":"ammonium_nitrogen/#see-also","title":"See Also","text":""},{"location":"ammonium_nitrogen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ammonium_nitrogen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ammonium_nitrogen/#schema-source","title":"Schema Source","text":""},{"location":"ammonium_nitrogen/#linkml-source","title":"LinkML Source","text":"
name: ammonium_nitrogen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of ammonium nitrogen in the sample\ntitle: ammonium nitrogen\nexamples:\n- value: 2.3 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- ammonium_nitrogen\n- NH4-N\nrank: 1000\nalias: ammonium_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"amount_light/","title":"Slot: amount of light (amount_light)","text":"

The unit of illuminance and luminous emittance, measuring luminous flux per unit area

URI: MIXS:0000140

"},{"location":"amount_light/#inheritance","title":"Inheritance","text":""},{"location":"amount_light/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"amount_light/#properties","title":"Properties","text":""},{"location":"amount_light/#aliases","title":"Aliases","text":""},{"location":"amount_light/#examples","title":"Examples","text":"Value"},{"location":"amount_light/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"amount_light/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"amount_light/#schema-source","title":"Schema Source","text":""},{"location":"amount_light/#linkml-source","title":"LinkML Source","text":"
name: amount_light\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: lux, lumens per square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The unit of illuminance and luminous emittance, measuring luminous flux\n  per unit area\ntitle: amount of light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount of light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000140\nalias: amount_light\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"analysis_identifiers/","title":"Slot: analysis_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:analysis_identifiers

"},{"location":"analysis_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"analysis_identifiers/#properties","title":"Properties","text":""},{"location":"analysis_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"analysis_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"analysis_identifiers/#linkml-source","title":"LinkML Source","text":"
name: analysis_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"analysis_type/","title":"Slot: analysis/data type (analysis_type)","text":"

Select all the data types associated or available for this biosample

URI: nmdc:analysis_type

"},{"location":"analysis_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"analysis_type/#properties","title":"Properties","text":""},{"location":"analysis_type/#examples","title":"Examples","text":"Value metagenomics; metabolomics; proteomics"},{"location":"analysis_type/#see-also","title":"See Also","text":""},{"location":"analysis_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"analysis_type/#schema-source","title":"Schema Source","text":""},{"location":"analysis_type/#linkml-source","title":"LinkML Source","text":"
name: analysis_type\ndescription: Select all the data types associated or available for this biosample\ntitle: analysis/data type\nexamples:\n- value: metagenomics; metabolomics; proteomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIxS:investigation_type\nrank: 3\nalias: analysis_type\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: AnalysisTypeEnum\nrecommended: true\nmultivalued: true\n\n
"},{"location":"analyte_category/","title":"Slot: analyte_category","text":"

The type of analyte(s) that were measured in the data generation process and analyzed

_ in the Workflow Chain_

__

URI: nmdc:analyte_category

"},{"location":"analyte_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"analyte_category/#properties","title":"Properties","text":""},{"location":"analyte_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"analyte_category/#schema-source","title":"Schema Source","text":""},{"location":"analyte_category/#linkml-source","title":"LinkML Source","text":"
name: analyte_category\ndescription: \"The type of analyte(s) that were measured in the data generation process\\\n  \\ and analyzed\\n  in the Workflow Chain\\n\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: analyte_category\ndomain_of:\n- DataGeneration\nrange: AnalyteCategoryEnum\nrequired: true\n\n
"},{"location":"ances_data/","title":"Slot: ancestral data (ances_data)","text":"

Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)

URI: MIXS:0000247

"},{"location":"ances_data/#inheritance","title":"Inheritance","text":""},{"location":"ances_data/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ances_data/#properties","title":"Properties","text":""},{"location":"ances_data/#aliases","title":"Aliases","text":""},{"location":"ances_data/#examples","title":"Examples","text":"Value A/3*B"},{"location":"ances_data/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ances_data/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"ances_data/#schema-source","title":"Schema Source","text":""},{"location":"ances_data/#linkml-source","title":"LinkML Source","text":"
name: ances_data\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information about either pedigree or other ancestral information description\n  (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A\n  x B) x B] x B)\ntitle: ancestral data\nexamples:\n- value: A/3*B\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ancestral data\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000247\nalias: ances_data\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"annual_precpt/","title":"Slot: mean annual precipitation (annual_precpt)","text":"

The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.

URI: MIXS:0000644

"},{"location":"annual_precpt/#inheritance","title":"Inheritance","text":""},{"location":"annual_precpt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"annual_precpt/#properties","title":"Properties","text":""},{"location":"annual_precpt/#aliases","title":"Aliases","text":""},{"location":"annual_precpt/#examples","title":"Examples","text":"Value"},{"location":"annual_precpt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"annual_precpt/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"annual_precpt/#schema-source","title":"Schema Source","text":""},{"location":"annual_precpt/#linkml-source","title":"LinkML Source","text":"
name: annual_precpt\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average of all annual precipitation values known, or an estimated\n  equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean annual precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000644\nalias: annual_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"annual_temp/","title":"Slot: mean annual temperature (annual_temp)","text":"

Mean annual temperature

URI: MIXS:0000642

"},{"location":"annual_temp/#inheritance","title":"Inheritance","text":""},{"location":"annual_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"annual_temp/#properties","title":"Properties","text":""},{"location":"annual_temp/#aliases","title":"Aliases","text":""},{"location":"annual_temp/#examples","title":"Examples","text":"Value 12.5 degree Celsius"},{"location":"annual_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"annual_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"annual_temp/#schema-source","title":"Schema Source","text":""},{"location":"annual_temp/#linkml-source","title":"LinkML Source","text":"
name: annual_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Mean annual temperature\ntitle: mean annual temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000642\nalias: annual_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"antibiotic_regm/","title":"Slot: antibiotic regimen (antibiotic_regm)","text":"

Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens

URI: MIXS:0000553

"},{"location":"antibiotic_regm/#inheritance","title":"Inheritance","text":""},{"location":"antibiotic_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"antibiotic_regm/#properties","title":"Properties","text":""},{"location":"antibiotic_regm/#aliases","title":"Aliases","text":""},{"location":"antibiotic_regm/#examples","title":"Examples","text":"Value penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"antibiotic_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"antibiotic_regm/#annotations","title":"Annotations","text":"property value expected_value antibiotic name;antibiotic amount;treatment interval and duration"},{"location":"antibiotic_regm/#schema-source","title":"Schema Source","text":""},{"location":"antibiotic_regm/#linkml-source","title":"LinkML Source","text":"
name: antibiotic_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: antibiotic name;antibiotic amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving antibiotic administration; should\n  include the name of antibiotic, amount administered, treatment regimen including\n  how many times the treatment was repeated, how long each treatment lasted, and the\n  start and end time of the entire treatment; can include multiple antibiotic regimens\ntitle: antibiotic regimen\nexamples:\n- value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- antibiotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000553\nalias: antibiotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"api/","title":"Slot: API gravity (api)","text":"

API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)

URI: MIXS:0000157

"},{"location":"api/#inheritance","title":"Inheritance","text":""},{"location":"api/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"api/#properties","title":"Properties","text":""},{"location":"api/#aliases","title":"Aliases","text":""},{"location":"api/#examples","title":"Examples","text":"Value"},{"location":"api/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"api/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"api/#schema-source","title":"Schema Source","text":""},{"location":"api/#linkml-source","title":"LinkML Source","text":"
name: api\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degrees API\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'API gravity is a measure of how heavy or light a petroleum liquid is\n  compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e\n  API)'\ntitle: API gravity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- API gravity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000157\nalias: api\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"applied_roles/","title":"Slot: applied_roles","text":"

URI: nmdc:applied_roles

"},{"location":"applied_roles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applied_roles/#properties","title":"Properties","text":""},{"location":"applied_roles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"applied_roles/#annotations","title":"Annotations","text":"property value tooltip Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/"},{"location":"applied_roles/#schema-source","title":"Schema Source","text":""},{"location":"applied_roles/#linkml-source","title":"LinkML Source","text":"
name: applied_roles\nannotations:\n  tooltip:\n    tag: tooltip\n    value: 'Identify all CRediT roles associated with this contributor. CRediT Information:\n      https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: applied_roles\ndomain_of:\n- CreditAssociation\nrange: CreditEnum\nrequired: true\nmultivalued: true\n\n
"},{"location":"applies_to_person/","title":"Slot: applies_to_person","text":"

URI: nmdc:applies_to_person

"},{"location":"applies_to_person/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applies_to_person/#properties","title":"Properties","text":""},{"location":"applies_to_person/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"applies_to_person/#schema-source","title":"Schema Source","text":""},{"location":"applies_to_person/#linkml-source","title":"LinkML Source","text":"
name: applies_to_person\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: applies_to_person\ndomain_of:\n- CreditAssociation\nrange: PersonValue\nrequired: true\n\n
"},{"location":"arch_struc/","title":"Slot: architectural structure (arch_struc)","text":"

An architectural structure is a human-made, free-standing, immobile outdoor construction

URI: MIXS:0000774

"},{"location":"arch_struc/#inheritance","title":"Inheritance","text":""},{"location":"arch_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"arch_struc/#properties","title":"Properties","text":""},{"location":"arch_struc/#aliases","title":"Aliases","text":""},{"location":"arch_struc/#examples","title":"Examples","text":"Value shed"},{"location":"arch_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"arch_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"arch_struc/#schema-source","title":"Schema Source","text":""},{"location":"arch_struc/#linkml-source","title":"LinkML Source","text":"
name: arch_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: An architectural structure is a human-made, free-standing, immobile outdoor\n  construction\ntitle: architectural structure\nexamples:\n- value: shed\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- architectural structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000774\nalias: arch_struc\ndomain_of:\n- Biosample\nrange: arch_struc_enum\nmultivalued: false\n\n
"},{"location":"aromatics_pc/","title":"Slot: aromatics wt% (aromatics_pc)","text":"

Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)

URI: MIXS:0000133

"},{"location":"aromatics_pc/#inheritance","title":"Inheritance","text":""},{"location":"aromatics_pc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"aromatics_pc/#properties","title":"Properties","text":""},{"location":"aromatics_pc/#aliases","title":"Aliases","text":""},{"location":"aromatics_pc/#examples","title":"Examples","text":"Value"},{"location":"aromatics_pc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"aromatics_pc/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"aromatics_pc/#schema-source","title":"Schema Source","text":""},{"location":"aromatics_pc/#linkml-source","title":"LinkML Source","text":"
name: aromatics_pc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n  that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n  There are three main methods to obtain SARA results. The most popular one is known\n  as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: aromatics wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aromatics wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000133\nalias: aromatics_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"asm_score/","title":"Slot: asm_score","text":"

A score for comparing metagenomic assembly quality from same sample.

URI: nmdc:asm_score

"},{"location":"asm_score/#inheritance","title":"Inheritance","text":""},{"location":"asm_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"asm_score/#properties","title":"Properties","text":""},{"location":"asm_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"asm_score/#schema-source","title":"Schema Source","text":""},{"location":"asm_score/#linkml-source","title":"LinkML Source","text":"
name: asm_score\ndescription: A score for comparing metagenomic assembly quality from same sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: asm_score\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"asphaltenes_pc/","title":"Slot: asphaltenes wt% (asphaltenes_pc)","text":"

Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)

URI: MIXS:0000135

"},{"location":"asphaltenes_pc/#inheritance","title":"Inheritance","text":""},{"location":"asphaltenes_pc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"asphaltenes_pc/#properties","title":"Properties","text":""},{"location":"asphaltenes_pc/#aliases","title":"Aliases","text":""},{"location":"asphaltenes_pc/#examples","title":"Examples","text":"Value"},{"location":"asphaltenes_pc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"asphaltenes_pc/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"asphaltenes_pc/#schema-source","title":"Schema Source","text":""},{"location":"asphaltenes_pc/#linkml-source","title":"LinkML Source","text":"
name: asphaltenes_pc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n  that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n  There are three main methods to obtain SARA results. The most popular one is known\n  as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: asphaltenes wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- asphaltenes wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000135\nalias: asphaltenes_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"assembly_identifiers/","title":"Slot: assembly_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:assembly_identifiers

"},{"location":"assembly_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"assembly_identifiers/#properties","title":"Properties","text":""},{"location":"assembly_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"assembly_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"assembly_identifiers/#linkml-source","title":"LinkML Source","text":"
name: assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: assembly_identifiers\nrange: string\n\n
"},{"location":"associated_dois/","title":"Slot: associated_dois","text":"

A list of DOIs associated with a resource, such as a list of DOIS associated with a Study.

URI: nmdc:associated_dois

"},{"location":"associated_dois/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"associated_dois/#properties","title":"Properties","text":""},{"location":"associated_dois/#aliases","title":"Aliases","text":""},{"location":"associated_dois/#examples","title":"Examples","text":"Value [{'doi': 'doi:10.46936/intm.proj.2021.60141/60000423', 'doi_provider': 'emsl', 'doi_category': 'award_doi'}, {'doi': 'doi:10.1101/2022.12.12.520098', 'doi_category': 'publication_doi'}, {'doi': 'doi:10.48321/D1Z60Q', 'doi_category': 'data_management_plan_doi', 'doi_provider': 'gsc'}]"},{"location":"associated_dois/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"associated_dois/#schema-source","title":"Schema Source","text":""},{"location":"associated_dois/#linkml-source","title":"LinkML Source","text":"
name: associated_dois\ndescription: A list of DOIs associated with a resource, such as a list of DOIS associated\n  with a Study.\nexamples:\n- value: '[{''doi'': ''doi:10.46936/intm.proj.2021.60141/60000423'', ''doi_provider'':\n    ''emsl'', ''doi_category'': ''award_doi''}, {''doi'': ''doi:10.1101/2022.12.12.520098'',\n    ''doi_category'': ''publication_doi''}, {''doi'': ''doi:10.48321/D1Z60Q'', ''doi_category'':\n    ''data_management_plan_doi'', ''doi_provider'': ''gsc''}]'\n  description: Provides a list of two DOIs; specifically, an EMSL award DOI and a\n    publication DOI.\nin_subset:\n- data_portal_subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Associated DOIs\n- Associated digital object identifiers\nrank: 1000\nalias: associated_dois\ndomain_of:\n- Study\nrange: Doi\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"associated_studies/","title":"Slot: associated_studies","text":"

The study associated with a resource.

URI: nmdc:associated_studies

"},{"location":"associated_studies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... yes Biosample Biological source material which can be characterized by an experiment yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"associated_studies/#properties","title":"Properties","text":""},{"location":"associated_studies/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"associated_studies/#schema-source","title":"Schema Source","text":""},{"location":"associated_studies/#linkml-source","title":"LinkML Source","text":"
name: associated_studies\ndescription: The study associated with a resource.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: associated_studies\ndomain_of:\n- Biosample\n- DataGeneration\nrange: Study\nrequired: true\nmultivalued: true\nstructured_pattern:\n  syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n  interpolated: true\n\n
"},{"location":"atmospheric_data/","title":"Slot: atmospheric data (atmospheric_data)","text":"

Measurement of atmospheric data; can include multiple data

URI: MIXS:0001097

"},{"location":"atmospheric_data/#inheritance","title":"Inheritance","text":""},{"location":"atmospheric_data/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"atmospheric_data/#properties","title":"Properties","text":""},{"location":"atmospheric_data/#aliases","title":"Aliases","text":""},{"location":"atmospheric_data/#examples","title":"Examples","text":"Value wind speed;9 knots"},{"location":"atmospheric_data/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"atmospheric_data/#annotations","title":"Annotations","text":"property value expected_value atmospheric data name;measurement value"},{"location":"atmospheric_data/#schema-source","title":"Schema Source","text":""},{"location":"atmospheric_data/#linkml-source","title":"LinkML Source","text":"
name: atmospheric_data\nannotations:\n  expected_value:\n    tag: expected_value\n    value: atmospheric data name;measurement value\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Measurement of atmospheric data; can include multiple data\ntitle: atmospheric data\nexamples:\n- value: wind speed;9 knots\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- atmospheric data\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0001097\nalias: atmospheric_data\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"avg_dew_point/","title":"Slot: average dew point (avg_dew_point)","text":"

The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day

URI: MIXS:0000141

"},{"location":"avg_dew_point/#inheritance","title":"Inheritance","text":""},{"location":"avg_dew_point/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"avg_dew_point/#properties","title":"Properties","text":""},{"location":"avg_dew_point/#aliases","title":"Aliases","text":""},{"location":"avg_dew_point/#examples","title":"Examples","text":"Value 25.5 degree Celsius"},{"location":"avg_dew_point/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"avg_dew_point/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"avg_dew_point/#schema-source","title":"Schema Source","text":""},{"location":"avg_dew_point/#linkml-source","title":"LinkML Source","text":"
name: avg_dew_point\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average of dew point measures taken at the beginning of every hour\n  over a 24 hour period on the sampling day\ntitle: average dew point\nexamples:\n- value: 25.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000141\nalias: avg_dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"avg_occup/","title":"Slot: average daily occupancy (avg_occup)","text":"

Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.

URI: MIXS:0000775

"},{"location":"avg_occup/#inheritance","title":"Inheritance","text":""},{"location":"avg_occup/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"avg_occup/#properties","title":"Properties","text":""},{"location":"avg_occup/#aliases","title":"Aliases","text":""},{"location":"avg_occup/#examples","title":"Examples","text":"Value 2"},{"location":"avg_occup/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"avg_occup/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"avg_occup/#schema-source","title":"Schema Source","text":""},{"location":"avg_occup/#linkml-source","title":"LinkML Source","text":"
name: avg_occup\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Daily average occupancy of room. Indicate the number of person(s) daily\n  occupying the sampling room.\ntitle: average daily occupancy\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average daily occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000775\nalias: avg_occup\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"avg_temp/","title":"Slot: average temperature (avg_temp)","text":"

The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day

URI: MIXS:0000142

"},{"location":"avg_temp/#inheritance","title":"Inheritance","text":""},{"location":"avg_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"avg_temp/#properties","title":"Properties","text":""},{"location":"avg_temp/#aliases","title":"Aliases","text":""},{"location":"avg_temp/#examples","title":"Examples","text":"Value 12.5 degree Celsius"},{"location":"avg_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"avg_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"avg_temp/#schema-source","title":"Schema Source","text":""},{"location":"avg_temp/#linkml-source","title":"LinkML Source","text":"
name: avg_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average of temperatures taken at the beginning of every hour over\n  a 24 hour period on the sampling day\ntitle: average temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000142\nalias: avg_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"bac_prod/","title":"Slot: bacterial production (bac_prod)","text":"

Bacterial production in the water column measured by isotope uptake

URI: MIXS:0000683

"},{"location":"bac_prod/#inheritance","title":"Inheritance","text":""},{"location":"bac_prod/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bac_prod/#properties","title":"Properties","text":""},{"location":"bac_prod/#aliases","title":"Aliases","text":""},{"location":"bac_prod/#examples","title":"Examples","text":"Value 5 milligram per cubic meter per day"},{"location":"bac_prod/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bac_prod/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bac_prod/#schema-source","title":"Schema Source","text":""},{"location":"bac_prod/#linkml-source","title":"LinkML Source","text":"
name: bac_prod\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter per day\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Bacterial production in the water column measured by isotope uptake\ntitle: bacterial production\nexamples:\n- value: 5 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000683\nalias: bac_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"bac_resp/","title":"Slot: bacterial respiration (bac_resp)","text":"

Measurement of bacterial respiration in the water column

URI: MIXS:0000684

"},{"location":"bac_resp/#inheritance","title":"Inheritance","text":""},{"location":"bac_resp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bac_resp/#properties","title":"Properties","text":""},{"location":"bac_resp/#aliases","title":"Aliases","text":""},{"location":"bac_resp/#examples","title":"Examples","text":"Value 300 micromole oxygen per liter per hour"},{"location":"bac_resp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bac_resp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bac_resp/#schema-source","title":"Schema Source","text":""},{"location":"bac_resp/#linkml-source","title":"LinkML Source","text":"
name: bac_resp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter per day, micromole oxygen per liter per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of bacterial respiration in the water column\ntitle: bacterial respiration\nexamples:\n- value: 300 micromole oxygen per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial respiration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000684\nalias: bac_resp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"bacteria_carb_prod/","title":"Slot: bacterial carbon production (bacteria_carb_prod)","text":"

Measurement of bacterial carbon production

URI: MIXS:0000173

"},{"location":"bacteria_carb_prod/#inheritance","title":"Inheritance","text":""},{"location":"bacteria_carb_prod/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bacteria_carb_prod/#properties","title":"Properties","text":""},{"location":"bacteria_carb_prod/#aliases","title":"Aliases","text":""},{"location":"bacteria_carb_prod/#examples","title":"Examples","text":"Value 2.53 microgram per liter per hour"},{"location":"bacteria_carb_prod/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bacteria_carb_prod/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bacteria_carb_prod/#schema-source","title":"Schema Source","text":""},{"location":"bacteria_carb_prod/#linkml-source","title":"LinkML Source","text":"
name: bacteria_carb_prod\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: nanogram per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of bacterial carbon production\ntitle: bacterial carbon production\nexamples:\n- value: 2.53 microgram per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial carbon production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000173\nalias: bacteria_carb_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"barometric_press/","title":"Slot: barometric pressure (barometric_press)","text":"

Force per unit area exerted against a surface by the weight of air above that surface

URI: MIXS:0000096

"},{"location":"barometric_press/#inheritance","title":"Inheritance","text":""},{"location":"barometric_press/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"barometric_press/#properties","title":"Properties","text":""},{"location":"barometric_press/#aliases","title":"Aliases","text":""},{"location":"barometric_press/#examples","title":"Examples","text":"Value 5 millibar"},{"location":"barometric_press/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"barometric_press/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"barometric_press/#schema-source","title":"Schema Source","text":""},{"location":"barometric_press/#linkml-source","title":"LinkML Source","text":"
name: barometric_press\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millibar\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Force per unit area exerted against a surface by the weight of air above\n  that surface\ntitle: barometric pressure\nexamples:\n- value: 5 millibar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- barometric pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000096\nalias: barometric_press\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"basin/","title":"Slot: basin name (basin)","text":"

Name of the basin (e.g. Campos)

URI: MIXS:0000290

"},{"location":"basin/#inheritance","title":"Inheritance","text":""},{"location":"basin/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"basin/#properties","title":"Properties","text":""},{"location":"basin/#aliases","title":"Aliases","text":""},{"location":"basin/#examples","title":"Examples","text":"Value"},{"location":"basin/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"basin/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"basin/#schema-source","title":"Schema Source","text":""},{"location":"basin/#linkml-source","title":"LinkML Source","text":"
name: basin\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of the basin (e.g. Campos)\ntitle: basin name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- basin name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000290\nalias: basin\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"bathroom_count/","title":"Slot: bathroom count (bathroom_count)","text":"

The number of bathrooms in the building

URI: MIXS:0000776

"},{"location":"bathroom_count/#inheritance","title":"Inheritance","text":""},{"location":"bathroom_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bathroom_count/#properties","title":"Properties","text":""},{"location":"bathroom_count/#aliases","title":"Aliases","text":""},{"location":"bathroom_count/#examples","title":"Examples","text":"Value 1"},{"location":"bathroom_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bathroom_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"bathroom_count/#schema-source","title":"Schema Source","text":""},{"location":"bathroom_count/#linkml-source","title":"LinkML Source","text":"
name: bathroom_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of bathrooms in the building\ntitle: bathroom count\nexamples:\n- value: '1'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bathroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000776\nalias: bathroom_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"bedroom_count/","title":"Slot: bedroom count (bedroom_count)","text":"

The number of bedrooms in the building

URI: MIXS:0000777

"},{"location":"bedroom_count/#inheritance","title":"Inheritance","text":""},{"location":"bedroom_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bedroom_count/#properties","title":"Properties","text":""},{"location":"bedroom_count/#aliases","title":"Aliases","text":""},{"location":"bedroom_count/#examples","title":"Examples","text":"Value 2"},{"location":"bedroom_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bedroom_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"bedroom_count/#schema-source","title":"Schema Source","text":""},{"location":"bedroom_count/#linkml-source","title":"LinkML Source","text":"
name: bedroom_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of bedrooms in the building\ntitle: bedroom count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bedroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000777\nalias: bedroom_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"benzene/","title":"Slot: benzene (benzene)","text":"

Concentration of benzene in the sample

URI: MIXS:0000153

"},{"location":"benzene/#inheritance","title":"Inheritance","text":""},{"location":"benzene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"benzene/#properties","title":"Properties","text":""},{"location":"benzene/#aliases","title":"Aliases","text":""},{"location":"benzene/#examples","title":"Examples","text":"Value"},{"location":"benzene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"benzene/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"benzene/#schema-source","title":"Schema Source","text":""},{"location":"benzene/#linkml-source","title":"LinkML Source","text":"
name: benzene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of benzene in the sample\ntitle: benzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- benzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000153\nalias: benzene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"best_protein/","title":"Slot: best_protein","text":"

the specific protein identifier most correctly associated with the peptide sequence

URI: nmdc:best_protein

"},{"location":"best_protein/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes"},{"location":"best_protein/#properties","title":"Properties","text":""},{"location":"best_protein/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"best_protein/#schema-source","title":"Schema Source","text":""},{"location":"best_protein/#linkml-source","title":"LinkML Source","text":"
name: best_protein\ndescription: the specific protein identifier most correctly associated with the peptide\n  sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: best_protein\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\n\n
"},{"location":"bin_name/","title":"Slot: bin_name","text":"

URI: nmdc:bin_name

"},{"location":"bin_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_name/#properties","title":"Properties","text":""},{"location":"bin_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bin_name/#schema-source","title":"Schema Source","text":""},{"location":"bin_name/#linkml-source","title":"LinkML Source","text":"
name: bin_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_name\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"bin_quality/","title":"Slot: bin_quality","text":"

URI: nmdc:bin_quality

"},{"location":"bin_quality/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_quality/#properties","title":"Properties","text":""},{"location":"bin_quality/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bin_quality/#schema-source","title":"Schema Source","text":""},{"location":"bin_quality/#linkml-source","title":"LinkML Source","text":"
name: bin_quality\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_quality\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"binned_contig_num/","title":"Slot: binned_contig_num","text":"

URI: nmdc:binned_contig_num

"},{"location":"binned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"binned_contig_num/#properties","title":"Properties","text":""},{"location":"binned_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"binned_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"binned_contig_num/#linkml-source","title":"LinkML Source","text":"
name: binned_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: binned_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"biochem_oxygen_dem/","title":"Slot: biochemical oxygen demand (biochem_oxygen_dem)","text":"

Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period

URI: MIXS:0000653

"},{"location":"biochem_oxygen_dem/#inheritance","title":"Inheritance","text":""},{"location":"biochem_oxygen_dem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biochem_oxygen_dem/#properties","title":"Properties","text":""},{"location":"biochem_oxygen_dem/#aliases","title":"Aliases","text":""},{"location":"biochem_oxygen_dem/#examples","title":"Examples","text":"Value"},{"location":"biochem_oxygen_dem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biochem_oxygen_dem/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"biochem_oxygen_dem/#schema-source","title":"Schema Source","text":""},{"location":"biochem_oxygen_dem/#linkml-source","title":"LinkML Source","text":"
name: biochem_oxygen_dem\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Amount of dissolved oxygen needed by aerobic biological organisms in\n  a body of water to break down organic material present in a given water sample at\n  certain temperature over a specific time period\ntitle: biochemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biochemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000653\nalias: biochem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"biocide/","title":"Slot: biocide administration (biocide)","text":"

List of biocides (commercial name of product and supplier) and date of administration

URI: MIXS:0001011

"},{"location":"biocide/#inheritance","title":"Inheritance","text":""},{"location":"biocide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biocide/#properties","title":"Properties","text":""},{"location":"biocide/#aliases","title":"Aliases","text":""},{"location":"biocide/#examples","title":"Examples","text":"Value ALPHA 1427;Baker Hughes;2008-01-23"},{"location":"biocide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biocide/#annotations","title":"Annotations","text":"property value expected_value name;name;timestamp"},{"location":"biocide/#schema-source","title":"Schema Source","text":""},{"location":"biocide/#linkml-source","title":"LinkML Source","text":"
name: biocide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;name;timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of biocides (commercial name of product and supplier) and date of\n  administration\ntitle: biocide administration\nexamples:\n- value: ALPHA 1427;Baker Hughes;2008-01-23\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001011\nalias: biocide\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"biocide_admin_method/","title":"Slot: biocide administration method (biocide_admin_method)","text":"

Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)

URI: MIXS:0000456

"},{"location":"biocide_admin_method/#inheritance","title":"Inheritance","text":""},{"location":"biocide_admin_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biocide_admin_method/#properties","title":"Properties","text":""},{"location":"biocide_admin_method/#aliases","title":"Aliases","text":""},{"location":"biocide_admin_method/#examples","title":"Examples","text":"Value"},{"location":"biocide_admin_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biocide_admin_method/#annotations","title":"Annotations","text":"property value expected_value measurement value;frequency;duration;duration"},{"location":"biocide_admin_method/#schema-source","title":"Schema Source","text":""},{"location":"biocide_admin_method/#linkml-source","title":"LinkML Source","text":"
name: biocide_admin_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;frequency;duration;duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Method of biocide administration (dose, frequency, duration, time elapsed\n  between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)\ntitle: biocide administration method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\nslot_uri: MIXS:0000456\nalias: biocide_admin_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"biogas_retention_time/","title":"Slot: biogas_retention_time","text":"

URI: nmdc:biogas_retention_time

"},{"location":"biogas_retention_time/#properties","title":"Properties","text":""},{"location":"biogas_retention_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biogas_retention_time/#schema-source","title":"Schema Source","text":""},{"location":"biogas_retention_time/#linkml-source","title":"LinkML Source","text":"
name: biogas_retention_time\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_retention_time\nrange: string\n\n
"},{"location":"biogas_temperature/","title":"Slot: biogas_temperature","text":"

URI: nmdc:biogas_temperature

"},{"location":"biogas_temperature/#properties","title":"Properties","text":""},{"location":"biogas_temperature/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biogas_temperature/#schema-source","title":"Schema Source","text":""},{"location":"biogas_temperature/#linkml-source","title":"LinkML Source","text":"
name: biogas_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_temperature\nrange: string\n\n
"},{"location":"biol_stat/","title":"Slot: biological status (biol_stat)","text":"

The level of genome modification.

URI: MIXS:0000858

"},{"location":"biol_stat/#inheritance","title":"Inheritance","text":""},{"location":"biol_stat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biol_stat/#properties","title":"Properties","text":""},{"location":"biol_stat/#aliases","title":"Aliases","text":""},{"location":"biol_stat/#examples","title":"Examples","text":"Value natural"},{"location":"biol_stat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biol_stat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"biol_stat/#schema-source","title":"Schema Source","text":""},{"location":"biol_stat/#linkml-source","title":"LinkML Source","text":"
name: biol_stat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The level of genome modification.\ntitle: biological status\nexamples:\n- value: natural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000858\nalias: biol_stat\ndomain_of:\n- Biosample\nrange: biol_stat_enum\nmultivalued: false\n\n
"},{"location":"biomass/","title":"Slot: biomass (biomass)","text":"

Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements

URI: MIXS:0000174

"},{"location":"biomass/#inheritance","title":"Inheritance","text":""},{"location":"biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biomass/#properties","title":"Properties","text":""},{"location":"biomass/#aliases","title":"Aliases","text":""},{"location":"biomass/#examples","title":"Examples","text":"Value total;20 gram"},{"location":"biomass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biomass/#annotations","title":"Annotations","text":"property value expected_value biomass type;measurement value"},{"location":"biomass/#schema-source","title":"Schema Source","text":""},{"location":"biomass/#linkml-source","title":"LinkML Source","text":"
name: biomass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: biomass type;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: ton, kilogram, gram\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n  e.g. Microbial, total. Can include multiple measurements\ntitle: biomass\nexamples:\n- value: total;20 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biomass\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000174\nalias: biomass\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biomaterial_purity/","title":"Slot: biomaterial_purity","text":"

URI: nmdc:biomaterial_purity

"},{"location":"biomaterial_purity/#inheritance","title":"Inheritance","text":""},{"location":"biomaterial_purity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProcessedSample no"},{"location":"biomaterial_purity/#properties","title":"Properties","text":""},{"location":"biomaterial_purity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biomaterial_purity/#schema-source","title":"Schema Source","text":""},{"location":"biomaterial_purity/#linkml-source","title":"LinkML Source","text":"
name: biomaterial_purity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biomaterial_purity\ndomain_of:\n- ProcessedSample\nrange: QuantityValue\n\n
"},{"location":"biosample_categories/","title":"Slot: Categories the biosample belongs to (biosample_categories)","text":"

URI: nmdc:biosample_categories

"},{"location":"biosample_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biosample_categories/#properties","title":"Properties","text":""},{"location":"biosample_categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biosample_categories/#schema-source","title":"Schema Source","text":""},{"location":"biosample_categories/#linkml-source","title":"LinkML Source","text":"
name: biosample_categories\ntitle: Categories the biosample belongs to\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biosample_categories\ndomain_of:\n- Biosample\nrange: BiosampleCategoryEnum\nmultivalued: true\n\n
"},{"location":"biosample_identifiers/","title":"Slot: biosample_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:biosample_identifiers

"},{"location":"biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"biosample_identifiers/#properties","title":"Properties","text":""},{"location":"biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: biosample_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"biosample_set/","title":"Slot: biosample_set","text":"

This property links a database object to the set of samples within it.

URI: nmdc:biosample_set

"},{"location":"biosample_set/#inheritance","title":"Inheritance","text":""},{"location":"biosample_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"biosample_set/#properties","title":"Properties","text":""},{"location":"biosample_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biosample_set/#schema-source","title":"Schema Source","text":""},{"location":"biosample_set/#linkml-source","title":"LinkML Source","text":"
name: biosample_set\ndescription: This property links a database object to the set of samples within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: biosample_set\ndomain_of:\n- Database\nrange: Biosample\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biotic_regm/","title":"Slot: biotic regimen (biotic_regm)","text":"

Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.

URI: MIXS:0001038

"},{"location":"biotic_regm/#inheritance","title":"Inheritance","text":""},{"location":"biotic_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biotic_regm/#properties","title":"Properties","text":""},{"location":"biotic_regm/#aliases","title":"Aliases","text":""},{"location":"biotic_regm/#examples","title":"Examples","text":"Value sample inoculated with Rhizobium spp. Culture"},{"location":"biotic_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_regm/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"biotic_regm/#schema-source","title":"Schema Source","text":""},{"location":"biotic_regm/#linkml-source","title":"LinkML Source","text":"
name: biotic_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information about treatment(s) involving use of biotic factors, such\n  as bacteria, viruses or fungi.\ntitle: biotic regimen\nexamples:\n- value: sample inoculated with Rhizobium spp. Culture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001038\nalias: biotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"biotic_relationship/","title":"Slot: observed biotic relationship (biotic_relationship)","text":"

Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object

URI: MIXS:0000028

"},{"location":"biotic_relationship/#inheritance","title":"Inheritance","text":""},{"location":"biotic_relationship/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biotic_relationship/#properties","title":"Properties","text":""},{"location":"biotic_relationship/#aliases","title":"Aliases","text":""},{"location":"biotic_relationship/#examples","title":"Examples","text":"Value free living"},{"location":"biotic_relationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_relationship/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"biotic_relationship/#schema-source","title":"Schema Source","text":""},{"location":"biotic_relationship/#linkml-source","title":"LinkML Source","text":"
name: biotic_relationship\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\ndescription: Description of relationship(s) between the subject organism and other\n  organism(s) it is associated with. E.g., parasite on species X; mutualist with species\n  Y. The target organism is the subject of the relationship, and the other organism(s)\n  is the object\ntitle: observed biotic relationship\nexamples:\n- value: free living\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed biotic relationship\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000028\nalias: biotic_relationship\ndomain_of:\n- Biosample\nrange: biotic_relationship_enum\nmultivalued: false\n\n
"},{"location":"bishomohopanol/","title":"Slot: bishomohopanol (bishomohopanol)","text":"

Concentration of bishomohopanol

URI: MIXS:0000175

"},{"location":"bishomohopanol/#inheritance","title":"Inheritance","text":""},{"location":"bishomohopanol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bishomohopanol/#properties","title":"Properties","text":""},{"location":"bishomohopanol/#aliases","title":"Aliases","text":""},{"location":"bishomohopanol/#examples","title":"Examples","text":"Value 14 microgram per liter"},{"location":"bishomohopanol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bishomohopanol/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bishomohopanol/#schema-source","title":"Schema Source","text":""},{"location":"bishomohopanol/#linkml-source","title":"LinkML Source","text":"
name: bishomohopanol\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, microgram per gram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of bishomohopanol\ntitle: bishomohopanol\nexamples:\n- value: 14 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bishomohopanol\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000175\nalias: bishomohopanol\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"blood_press_diast/","title":"Slot: host blood pressure diastolic (blood_press_diast)","text":"

Resting diastolic blood pressure, measured as mm mercury

URI: MIXS:0000258

"},{"location":"blood_press_diast/#inheritance","title":"Inheritance","text":""},{"location":"blood_press_diast/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"blood_press_diast/#properties","title":"Properties","text":""},{"location":"blood_press_diast/#aliases","title":"Aliases","text":""},{"location":"blood_press_diast/#examples","title":"Examples","text":"Value"},{"location":"blood_press_diast/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"blood_press_diast/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"blood_press_diast/#schema-source","title":"Schema Source","text":""},{"location":"blood_press_diast/#linkml-source","title":"LinkML Source","text":"
name: blood_press_diast\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter mercury\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Resting diastolic blood pressure, measured as mm mercury\ntitle: host blood pressure diastolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure diastolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000258\nalias: blood_press_diast\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"blood_press_syst/","title":"Slot: host blood pressure systolic (blood_press_syst)","text":"

Resting systolic blood pressure, measured as mm mercury

URI: MIXS:0000259

"},{"location":"blood_press_syst/#inheritance","title":"Inheritance","text":""},{"location":"blood_press_syst/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"blood_press_syst/#properties","title":"Properties","text":""},{"location":"blood_press_syst/#aliases","title":"Aliases","text":""},{"location":"blood_press_syst/#examples","title":"Examples","text":"Value"},{"location":"blood_press_syst/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"blood_press_syst/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"blood_press_syst/#schema-source","title":"Schema Source","text":""},{"location":"blood_press_syst/#linkml-source","title":"LinkML Source","text":"
name: blood_press_syst\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter mercury\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Resting systolic blood pressure, measured as mm mercury\ntitle: host blood pressure systolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure systolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000259\nalias: blood_press_syst\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"bromide/","title":"Slot: bromide (bromide)","text":"

Concentration of bromide

URI: MIXS:0000176

"},{"location":"bromide/#inheritance","title":"Inheritance","text":""},{"location":"bromide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bromide/#properties","title":"Properties","text":""},{"location":"bromide/#aliases","title":"Aliases","text":""},{"location":"bromide/#examples","title":"Examples","text":"Value 0.05 parts per million"},{"location":"bromide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bromide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bromide/#schema-source","title":"Schema Source","text":""},{"location":"bromide/#linkml-source","title":"LinkML Source","text":"
name: bromide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of bromide\ntitle: bromide\nexamples:\n- value: 0.05 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bromide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000176\nalias: bromide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"build_docs/","title":"Slot: design, construction, and operation documents (build_docs)","text":"

The building design, construction and operation documents

URI: MIXS:0000787

"},{"location":"build_docs/#inheritance","title":"Inheritance","text":""},{"location":"build_docs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"build_docs/#properties","title":"Properties","text":""},{"location":"build_docs/#aliases","title":"Aliases","text":""},{"location":"build_docs/#examples","title":"Examples","text":"Value maintenance plans"},{"location":"build_docs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"build_docs/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"build_docs/#schema-source","title":"Schema Source","text":""},{"location":"build_docs/#linkml-source","title":"LinkML Source","text":"
name: build_docs\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The building design, construction and operation documents\ntitle: design, construction, and operation documents\nexamples:\n- value: maintenance plans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- design, construction, and operation documents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000787\nalias: build_docs\ndomain_of:\n- Biosample\nrange: build_docs_enum\nmultivalued: false\n\n
"},{"location":"build_occup_type/","title":"Slot: building occupancy type (build_occup_type)","text":"

The primary function for which a building or discrete part of a building is intended to be used

URI: MIXS:0000761

"},{"location":"build_occup_type/#inheritance","title":"Inheritance","text":""},{"location":"build_occup_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"build_occup_type/#properties","title":"Properties","text":""},{"location":"build_occup_type/#aliases","title":"Aliases","text":""},{"location":"build_occup_type/#examples","title":"Examples","text":"Value market"},{"location":"build_occup_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"build_occup_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"build_occup_type/#schema-source","title":"Schema Source","text":""},{"location":"build_occup_type/#linkml-source","title":"LinkML Source","text":"
name: build_occup_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: The primary function for which a building or discrete part of a building\n  is intended to be used\ntitle: building occupancy type\nexamples:\n- value: market\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building occupancy type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000761\nalias: build_occup_type\ndomain_of:\n- Biosample\nrange: build_occup_type_enum\nmultivalued: true\n\n
"},{"location":"building_setting/","title":"Slot: building setting (building_setting)","text":"

A location (geography) where a building is set

URI: MIXS:0000768

"},{"location":"building_setting/#inheritance","title":"Inheritance","text":""},{"location":"building_setting/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"building_setting/#properties","title":"Properties","text":""},{"location":"building_setting/#aliases","title":"Aliases","text":""},{"location":"building_setting/#examples","title":"Examples","text":"Value rural"},{"location":"building_setting/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"building_setting/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"building_setting/#schema-source","title":"Schema Source","text":""},{"location":"building_setting/#linkml-source","title":"LinkML Source","text":"
name: building_setting\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A location (geography) where a building is set\ntitle: building setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building setting\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000768\nalias: building_setting\ndomain_of:\n- Biosample\nrange: building_setting_enum\nmultivalued: false\n\n
"},{"location":"built_struc_age/","title":"Slot: built structure age (built_struc_age)","text":"

The age of the built structure since construction

URI: MIXS:0000145

"},{"location":"built_struc_age/#inheritance","title":"Inheritance","text":""},{"location":"built_struc_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"built_struc_age/#properties","title":"Properties","text":""},{"location":"built_struc_age/#aliases","title":"Aliases","text":""},{"location":"built_struc_age/#examples","title":"Examples","text":"Value 15"},{"location":"built_struc_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"built_struc_age/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"built_struc_age/#schema-source","title":"Schema Source","text":""},{"location":"built_struc_age/#linkml-source","title":"LinkML Source","text":"
name: built_struc_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: year\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The age of the built structure since construction\ntitle: built structure age\nexamples:\n- value: '15'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000145\nalias: built_struc_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"built_struc_set/","title":"Slot: built structure setting (built_struc_set)","text":"

The characterization of the location of the built structure as high or low human density

URI: MIXS:0000778

"},{"location":"built_struc_set/#inheritance","title":"Inheritance","text":""},{"location":"built_struc_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"built_struc_set/#properties","title":"Properties","text":""},{"location":"built_struc_set/#aliases","title":"Aliases","text":""},{"location":"built_struc_set/#examples","title":"Examples","text":"Value rural"},{"location":"built_struc_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"built_struc_set/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"built_struc_set/#schema-source","title":"Schema Source","text":""},{"location":"built_struc_set/#linkml-source","title":"LinkML Source","text":"
name: built_struc_set\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The characterization of the location of the built structure as high or\n  low human density\ntitle: built structure setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure setting\nrank: 1000\nis_a: core field\nstring_serialization: '[urban|rural]'\nslot_uri: MIXS:0000778\nalias: built_struc_set\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"built_struc_type/","title":"Slot: built structure type (built_struc_type)","text":"

A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads

URI: MIXS:0000721

"},{"location":"built_struc_type/#inheritance","title":"Inheritance","text":""},{"location":"built_struc_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"built_struc_type/#properties","title":"Properties","text":""},{"location":"built_struc_type/#aliases","title":"Aliases","text":""},{"location":"built_struc_type/#examples","title":"Examples","text":"Value"},{"location":"built_struc_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"built_struc_type/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"built_struc_type/#schema-source","title":"Schema Source","text":""},{"location":"built_struc_type/#linkml-source","title":"LinkML Source","text":"
name: built_struc_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A physical structure that is a body or assemblage of bodies in space\n  to form a system capable of supporting loads\ntitle: built structure type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000721\nalias: built_struc_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"bulk_elect_conductivity/","title":"Slot: bulk electrical conductivity (bulk_elect_conductivity)","text":"

Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.

URI: nmdc:bulk_elect_conductivity

"},{"location":"bulk_elect_conductivity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bulk_elect_conductivity/#properties","title":"Properties","text":""},{"location":"bulk_elect_conductivity/#examples","title":"Examples","text":"Value JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')"},{"location":"bulk_elect_conductivity/#comments","title":"Comments","text":""},{"location":"bulk_elect_conductivity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bulk_elect_conductivity/#schema-source","title":"Schema Source","text":""},{"location":"bulk_elect_conductivity/#linkml-source","title":"LinkML Source","text":"
name: bulk_elect_conductivity\ndescription: Electrical conductivity is a measure of the ability to carry electric\n  current, which is mostly dictated by the chemistry of and amount of water.\ntitle: bulk electrical conductivity\ncomments:\n- Provide the value output of the field instrument.\nexamples:\n- value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')\n  description: The conductivity measurement was 0.017 millisiemens per centimeter.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bulk_elect_conductivity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"calcium/","title":"Slot: calcium (calcium)","text":"

Concentration of calcium in the sample

URI: MIXS:0000432

"},{"location":"calcium/#inheritance","title":"Inheritance","text":""},{"location":"calcium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"calcium/#properties","title":"Properties","text":""},{"location":"calcium/#aliases","title":"Aliases","text":""},{"location":"calcium/#examples","title":"Examples","text":"Value 0.2 micromole per liter"},{"location":"calcium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calcium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"calcium/#schema-source","title":"Schema Source","text":""},{"location":"calcium/#linkml-source","title":"LinkML Source","text":"
name: calcium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, micromole per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of calcium in the sample\ntitle: calcium\nexamples:\n- value: 0.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- calcium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000432\nalias: calcium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"calibration_object/","title":"Slot: calibration_object","text":"

the file containing calibration data object

URI: nmdc:calibration_object

"},{"location":"calibration_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process no"},{"location":"calibration_object/#properties","title":"Properties","text":""},{"location":"calibration_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calibration_object/#schema-source","title":"Schema Source","text":""},{"location":"calibration_object/#linkml-source","title":"LinkML Source","text":"
name: calibration_object\ndescription: the file containing calibration data object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_object\ndomain_of:\n- CalibrationInformation\nrange: DataObject\n\n
"},{"location":"calibration_set/","title":"Slot: calibration_set","text":"

This property links a database object to the set of calibrations within it.

URI: nmdc:calibration_set

"},{"location":"calibration_set/#inheritance","title":"Inheritance","text":""},{"location":"calibration_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"calibration_set/#properties","title":"Properties","text":""},{"location":"calibration_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calibration_set/#schema-source","title":"Schema Source","text":""},{"location":"calibration_set/#linkml-source","title":"LinkML Source","text":"
name: calibration_set\ndescription: This property links a database object to the set of calibrations within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: calibration_set\ndomain_of:\n- Database\nrange: CalibrationInformation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"calibration_standard/","title":"Slot: calibration_standard","text":"

the reference standard(s) used for calibration

URI: nmdc:calibration_standard

"},{"location":"calibration_standard/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process no"},{"location":"calibration_standard/#properties","title":"Properties","text":""},{"location":"calibration_standard/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calibration_standard/#schema-source","title":"Schema Source","text":""},{"location":"calibration_standard/#linkml-source","title":"LinkML Source","text":"
name: calibration_standard\ndescription: the reference standard(s) used for calibration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_standard\ndomain_of:\n- CalibrationInformation\nrange: CalibrationStandardEnum\n\n
"},{"location":"calibration_target/","title":"Slot: calibration_target","text":"

the target measurement of the calibration

URI: nmdc:calibration_target

"},{"location":"calibration_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process yes"},{"location":"calibration_target/#properties","title":"Properties","text":""},{"location":"calibration_target/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calibration_target/#schema-source","title":"Schema Source","text":""},{"location":"calibration_target/#linkml-source","title":"LinkML Source","text":"
name: calibration_target\ndescription: the target measurement of the calibration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_target\ndomain_of:\n- CalibrationInformation\nrange: CalibrationTargetEnum\n\n
"},{"location":"carb_dioxide/","title":"Slot: carbon dioxide (carb_dioxide)","text":"

Carbon dioxide (gas) amount or concentration at the time of sampling

URI: MIXS:0000097

"},{"location":"carb_dioxide/#inheritance","title":"Inheritance","text":""},{"location":"carb_dioxide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"carb_dioxide/#properties","title":"Properties","text":""},{"location":"carb_dioxide/#aliases","title":"Aliases","text":""},{"location":"carb_dioxide/#examples","title":"Examples","text":"Value 410 parts per million"},{"location":"carb_dioxide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"carb_dioxide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"carb_dioxide/#schema-source","title":"Schema Source","text":""},{"location":"carb_dioxide/#linkml-source","title":"LinkML Source","text":"
name: carb_dioxide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Carbon dioxide (gas) amount or concentration at the time of sampling\ntitle: carbon dioxide\nexamples:\n- value: 410 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000097\nalias: carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"carb_monoxide/","title":"Slot: carbon monoxide (carb_monoxide)","text":"

Carbon monoxide (gas) amount or concentration at the time of sampling

URI: MIXS:0000098

"},{"location":"carb_monoxide/#inheritance","title":"Inheritance","text":""},{"location":"carb_monoxide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"carb_monoxide/#properties","title":"Properties","text":""},{"location":"carb_monoxide/#aliases","title":"Aliases","text":""},{"location":"carb_monoxide/#examples","title":"Examples","text":"Value 0.1 parts per million"},{"location":"carb_monoxide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"carb_monoxide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"carb_monoxide/#schema-source","title":"Schema Source","text":""},{"location":"carb_monoxide/#linkml-source","title":"LinkML Source","text":"
name: carb_monoxide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Carbon monoxide (gas) amount or concentration at the time of sampling\ntitle: carbon monoxide\nexamples:\n- value: 0.1 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon monoxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000098\nalias: carb_monoxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"carb_nitro_ratio/","title":"Slot: carbon/nitrogen ratio (carb_nitro_ratio)","text":"

Ratio of amount or concentrations of carbon to nitrogen

URI: MIXS:0000310

"},{"location":"carb_nitro_ratio/#inheritance","title":"Inheritance","text":""},{"location":"carb_nitro_ratio/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"carb_nitro_ratio/#properties","title":"Properties","text":""},{"location":"carb_nitro_ratio/#aliases","title":"Aliases","text":""},{"location":"carb_nitro_ratio/#examples","title":"Examples","text":"Value 0.417361111"},{"location":"carb_nitro_ratio/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"carb_nitro_ratio/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"carb_nitro_ratio/#schema-source","title":"Schema Source","text":""},{"location":"carb_nitro_ratio/#linkml-source","title":"LinkML Source","text":"
name: carb_nitro_ratio\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Ratio of amount or concentrations of carbon to nitrogen\ntitle: carbon/nitrogen ratio\nexamples:\n- value: '0.417361111'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon/nitrogen ratio\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000310\nalias: carb_nitro_ratio\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ceil_area/","title":"Slot: ceiling area (ceil_area)","text":"

The area of the ceiling space within the room

URI: MIXS:0000148

"},{"location":"ceil_area/#inheritance","title":"Inheritance","text":""},{"location":"ceil_area/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_area/#properties","title":"Properties","text":""},{"location":"ceil_area/#aliases","title":"Aliases","text":""},{"location":"ceil_area/#examples","title":"Examples","text":"Value 25 square meter"},{"location":"ceil_area/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_area/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ceil_area/#schema-source","title":"Schema Source","text":""},{"location":"ceil_area/#linkml-source","title":"LinkML Source","text":"
name: ceil_area\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The area of the ceiling space within the room\ntitle: ceiling area\nexamples:\n- value: 25 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000148\nalias: ceil_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ceil_cond/","title":"Slot: ceiling condition (ceil_cond)","text":"

The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas

URI: MIXS:0000779

"},{"location":"ceil_cond/#inheritance","title":"Inheritance","text":""},{"location":"ceil_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_cond/#properties","title":"Properties","text":""},{"location":"ceil_cond/#aliases","title":"Aliases","text":""},{"location":"ceil_cond/#examples","title":"Examples","text":"Value damaged"},{"location":"ceil_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_cond/#schema-source","title":"Schema Source","text":""},{"location":"ceil_cond/#linkml-source","title":"LinkML Source","text":"
name: ceil_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the ceiling at the time of sampling; photos\n  or video preferred; use drawings to indicate location of damaged areas\ntitle: ceiling condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000779\nalias: ceil_cond\ndomain_of:\n- Biosample\nrange: ceil_cond_enum\nmultivalued: false\n\n
"},{"location":"ceil_finish_mat/","title":"Slot: ceiling finish material (ceil_finish_mat)","text":"

The type of material used to finish a ceiling

URI: MIXS:0000780

"},{"location":"ceil_finish_mat/#inheritance","title":"Inheritance","text":""},{"location":"ceil_finish_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_finish_mat/#properties","title":"Properties","text":""},{"location":"ceil_finish_mat/#aliases","title":"Aliases","text":""},{"location":"ceil_finish_mat/#examples","title":"Examples","text":"Value stucco"},{"location":"ceil_finish_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_finish_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_finish_mat/#schema-source","title":"Schema Source","text":""},{"location":"ceil_finish_mat/#linkml-source","title":"LinkML Source","text":"
name: ceil_finish_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of material used to finish a ceiling\ntitle: ceiling finish material\nexamples:\n- value: stucco\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000780\nalias: ceil_finish_mat\ndomain_of:\n- Biosample\nrange: ceil_finish_mat_enum\nmultivalued: false\n\n
"},{"location":"ceil_struc/","title":"Slot: ceiling structure (ceil_struc)","text":"

The construction format of the ceiling

URI: MIXS:0000782

"},{"location":"ceil_struc/#inheritance","title":"Inheritance","text":""},{"location":"ceil_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_struc/#properties","title":"Properties","text":""},{"location":"ceil_struc/#aliases","title":"Aliases","text":""},{"location":"ceil_struc/#examples","title":"Examples","text":"Value concrete"},{"location":"ceil_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_struc/#schema-source","title":"Schema Source","text":""},{"location":"ceil_struc/#linkml-source","title":"LinkML Source","text":"
name: ceil_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The construction format of the ceiling\ntitle: ceiling structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling structure\nrank: 1000\nis_a: core field\nstring_serialization: '[wood frame|concrete]'\nslot_uri: MIXS:0000782\nalias: ceil_struc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ceil_texture/","title":"Slot: ceiling texture (ceil_texture)","text":"

The feel, appearance, or consistency of a ceiling surface

URI: MIXS:0000783

"},{"location":"ceil_texture/#inheritance","title":"Inheritance","text":""},{"location":"ceil_texture/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_texture/#properties","title":"Properties","text":""},{"location":"ceil_texture/#aliases","title":"Aliases","text":""},{"location":"ceil_texture/#examples","title":"Examples","text":"Value popcorn"},{"location":"ceil_texture/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_texture/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_texture/#schema-source","title":"Schema Source","text":""},{"location":"ceil_texture/#linkml-source","title":"LinkML Source","text":"
name: ceil_texture\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The feel, appearance, or consistency of a ceiling surface\ntitle: ceiling texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000783\nalias: ceil_texture\ndomain_of:\n- Biosample\nrange: ceil_texture_enum\nmultivalued: false\n\n
"},{"location":"ceil_thermal_mass/","title":"Slot: ceiling thermal mass (ceil_thermal_mass)","text":"

The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow

URI: MIXS:0000143

"},{"location":"ceil_thermal_mass/#inheritance","title":"Inheritance","text":""},{"location":"ceil_thermal_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_thermal_mass/#properties","title":"Properties","text":""},{"location":"ceil_thermal_mass/#aliases","title":"Aliases","text":""},{"location":"ceil_thermal_mass/#examples","title":"Examples","text":"Value"},{"location":"ceil_thermal_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_thermal_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ceil_thermal_mass/#schema-source","title":"Schema Source","text":""},{"location":"ceil_thermal_mass/#linkml-source","title":"LinkML Source","text":"
name: ceil_thermal_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: joule per degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The ability of the ceiling to provide inertia against temperature fluctuations.\n  Generally this means concrete that is exposed. A metal deck that supports a concrete\n  slab will act thermally as long as it is exposed to room air flow\ntitle: ceiling thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000143\nalias: ceil_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ceil_type/","title":"Slot: ceiling type (ceil_type)","text":"

The type of ceiling according to the ceiling's appearance or construction

URI: MIXS:0000784

"},{"location":"ceil_type/#inheritance","title":"Inheritance","text":""},{"location":"ceil_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_type/#properties","title":"Properties","text":""},{"location":"ceil_type/#aliases","title":"Aliases","text":""},{"location":"ceil_type/#examples","title":"Examples","text":"Value coffered"},{"location":"ceil_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_type/#schema-source","title":"Schema Source","text":""},{"location":"ceil_type/#linkml-source","title":"LinkML Source","text":"
name: ceil_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of ceiling according to the ceiling's appearance or construction\ntitle: ceiling type\nexamples:\n- value: coffered\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000784\nalias: ceil_type\ndomain_of:\n- Biosample\nrange: ceil_type_enum\nmultivalued: false\n\n
"},{"location":"ceil_water_mold/","title":"Slot: ceiling signs of water/mold (ceil_water_mold)","text":"

Signs of the presence of mold or mildew on the ceiling

URI: MIXS:0000781

"},{"location":"ceil_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"ceil_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_water_mold/#properties","title":"Properties","text":""},{"location":"ceil_water_mold/#aliases","title":"Aliases","text":""},{"location":"ceil_water_mold/#examples","title":"Examples","text":"Value presence of mold visible"},{"location":"ceil_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"ceil_water_mold/#linkml-source","title":"LinkML Source","text":"
name: ceil_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on the ceiling\ntitle: ceiling signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000781\nalias: ceil_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"chem_administration/","title":"Slot: chemical administration (chem_administration)","text":"

List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi

URI: MIXS:0000751

"},{"location":"chem_administration/#inheritance","title":"Inheritance","text":""},{"location":"chem_administration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_administration/#properties","title":"Properties","text":""},{"location":"chem_administration/#aliases","title":"Aliases","text":""},{"location":"chem_administration/#examples","title":"Examples","text":"Value agar [CHEBI:2509];2018-05-11T20:00Z"},{"location":"chem_administration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_administration/#annotations","title":"Annotations","text":"property value expected_value CHEBI;timestamp"},{"location":"chem_administration/#schema-source","title":"Schema Source","text":""},{"location":"chem_administration/#linkml-source","title":"LinkML Source","text":"
name: chem_administration\nannotations:\n  expected_value:\n    tag: expected_value\n    value: CHEBI;timestamp\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: List of chemical compounds administered to the host or site where sampling\n  occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple\n  compounds. For chemical entities of biological interest ontology (chebi) (v 163),\n  http://purl.bioontology.org/ontology/chebi\ntitle: chemical administration\nexamples:\n- value: agar [CHEBI:2509];2018-05-11T20:00Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical administration\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]};{timestamp}'\nslot_uri: MIXS:0000751\nalias: chem_administration\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"chem_mutagen/","title":"Slot: chemical mutagen (chem_mutagen)","text":"

Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens

URI: MIXS:0000555

"},{"location":"chem_mutagen/#inheritance","title":"Inheritance","text":""},{"location":"chem_mutagen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_mutagen/#properties","title":"Properties","text":""},{"location":"chem_mutagen/#aliases","title":"Aliases","text":""},{"location":"chem_mutagen/#examples","title":"Examples","text":"Value nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"chem_mutagen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_mutagen/#annotations","title":"Annotations","text":"property value expected_value mutagen name;mutagen amount;treatment interval and duration"},{"location":"chem_mutagen/#schema-source","title":"Schema Source","text":""},{"location":"chem_mutagen/#linkml-source","title":"LinkML Source","text":"
name: chem_mutagen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: mutagen name;mutagen amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Treatment involving use of mutagens; should include the name of mutagen,\n  amount administered, treatment regimen including how many times the treatment was\n  repeated, how long each treatment lasted, and the start and end time of the entire\n  treatment; can include multiple mutagen regimens\ntitle: chemical mutagen\nexamples:\n- value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical mutagen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000555\nalias: chem_mutagen\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"chem_oxygen_dem/","title":"Slot: chemical oxygen demand (chem_oxygen_dem)","text":"

A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite

URI: MIXS:0000656

"},{"location":"chem_oxygen_dem/#inheritance","title":"Inheritance","text":""},{"location":"chem_oxygen_dem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_oxygen_dem/#properties","title":"Properties","text":""},{"location":"chem_oxygen_dem/#aliases","title":"Aliases","text":""},{"location":"chem_oxygen_dem/#examples","title":"Examples","text":"Value"},{"location":"chem_oxygen_dem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_oxygen_dem/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"chem_oxygen_dem/#schema-source","title":"Schema Source","text":""},{"location":"chem_oxygen_dem/#linkml-source","title":"LinkML Source","text":"
name: chem_oxygen_dem\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A measure of the capacity of water to consume oxygen during the decomposition\n  of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite\ntitle: chemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000656\nalias: chem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"chem_treat_method/","title":"Slot: chemical treatment method (chem_treat_method)","text":"

Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)

URI: MIXS:0000457

"},{"location":"chem_treat_method/#inheritance","title":"Inheritance","text":""},{"location":"chem_treat_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_treat_method/#properties","title":"Properties","text":""},{"location":"chem_treat_method/#aliases","title":"Aliases","text":""},{"location":"chem_treat_method/#examples","title":"Examples","text":"Value"},{"location":"chem_treat_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_treat_method/#annotations","title":"Annotations","text":"property value expected_value measurement value;frequency;duration;duration"},{"location":"chem_treat_method/#schema-source","title":"Schema Source","text":""},{"location":"chem_treat_method/#linkml-source","title":"LinkML Source","text":"
name: chem_treat_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;frequency;duration;duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Method of chemical administration(dose, frequency, duration, time elapsed\n  between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)\ntitle: chemical treatment method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\nslot_uri: MIXS:0000457\nalias: chem_treat_method\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"chem_treatment/","title":"Slot: chemical treatment (chem_treatment)","text":"

List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included

URI: MIXS:0001012

"},{"location":"chem_treatment/#inheritance","title":"Inheritance","text":""},{"location":"chem_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_treatment/#properties","title":"Properties","text":""},{"location":"chem_treatment/#aliases","title":"Aliases","text":""},{"location":"chem_treatment/#examples","title":"Examples","text":"Value ACCENT 1125;DOW;2010-11-17"},{"location":"chem_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_treatment/#annotations","title":"Annotations","text":"property value expected_value name;name;timestamp"},{"location":"chem_treatment/#schema-source","title":"Schema Source","text":""},{"location":"chem_treatment/#linkml-source","title":"LinkML Source","text":"
name: chem_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;name;timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of chemical compounds administered upstream the sampling location\n  where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n  demulsifiers, and other production chemicals etc.). The commercial name of the product\n  and name of the supplier should be provided. The date of administration should also\n  be included\ntitle: chemical treatment\nexamples:\n- value: ACCENT 1125;DOW;2010-11-17\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001012\nalias: chem_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"chemical_conversion_category/","title":"Slot: chemical_conversion_category","text":"

The type of chemical conversion process.

URI: nmdc:chemical_conversion_category

"},{"location":"chemical_conversion_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no"},{"location":"chemical_conversion_category/#properties","title":"Properties","text":""},{"location":"chemical_conversion_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chemical_conversion_category/#schema-source","title":"Schema Source","text":""},{"location":"chemical_conversion_category/#linkml-source","title":"LinkML Source","text":"
name: chemical_conversion_category\ndescription: The type of chemical conversion process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_conversion_category\ndomain_of:\n- ChemicalConversionProcess\nrange: ChemicalConversionCategoryEnum\n\n
"},{"location":"chemical_entity_set/","title":"Slot: chemical_entity_set","text":"

This property links a database object to the set of chemical entities within it.

URI: nmdc:chemical_entity_set

"},{"location":"chemical_entity_set/#inheritance","title":"Inheritance","text":""},{"location":"chemical_entity_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"chemical_entity_set/#properties","title":"Properties","text":""},{"location":"chemical_entity_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chemical_entity_set/#schema-source","title":"Schema Source","text":""},{"location":"chemical_entity_set/#linkml-source","title":"LinkML Source","text":"
name: chemical_entity_set\ndescription: This property links a database object to the set of chemical entities\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: chemical_entity_set\ndomain_of:\n- Database\nrange: ChemicalEntity\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"chemical_formula/","title":"Slot: chemical_formula","text":"

A generic grouping for molecular formulae and empirical formulae

URI: nmdc:chemical_formula

"},{"location":"chemical_formula/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"chemical_formula/#properties","title":"Properties","text":""},{"location":"chemical_formula/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chemical_formula/#schema-source","title":"Schema Source","text":""},{"location":"chemical_formula/#linkml-source","title":"LinkML Source","text":"
name: chemical_formula\ndescription: A generic grouping for molecular formulae and empirical formulae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_formula\ndomain_of:\n- ChemicalEntity\nrange: string\n\n
"},{"location":"chimera_check/","title":"Slot: chimera check software (chimera_check)","text":"

Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.

URI: MIXS:0000052

"},{"location":"chimera_check/#inheritance","title":"Inheritance","text":""},{"location":"chimera_check/#properties","title":"Properties","text":""},{"location":"chimera_check/#aliases","title":"Aliases","text":""},{"location":"chimera_check/#examples","title":"Examples","text":"Value uchime;v4.1;default parameters"},{"location":"chimera_check/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chimera_check/#annotations","title":"Annotations","text":"property value expected_value name and version of software, parameters used"},{"location":"chimera_check/#schema-source","title":"Schema Source","text":""},{"location":"chimera_check/#linkml-source","title":"LinkML Source","text":"
name: chimera_check\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name and version of software, parameters used\ndescription: Tool(s) used for chimera checking, including version number and parameters,\n  to discover and remove chimeric sequences. A chimeric sequence is comprised of two\n  or more phylogenetically distinct parent sequences.\ntitle: chimera check software\nexamples:\n- value: uchime;v4.1;default parameters\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chimera check software\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{software};{version};{parameters}'\nslot_uri: MIXS:0000052\nalias: chimera_check\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"chloride/","title":"Slot: chloride (chloride)","text":"

Concentration of chloride in the sample

URI: MIXS:0000429

"},{"location":"chloride/#inheritance","title":"Inheritance","text":""},{"location":"chloride/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chloride/#properties","title":"Properties","text":""},{"location":"chloride/#aliases","title":"Aliases","text":""},{"location":"chloride/#examples","title":"Examples","text":"Value 5000 milligram per liter"},{"location":"chloride/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chloride/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"chloride/#schema-source","title":"Schema Source","text":""},{"location":"chloride/#linkml-source","title":"LinkML Source","text":"
name: chloride\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of chloride in the sample\ntitle: chloride\nexamples:\n- value: 5000 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chloride\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000429\nalias: chloride\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"chlorophyll/","title":"Slot: chlorophyll (chlorophyll)","text":"

Concentration of chlorophyll

URI: MIXS:0000177

"},{"location":"chlorophyll/#inheritance","title":"Inheritance","text":""},{"location":"chlorophyll/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chlorophyll/#properties","title":"Properties","text":""},{"location":"chlorophyll/#aliases","title":"Aliases","text":""},{"location":"chlorophyll/#examples","title":"Examples","text":"Value 5 milligram per cubic meter"},{"location":"chlorophyll/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chlorophyll/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"chlorophyll/#schema-source","title":"Schema Source","text":""},{"location":"chlorophyll/#linkml-source","title":"LinkML Source","text":"
name: chlorophyll\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter, microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of chlorophyll\ntitle: chlorophyll\nexamples:\n- value: 5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chlorophyll\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000177\nalias: chlorophyll\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"chromatographic_category/","title":"Slot: chromatographic_category","text":"

The type of chromatography used in a process.

URI: nmdc:chromatographic_category

"},{"location":"chromatographic_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no"},{"location":"chromatographic_category/#properties","title":"Properties","text":""},{"location":"chromatographic_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chromatographic_category/#schema-source","title":"Schema Source","text":""},{"location":"chromatographic_category/#linkml-source","title":"LinkML Source","text":"
name: chromatographic_category\ndescription: The type of chromatography used in a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chromatographic_category\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: ChromatographicCategoryEnum\n\n
"},{"location":"climate_environment/","title":"Slot: climate environment (climate_environment)","text":"

Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates

URI: MIXS:0001040

"},{"location":"climate_environment/#inheritance","title":"Inheritance","text":""},{"location":"climate_environment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"climate_environment/#properties","title":"Properties","text":""},{"location":"climate_environment/#aliases","title":"Aliases","text":""},{"location":"climate_environment/#examples","title":"Examples","text":"Value tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"climate_environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"climate_environment/#annotations","title":"Annotations","text":"property value expected_value climate name;treatment interval and duration"},{"location":"climate_environment/#schema-source","title":"Schema Source","text":""},{"location":"climate_environment/#linkml-source","title":"LinkML Source","text":"
name: climate_environment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: climate name;treatment interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Treatment involving an exposure to a particular climate; treatment regimen\n  including how many times the treatment was repeated, how long each treatment lasted,\n  and the start and end time of the entire treatment; can include multiple climates\ntitle: climate environment\nexamples:\n- value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- climate environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001040\nalias: climate_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"collected_from/","title":"Slot: collected_from","text":"

The Site from which a Biosample was collected

URI: nmdc:collected_from

"},{"location":"collected_from/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"collected_from/#properties","title":"Properties","text":""},{"location":"collected_from/#comments","title":"Comments","text":""},{"location":"collected_from/#todos","title":"TODOs","text":""},{"location":"collected_from/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collected_from/#schema-source","title":"Schema Source","text":""},{"location":"collected_from/#linkml-source","title":"LinkML Source","text":"
name: collected_from\ndescription: The Site from which a Biosample was collected\ntodos:\n- add an OBO slot_uri ?\ncomments:\n- this illustrates implementing a Biosample relation with a (binary) slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: collected_from\ndomain_of:\n- Biosample\nrange: FieldResearchSite\n\n
"},{"location":"collecting_biosamples_from_site_set/","title":"Slot: collecting_biosamples_from_site_set","text":"

URI: nmdc:collecting_biosamples_from_site_set

"},{"location":"collecting_biosamples_from_site_set/#inheritance","title":"Inheritance","text":""},{"location":"collecting_biosamples_from_site_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"collecting_biosamples_from_site_set/#properties","title":"Properties","text":""},{"location":"collecting_biosamples_from_site_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collecting_biosamples_from_site_set/#schema-source","title":"Schema Source","text":""},{"location":"collecting_biosamples_from_site_set/#linkml-source","title":"LinkML Source","text":"
name: collecting_biosamples_from_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: collecting_biosamples_from_site_set\ndomain_of:\n- Database\nrange: CollectingBiosamplesFromSite\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"collection_date/","title":"Slot: collection date (collection_date)","text":"

The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant

URI: MIXS:0000011

"},{"location":"collection_date/#inheritance","title":"Inheritance","text":""},{"location":"collection_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_date/#properties","title":"Properties","text":""},{"location":"collection_date/#aliases","title":"Aliases","text":""},{"location":"collection_date/#examples","title":"Examples","text":"Value 2018-05-11T10:00:00+01:00; 2018-05-11"},{"location":"collection_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collection_date/#annotations","title":"Annotations","text":"property value expected_value date and time"},{"location":"collection_date/#schema-source","title":"Schema Source","text":""},{"location":"collection_date/#linkml-source","title":"LinkML Source","text":"
name: collection_date\nannotations:\n  expected_value:\n    tag: expected_value\n    value: date and time\ndescription: 'The time of sampling, either as an instance (single point in time) or\n  interval. In case no exact time is available, the date/time can be right truncated\n  i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n  2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\ntitle: collection date\nexamples:\n- value: 2018-05-11T10:00:00+01:00; 2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- collection date\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000011\nalias: collection_date\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"collection_date_inc/","title":"Slot: incubation collection date (collection_date_inc)","text":"

Date the incubation was harvested/collected/ended. Only relevant for incubation samples.

URI: nmdc:collection_date_inc

"},{"location":"collection_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_date_inc/#properties","title":"Properties","text":""},{"location":"collection_date_inc/#examples","title":"Examples","text":"Value 2021-04-15, 2021-04 and 2021 are all acceptable."},{"location":"collection_date_inc/#comments","title":"Comments","text":""},{"location":"collection_date_inc/#see-also","title":"See Also","text":""},{"location":"collection_date_inc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collection_date_inc/#schema-source","title":"Schema Source","text":""},{"location":"collection_date_inc/#linkml-source","title":"LinkML Source","text":"
name: collection_date_inc\ndescription: Date the incubation was harvested/collected/ended. Only relevant for\n  incubation samples.\ntitle: incubation collection date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n  date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n  all acceptable.\nexamples:\n- value: 2021-04-15, 2021-04 and 2021 are all acceptable.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 2\nstring_serialization: '{date, arbitrary precision}'\nalias: collection_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"collection_time/","title":"Slot: collection time, GMT (collection_time)","text":"

The time of sampling, either as an instance (single point) or interval.

URI: nmdc:collection_time

"},{"location":"collection_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time/#properties","title":"Properties","text":""},{"location":"collection_time/#examples","title":"Examples","text":"Value 13:33 or 13:33:55"},{"location":"collection_time/#comments","title":"Comments","text":""},{"location":"collection_time/#see-also","title":"See Also","text":""},{"location":"collection_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collection_time/#schema-source","title":"Schema Source","text":""},{"location":"collection_time/#linkml-source","title":"LinkML Source","text":"
name: collection_time\ndescription: The time of sampling, either as an instance (single point) or interval.\ntitle: collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n  only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 1\nstring_serialization: '{time, seconds optional}'\nalias: collection_time\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"collection_time_inc/","title":"Slot: incubation collection time, GMT (collection_time_inc)","text":"

Time the incubation was harvested/collected/ended. Only relevant for incubation samples.

URI: nmdc:collection_time_inc

"},{"location":"collection_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time_inc/#properties","title":"Properties","text":""},{"location":"collection_time_inc/#examples","title":"Examples","text":"Value 13:33 or 13:33:55"},{"location":"collection_time_inc/#comments","title":"Comments","text":""},{"location":"collection_time_inc/#see-also","title":"See Also","text":""},{"location":"collection_time_inc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collection_time_inc/#schema-source","title":"Schema Source","text":""},{"location":"collection_time_inc/#linkml-source","title":"LinkML Source","text":"
name: collection_time_inc\ndescription: Time the incubation was harvested/collected/ended. Only relevant for\n  incubation samples.\ntitle: incubation collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n  only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 3\nstring_serialization: '{time, seconds optional}'\nalias: collection_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"community/","title":"Slot: community","text":"

URI: nmdc:community

"},{"location":"community/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"community/#properties","title":"Properties","text":""},{"location":"community/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"community/#schema-source","title":"Schema Source","text":""},{"location":"community/#linkml-source","title":"LinkML Source","text":"
name: community\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: community\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"completeness/","title":"Slot: completeness","text":"

URI: nmdc:completeness

"},{"location":"completeness/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"completeness/#properties","title":"Properties","text":""},{"location":"completeness/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"completeness/#schema-source","title":"Schema Source","text":""},{"location":"completeness/#linkml-source","title":"LinkML Source","text":"
name: completeness\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completeness\ndomain_of:\n- EukEval\n- MagBin\nrange: float\n\n
"},{"location":"completion_date/","title":"Slot: completion_date","text":"

URI: nmdc:completion_date

"},{"location":"completion_date/#properties","title":"Properties","text":""},{"location":"completion_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"completion_date/#schema-source","title":"Schema Source","text":""},{"location":"completion_date/#linkml-source","title":"LinkML Source","text":"
name: completion_date\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completion_date\nrange: string\n\n
"},{"location":"compression_type/","title":"Slot: compression_type","text":"

If provided, specifies the compression type

URI: nmdc:compression_type

"},{"location":"compression_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"compression_type/#properties","title":"Properties","text":""},{"location":"compression_type/#examples","title":"Examples","text":"Value gzip"},{"location":"compression_type/#todos","title":"TODOs","text":""},{"location":"compression_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"compression_type/#schema-source","title":"Schema Source","text":""},{"location":"compression_type/#linkml-source","title":"LinkML Source","text":"
name: compression_type\ndescription: If provided, specifies the compression type\ntodos:\n- consider setting the range to an enum\nexamples:\n- value: gzip\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: compression_type\ndomain_of:\n- DataObject\nrange: string\n\n
"},{"location":"concentration/","title":"Slot: concentration","text":"

The concentration of a substance used in a process

URI: nmdc:concentration

"},{"location":"concentration/#inheritance","title":"Inheritance","text":""},{"location":"concentration/#properties","title":"Properties","text":""},{"location":"concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"concentration/#schema-source","title":"Schema Source","text":""},{"location":"concentration/#linkml-source","title":"LinkML Source","text":"
name: concentration\ndescription: The concentration of a substance used in a process\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: concentration\nrange: QuantityValue\n\n
"},{"location":"conditionings/","title":"Slot: conditionings","text":"

Preliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized.

URI: nmdc:conditionings

"},{"location":"conditionings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"conditionings/#properties","title":"Properties","text":""},{"location":"conditionings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"conditionings/#schema-source","title":"Schema Source","text":""},{"location":"conditionings/#linkml-source","title":"LinkML Source","text":"
name: conditionings\ndescription: Preliminary treatment of either phase with a suitable solution of the\n  other phase (in the absence of main extractable solute(s)) so that when the subsequent\n  equilibration is carried out changes in the (volume) phase ratio or in the concentrations\n  of other components are minimized.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: conditionings\ndomain_of:\n- FiltrationProcess\nrange: string\nmultivalued: true\n\n
"},{"location":"conduc/","title":"Slot: conductivity (conduc)","text":"

Electrical conductivity of water

URI: MIXS:0000692

"},{"location":"conduc/#inheritance","title":"Inheritance","text":""},{"location":"conduc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"conduc/#properties","title":"Properties","text":""},{"location":"conduc/#aliases","title":"Aliases","text":""},{"location":"conduc/#examples","title":"Examples","text":"Value 10 milliSiemens per centimeter"},{"location":"conduc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"conduc/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"conduc/#schema-source","title":"Schema Source","text":""},{"location":"conduc/#linkml-source","title":"LinkML Source","text":"
name: conduc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milliSiemens per centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Electrical conductivity of water\ntitle: conductivity\nexamples:\n- value: 10 milliSiemens per centimeter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- conductivity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000692\nalias: conduc\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"configuration_set/","title":"Slot: configuration_set","text":"

This property links a database object to the set of configurations within it.

URI: nmdc:configuration_set

"},{"location":"configuration_set/#inheritance","title":"Inheritance","text":""},{"location":"configuration_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"configuration_set/#properties","title":"Properties","text":""},{"location":"configuration_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"configuration_set/#schema-source","title":"Schema Source","text":""},{"location":"configuration_set/#linkml-source","title":"LinkML Source","text":"
name: configuration_set\ndescription: This property links a database object to the set of configurations within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: configuration_set\ndomain_of:\n- Database\nrange: Configuration\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"contained_in/","title":"Slot: contained_in","text":"

A type of container.

URI: nmdc:contained_in

"},{"location":"contained_in/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot StorageProcess A planned process with the objective to preserve and protect material entitie... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no"},{"location":"contained_in/#properties","title":"Properties","text":""},{"location":"contained_in/#examples","title":"Examples","text":"Value test tube falcon tube whirlpak"},{"location":"contained_in/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"contained_in/#schema-source","title":"Schema Source","text":""},{"location":"contained_in/#linkml-source","title":"LinkML Source","text":"
name: contained_in\ndescription: A type of container.\nexamples:\n- value: test tube\n- value: falcon tube\n- value: whirlpak\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contained_in\ndomain_of:\n- SubSamplingProcess\n- StorageProcess\nrange: ContainerCategoryEnum\n\n
"},{"location":"container_size/","title":"Slot: container_size","text":"

The volume of the container an analyte is stored in or an activity takes place in

URI: nmdc:container_size

"},{"location":"container_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no"},{"location":"container_size/#properties","title":"Properties","text":""},{"location":"container_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"container_size/#schema-source","title":"Schema Source","text":""},{"location":"container_size/#linkml-source","title":"LinkML Source","text":"
name: container_size\ndescription: The volume of the container an analyte is stored in or an activity takes\n  place in\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: container_size\ndomain_of:\n- SubSamplingProcess\n- FiltrationProcess\nrange: QuantityValue\n\n
"},{"location":"contamination/","title":"Slot: contamination","text":"

URI: nmdc:contamination

"},{"location":"contamination/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"contamination/#properties","title":"Properties","text":""},{"location":"contamination/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"contamination/#schema-source","title":"Schema Source","text":""},{"location":"contamination/#linkml-source","title":"LinkML Source","text":"
name: contamination\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contamination\ndomain_of:\n- EukEval\n- MagBin\nrange: float\n\n
"},{"location":"contig_bp/","title":"Slot: contig_bp","text":"

Total size in bp of all contigs.

URI: nmdc:contig_bp

"},{"location":"contig_bp/#inheritance","title":"Inheritance","text":""},{"location":"contig_bp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"contig_bp/#properties","title":"Properties","text":""},{"location":"contig_bp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"contig_bp/#schema-source","title":"Schema Source","text":""},{"location":"contig_bp/#linkml-source","title":"LinkML Source","text":"
name: contig_bp\ndescription: Total size in bp of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contig_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"contigs/","title":"Slot: contigs","text":"

The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase

URI: nmdc:contigs

"},{"location":"contigs/#inheritance","title":"Inheritance","text":""},{"location":"contigs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"contigs/#properties","title":"Properties","text":""},{"location":"contigs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"contigs/#schema-source","title":"Schema Source","text":""},{"location":"contigs/#linkml-source","title":"LinkML Source","text":"
name: contigs\ndescription: The sum of the (length*log(length)) of all contigs, times some constant.  Increase\n  the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contigs\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"cool_syst_id/","title":"Slot: cooling system identifier (cool_syst_id)","text":"

The cooling system identifier

URI: MIXS:0000785

"},{"location":"cool_syst_id/#inheritance","title":"Inheritance","text":""},{"location":"cool_syst_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"cool_syst_id/#properties","title":"Properties","text":""},{"location":"cool_syst_id/#aliases","title":"Aliases","text":""},{"location":"cool_syst_id/#examples","title":"Examples","text":"Value 12345"},{"location":"cool_syst_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cool_syst_id/#annotations","title":"Annotations","text":"property value expected_value unique identifier"},{"location":"cool_syst_id/#schema-source","title":"Schema Source","text":""},{"location":"cool_syst_id/#linkml-source","title":"LinkML Source","text":"
name: cool_syst_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: unique identifier\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The cooling system identifier\ntitle: cooling system identifier\nexamples:\n- value: '12345'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- cooling system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000785\nalias: cool_syst_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"core_field/","title":"Slot: core_field","text":"

basic fields

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:core_field

"},{"location":"core_field/#inheritance","title":"Inheritance","text":""},{"location":"core_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"core_field/#properties","title":"Properties","text":""},{"location":"core_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core_field/#schema-source","title":"Schema Source","text":""},{"location":"core_field/#linkml-source","title":"LinkML Source","text":"
name: core field\ndescription: basic fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: core_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"count/","title":"Slot: count","text":"

URI: nmdc:count

"},{"location":"count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"count/#properties","title":"Properties","text":""},{"location":"count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"count/#schema-source","title":"Schema Source","text":""},{"location":"count/#linkml-source","title":"LinkML Source","text":"
name: count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: count\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: integer\nrequired: true\n\n
"},{"location":"crop_rotation/","title":"Slot: history/crop rotation (crop_rotation)","text":"

Whether or not crop is rotated, and if yes, rotation schedule

URI: MIXS:0000318

"},{"location":"crop_rotation/#inheritance","title":"Inheritance","text":""},{"location":"crop_rotation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"crop_rotation/#properties","title":"Properties","text":""},{"location":"crop_rotation/#aliases","title":"Aliases","text":""},{"location":"crop_rotation/#examples","title":"Examples","text":"Value yes;R2/2017-01-01/2018-12-31/P6M"},{"location":"crop_rotation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"crop_rotation/#annotations","title":"Annotations","text":"property value expected_value crop rotation status;schedule"},{"location":"crop_rotation/#schema-source","title":"Schema Source","text":""},{"location":"crop_rotation/#linkml-source","title":"LinkML Source","text":"
name: crop_rotation\nannotations:\n  expected_value:\n    tag: expected_value\n    value: crop rotation status;schedule\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Whether or not crop is rotated, and if yes, rotation schedule\ntitle: history/crop rotation\nexamples:\n- value: yes;R2/2017-01-01/2018-12-31/P6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/crop rotation\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000318\nalias: crop_rotation\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ctg_l50/","title":"Slot: ctg_l50","text":"

Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.

URI: nmdc:ctg_l50

"},{"location":"ctg_l50/#inheritance","title":"Inheritance","text":""},{"location":"ctg_l50/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"ctg_l50/#properties","title":"Properties","text":""},{"location":"ctg_l50/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_l50/#schema-source","title":"Schema Source","text":""},{"location":"ctg_l50/#linkml-source","title":"LinkML Source","text":"
name: ctg_l50\ndescription: Given a set of contigs, the L50 is defined as the sequence length of\n  the shortest contig at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_l90/","title":"Slot: ctg_l90","text":"

The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.

URI: nmdc:ctg_l90

"},{"location":"ctg_l90/#inheritance","title":"Inheritance","text":""},{"location":"ctg_l90/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"ctg_l90/#properties","title":"Properties","text":""},{"location":"ctg_l90/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_l90/#schema-source","title":"Schema Source","text":""},{"location":"ctg_l90/#linkml-source","title":"LinkML Source","text":"
name: ctg_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n  length for which the collection of all contigs of that length or longer contains\n  at least 90% of the sum of the lengths of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_logsum/","title":"Slot: ctg_logsum","text":"

Maximum contig length.

URI: nmdc:ctg_logsum

"},{"location":"ctg_logsum/#inheritance","title":"Inheritance","text":""},{"location":"ctg_logsum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"ctg_logsum/#properties","title":"Properties","text":""},{"location":"ctg_logsum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_logsum/#schema-source","title":"Schema Source","text":""},{"location":"ctg_logsum/#linkml-source","title":"LinkML Source","text":"
name: ctg_logsum\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_max/","title":"Slot: ctg_max","text":"

Maximum contig length.

URI: nmdc:ctg_max

"},{"location":"ctg_max/#inheritance","title":"Inheritance","text":""},{"location":"ctg_max/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"ctg_max/#properties","title":"Properties","text":""},{"location":"ctg_max/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_max/#schema-source","title":"Schema Source","text":""},{"location":"ctg_max/#linkml-source","title":"LinkML Source","text":"
name: ctg_max\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_n50/","title":"Slot: ctg_n50","text":"

Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.

URI: nmdc:ctg_n50

"},{"location":"ctg_n50/#inheritance","title":"Inheritance","text":""},{"location":"ctg_n50/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"ctg_n50/#properties","title":"Properties","text":""},{"location":"ctg_n50/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_n50/#schema-source","title":"Schema Source","text":""},{"location":"ctg_n50/#linkml-source","title":"LinkML Source","text":"
name: ctg_n50\ndescription: Given a set of contigs, each with its own length, the N50 count is defined\n  as the smallest number_of_contigs whose length sum makes up half of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_n90/","title":"Slot: ctg_n90","text":"

Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.

URI: nmdc:ctg_n90

"},{"location":"ctg_n90/#inheritance","title":"Inheritance","text":""},{"location":"ctg_n90/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"ctg_n90/#properties","title":"Properties","text":""},{"location":"ctg_n90/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_n90/#schema-source","title":"Schema Source","text":""},{"location":"ctg_n90/#linkml-source","title":"LinkML Source","text":"
name: ctg_n90\ndescription: Given a set of contigs, each with its own length, the N90 count is defined\n  as the smallest number of contigs whose length sum makes up 90% of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_powsum/","title":"Slot: ctg_powsum","text":"

Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).

URI: nmdc:ctg_powsum

"},{"location":"ctg_powsum/#inheritance","title":"Inheritance","text":""},{"location":"ctg_powsum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"ctg_powsum/#properties","title":"Properties","text":""},{"location":"ctg_powsum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_powsum/#schema-source","title":"Schema Source","text":""},{"location":"ctg_powsum/#linkml-source","title":"LinkML Source","text":"
name: ctg_powsum\ndescription: Powersum of all contigs is the same as logsum except that it uses the\n  sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"cult_root_med/","title":"Slot: culture rooting medium (cult_root_med)","text":"

Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.

URI: MIXS:0001041

"},{"location":"cult_root_med/#inheritance","title":"Inheritance","text":""},{"location":"cult_root_med/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"cult_root_med/#properties","title":"Properties","text":""},{"location":"cult_root_med/#aliases","title":"Aliases","text":""},{"location":"cult_root_med/#examples","title":"Examples","text":"Value http://himedialabs.com/TD/PT158.pdf"},{"location":"cult_root_med/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cult_root_med/#annotations","title":"Annotations","text":"property value expected_value name, PMID,DOI or url"},{"location":"cult_root_med/#schema-source","title":"Schema Source","text":""},{"location":"cult_root_med/#linkml-source","title":"LinkML Source","text":"
name: cult_root_med\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name, PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name or reference for the hydroponic or in vitro culture rooting medium;\n  can be the name of a commonly used medium or reference to a specific medium, e.g.\n  Murashige and Skoog medium. If the medium has not been formally published, use the\n  rooting medium descriptors.\ntitle: culture rooting medium\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- culture rooting medium\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001041\nalias: cult_root_med\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"cur_land_use/","title":"Slot: current land use (cur_land_use)","text":"

Present state of sample site

URI: MIXS:0001080

"},{"location":"cur_land_use/#inheritance","title":"Inheritance","text":""},{"location":"cur_land_use/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"cur_land_use/#properties","title":"Properties","text":""},{"location":"cur_land_use/#aliases","title":"Aliases","text":""},{"location":"cur_land_use/#examples","title":"Examples","text":"Value conifers"},{"location":"cur_land_use/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cur_land_use/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"cur_land_use/#schema-source","title":"Schema Source","text":""},{"location":"cur_land_use/#linkml-source","title":"LinkML Source","text":"
name: cur_land_use\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Present state of sample site\ntitle: current land use\nexamples:\n- value: conifers\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current land use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001080\nalias: cur_land_use\ndomain_of:\n- Biosample\nrange: cur_land_use_enum\nmultivalued: false\n\n
"},{"location":"cur_vegetation/","title":"Slot: current vegetation (cur_vegetation)","text":"

Vegetation classification from one or more standard classification systems, or agricultural crop

URI: MIXS:0000312

"},{"location":"cur_vegetation/#inheritance","title":"Inheritance","text":""},{"location":"cur_vegetation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment yes"},{"location":"cur_vegetation/#properties","title":"Properties","text":""},{"location":"cur_vegetation/#aliases","title":"Aliases","text":""},{"location":"cur_vegetation/#examples","title":"Examples","text":"Value"},{"location":"cur_vegetation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cur_vegetation/#annotations","title":"Annotations","text":"property value expected_value current vegetation type"},{"location":"cur_vegetation/#schema-source","title":"Schema Source","text":""},{"location":"cur_vegetation/#linkml-source","title":"LinkML Source","text":"
name: cur_vegetation\nannotations:\n  expected_value:\n    tag: expected_value\n    value: current vegetation type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Vegetation classification from one or more standard classification systems,\n  or agricultural crop\ntitle: current vegetation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000312\nalias: cur_vegetation\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"cur_vegetation_meth/","title":"Slot: current vegetation method (cur_vegetation_meth)","text":"

Reference or method used in vegetation classification

URI: MIXS:0000314

"},{"location":"cur_vegetation_meth/#inheritance","title":"Inheritance","text":""},{"location":"cur_vegetation_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"cur_vegetation_meth/#properties","title":"Properties","text":""},{"location":"cur_vegetation_meth/#aliases","title":"Aliases","text":""},{"location":"cur_vegetation_meth/#examples","title":"Examples","text":"Value"},{"location":"cur_vegetation_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cur_vegetation_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"cur_vegetation_meth/#schema-source","title":"Schema Source","text":""},{"location":"cur_vegetation_meth/#linkml-source","title":"LinkML Source","text":"
name: cur_vegetation_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in vegetation classification\ntitle: current vegetation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000314\nalias: cur_vegetation_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"data_category/","title":"Slot: data_category","text":"

The category of the file, such as instrument data from data generation or processed data from a workflow execution.

URI: nmdc:data_category

"},{"location":"data_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_category/#properties","title":"Properties","text":""},{"location":"data_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"data_category/#schema-source","title":"Schema Source","text":""},{"location":"data_category/#linkml-source","title":"LinkML Source","text":"
name: data_category\ndescription: The category of the file, such as instrument data from data generation\n  or processed data from a workflow execution.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: data_category\ndomain_of:\n- DataObject\nrange: DataCategoryEnum\n\n
"},{"location":"data_generation_set/","title":"Slot: data_generation_set","text":"

This property links a database object to the set of data generations within it.

URI: nmdc:data_generation_set

"},{"location":"data_generation_set/#inheritance","title":"Inheritance","text":""},{"location":"data_generation_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"data_generation_set/#properties","title":"Properties","text":""},{"location":"data_generation_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"data_generation_set/#schema-source","title":"Schema Source","text":""},{"location":"data_generation_set/#linkml-source","title":"LinkML Source","text":"
name: data_generation_set\ndescription: This property links a database object to the set of data generations\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: data_generation_set\ndomain_of:\n- Database\nrange: DataGeneration\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"data_object_set/","title":"Slot: data_object_set","text":"

This property links a database object to the set of data objects within it.

URI: nmdc:data_object_set

"},{"location":"data_object_set/#inheritance","title":"Inheritance","text":""},{"location":"data_object_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"data_object_set/#properties","title":"Properties","text":""},{"location":"data_object_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"data_object_set/#schema-source","title":"Schema Source","text":""},{"location":"data_object_set/#linkml-source","title":"LinkML Source","text":"
name: data_object_set\ndescription: This property links a database object to the set of data objects within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: data_object_set\ndomain_of:\n- Database\nrange: DataObject\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"data_object_type/","title":"Slot: data_object_type","text":"

The type of file represented by the data object.

URI: nmdc:data_object_type

"},{"location":"data_object_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_object_type/#properties","title":"Properties","text":""},{"location":"data_object_type/#examples","title":"Examples","text":"Value FT ICR-MS Analysis Results GC-MS Metabolomics Results"},{"location":"data_object_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"data_object_type/#schema-source","title":"Schema Source","text":""},{"location":"data_object_type/#linkml-source","title":"LinkML Source","text":"
name: data_object_type\ndescription: The type of file represented by the data object.\nexamples:\n- value: FT ICR-MS Analysis Results\n- value: GC-MS Metabolomics Results\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: data_object_type\ndomain_of:\n- DataObject\nrange: FileTypeEnum\n\n
"},{"location":"date_created/","title":"Slot: date_created","text":"

from database class

URI: nmdc:date_created

"},{"location":"date_created/#properties","title":"Properties","text":""},{"location":"date_created/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"date_created/#schema-source","title":"Schema Source","text":""},{"location":"date_created/#linkml-source","title":"LinkML Source","text":"
name: date_created\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: date_created\nrange: string\n\n
"},{"location":"date_last_rain/","title":"Slot: date last rain (date_last_rain)","text":"

The date of the last time it rained

URI: MIXS:0000786

"},{"location":"date_last_rain/#inheritance","title":"Inheritance","text":""},{"location":"date_last_rain/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"date_last_rain/#properties","title":"Properties","text":""},{"location":"date_last_rain/#aliases","title":"Aliases","text":""},{"location":"date_last_rain/#examples","title":"Examples","text":"Value 2018-05-11:T14:30Z"},{"location":"date_last_rain/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"date_last_rain/#annotations","title":"Annotations","text":"property value expected_value timestamp"},{"location":"date_last_rain/#schema-source","title":"Schema Source","text":""},{"location":"date_last_rain/#linkml-source","title":"LinkML Source","text":"
name: date_last_rain\nannotations:\n  expected_value:\n    tag: expected_value\n    value: timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The date of the last time it rained\ntitle: date last rain\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- date last rain\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000786\nalias: date_last_rain\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"density/","title":"Slot: density (density)","text":"

Density of the sample, which is its mass per unit volume (aka volumetric mass density)

URI: MIXS:0000435

"},{"location":"density/#inheritance","title":"Inheritance","text":""},{"location":"density/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"density/#properties","title":"Properties","text":""},{"location":"density/#aliases","title":"Aliases","text":""},{"location":"density/#examples","title":"Examples","text":"Value 1000 kilogram per cubic meter"},{"location":"density/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"density/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"density/#schema-source","title":"Schema Source","text":""},{"location":"density/#linkml-source","title":"LinkML Source","text":"
name: density\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per cubic meter, gram per cubic centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Density of the sample, which is its mass per unit volume (aka volumetric\n  mass density)\ntitle: density\nexamples:\n- value: 1000 kilogram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000435\nalias: density\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"depos_env/","title":"Slot: depositional environment (depos_env)","text":"

Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000992

"},{"location":"depos_env/#inheritance","title":"Inheritance","text":""},{"location":"depos_env/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"depos_env/#properties","title":"Properties","text":""},{"location":"depos_env/#aliases","title":"Aliases","text":""},{"location":"depos_env/#examples","title":"Examples","text":"Value Continental - Alluvial"},{"location":"depos_env/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"depos_env/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"depos_env/#schema-source","title":"Schema Source","text":""},{"location":"depos_env/#linkml-source","title":"LinkML Source","text":"
name: depos_env\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n  If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: depositional environment\nexamples:\n- value: Continental - Alluvial\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000992\nalias: depos_env\ndomain_of:\n- Biosample\nrange: depos_env_enum\nmultivalued: false\n\n
"},{"location":"depth/","title":"Slot: depth (depth)","text":"

The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.

URI: MIXS:0000018

"},{"location":"depth/#inheritance","title":"Inheritance","text":""},{"location":"depth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"depth/#properties","title":"Properties","text":""},{"location":"depth/#aliases","title":"Aliases","text":""},{"location":"depth/#examples","title":"Examples","text":"Value 10 meter"},{"location":"depth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"depth/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"depth/#schema-source","title":"Schema Source","text":""},{"location":"depth/#linkml-source","title":"LinkML Source","text":"
name: depth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\ndescription: The vertical distance below local surface, e.g. for sediment or soil\n  samples depth is measured from sediment or soil surface, respectively. Depth can\n  be reported as an interval for subsurface samples.\ntitle: depth\nexamples:\n- value: 10 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000018\nalias: depth\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"description/","title":"Slot: description","text":"

a human-readable description of a thing

URI: dcterms:description

"},{"location":"description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no ImageValue An attribute value representing an image no Extraction A material separation in which a desired component of an input material is se... no NamedThing a databased entity or concept/class no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no WorkflowExecution Represents an instance of an execution of a particular workflow no Biosample Biological source material which can be characterized by an experiment no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no Configuration A set of parameters that define the actions of a process and is shared among ... no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no Site no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes MetabolomicsAnalysis no ProcessedSample no OntologyClass no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DataObject An object that primarily consists of symbols that represent information yes GeneProduct A molecule encoded by a gene that has an evolved function no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no Instrument A material entity that is designed to perform a function in a scientific inve... no MetatranscriptomeAssembly no ChemicalEntity An atom or molecule that can be represented with a chemical formula no FiltrationProcess The process of segregation of phases; e no MetagenomeSequencing Initial sequencing activity that precedes any analysis no EnvironmentalMaterialTerm no LibraryPreparation no Pooling physical combination of several instances of like material no MaterialEntity no CalibrationInformation A calibration object that is associated with a process no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no DataGeneration The methods and processes used to generate omics data from a biosample or org... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no OrthologyGroup A set of genes or gene products in which all members are orthologous no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no Study A study summarizes the overall goal of a research initiative and outlines the... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no Manifest no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"description/#properties","title":"Properties","text":""},{"location":"description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"description/#schema-source","title":"Schema Source","text":""},{"location":"description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a human-readable description of a thing\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: dcterms:description\nalias: description\ndomain_of:\n- ImageValue\n- NamedThing\nrange: string\n\n
"},{"location":"dew_point/","title":"Slot: dew point (dew_point)","text":"

The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.

URI: MIXS:0000129

"},{"location":"dew_point/#inheritance","title":"Inheritance","text":""},{"location":"dew_point/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dew_point/#properties","title":"Properties","text":""},{"location":"dew_point/#aliases","title":"Aliases","text":""},{"location":"dew_point/#examples","title":"Examples","text":"Value 22 degree Celsius"},{"location":"dew_point/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dew_point/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"dew_point/#schema-source","title":"Schema Source","text":""},{"location":"dew_point/#linkml-source","title":"LinkML Source","text":"
name: dew_point\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The temperature to which a given parcel of humid air must be cooled,\n  at constant barometric pressure, for water vapor to condense into water.\ntitle: dew point\nexamples:\n- value: 22 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000129\nalias: dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diether_lipids/","title":"Slot: diether lipids (diether_lipids)","text":"

Concentration of diether lipids; can include multiple types of diether lipids

URI: MIXS:0000178

"},{"location":"diether_lipids/#inheritance","title":"Inheritance","text":""},{"location":"diether_lipids/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diether_lipids/#properties","title":"Properties","text":""},{"location":"diether_lipids/#aliases","title":"Aliases","text":""},{"location":"diether_lipids/#examples","title":"Examples","text":"Value 0.2 nanogram per liter"},{"location":"diether_lipids/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diether_lipids/#annotations","title":"Annotations","text":"property value expected_value diether lipid name;measurement value"},{"location":"diether_lipids/#schema-source","title":"Schema Source","text":""},{"location":"diether_lipids/#linkml-source","title":"LinkML Source","text":"
name: diether_lipids\nannotations:\n  expected_value:\n    tag: expected_value\n    value: diether lipid name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: nanogram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of diether lipids; can include multiple types of diether\n  lipids\ntitle: diether lipids\nexamples:\n- value: 0.2 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- diether lipids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000178\nalias: diether_lipids\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"direct_infusion_category/","title":"Slot: direct_infusion_category","text":"

used when a processed sample is introduced into a mass spectrometer without chromatographic separation

URI: nmdc:direct_infusion_category

"},{"location":"direct_infusion_category/#properties","title":"Properties","text":""},{"location":"direct_infusion_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"direct_infusion_category/#schema-source","title":"Schema Source","text":""},{"location":"direct_infusion_category/#linkml-source","title":"LinkML Source","text":"
name: direct_infusion_category\ndescription: used when a processed sample is introduced into a mass spectrometer without\n  chromatographic separation\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: direct_infusion_category\nrange: DirectInfusionEnum\n\n
"},{"location":"display_order/","title":"Slot: display_order","text":"

When rendering information, this attribute to specify the order in which the information should be rendered.

URI: nmdc:display_order

"},{"location":"display_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ImageValue An attribute value representing an image no"},{"location":"display_order/#properties","title":"Properties","text":""},{"location":"display_order/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"display_order/#schema-source","title":"Schema Source","text":""},{"location":"display_order/#linkml-source","title":"LinkML Source","text":"
name: display_order\ndescription: When rendering information, this attribute to specify the order in which\n  the information should be rendered.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: display_order\ndomain_of:\n- ImageValue\nrange: integer\n\n
"},{"location":"diss_carb_dioxide/","title":"Slot: dissolved carbon dioxide (diss_carb_dioxide)","text":"

Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample

URI: MIXS:0000436

"},{"location":"diss_carb_dioxide/#inheritance","title":"Inheritance","text":""},{"location":"diss_carb_dioxide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_carb_dioxide/#properties","title":"Properties","text":""},{"location":"diss_carb_dioxide/#aliases","title":"Aliases","text":""},{"location":"diss_carb_dioxide/#examples","title":"Examples","text":"Value 5 milligram per liter"},{"location":"diss_carb_dioxide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_carb_dioxide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_carb_dioxide/#schema-source","title":"Schema Source","text":""},{"location":"diss_carb_dioxide/#linkml-source","title":"LinkML Source","text":"
name: diss_carb_dioxide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved carbon dioxide in the sample or liquid portion\n  of the sample\ntitle: dissolved carbon dioxide\nexamples:\n- value: 5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000436\nalias: diss_carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_hydrogen/","title":"Slot: dissolved hydrogen (diss_hydrogen)","text":"

Concentration of dissolved hydrogen

URI: MIXS:0000179

"},{"location":"diss_hydrogen/#inheritance","title":"Inheritance","text":""},{"location":"diss_hydrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_hydrogen/#properties","title":"Properties","text":""},{"location":"diss_hydrogen/#aliases","title":"Aliases","text":""},{"location":"diss_hydrogen/#examples","title":"Examples","text":"Value 0.3 micromole per liter"},{"location":"diss_hydrogen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_hydrogen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_hydrogen/#schema-source","title":"Schema Source","text":""},{"location":"diss_hydrogen/#linkml-source","title":"LinkML Source","text":"
name: diss_hydrogen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved hydrogen\ntitle: dissolved hydrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved hydrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000179\nalias: diss_hydrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_inorg_carb/","title":"Slot: dissolved inorganic carbon (diss_inorg_carb)","text":"

Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter

URI: MIXS:0000434

"},{"location":"diss_inorg_carb/#inheritance","title":"Inheritance","text":""},{"location":"diss_inorg_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_inorg_carb/#properties","title":"Properties","text":""},{"location":"diss_inorg_carb/#aliases","title":"Aliases","text":""},{"location":"diss_inorg_carb/#examples","title":"Examples","text":"Value 2059 micromole per kilogram"},{"location":"diss_inorg_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_inorg_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_inorg_carb/#schema-source","title":"Schema Source","text":""},{"location":"diss_inorg_carb/#linkml-source","title":"LinkML Source","text":"
name: diss_inorg_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Dissolved inorganic carbon concentration in the sample, typically measured\n  after filtering the sample using a 0.45 micrometer filter\ntitle: dissolved inorganic carbon\nexamples:\n- value: 2059 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000434\nalias: diss_inorg_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_inorg_nitro/","title":"Slot: dissolved inorganic nitrogen (diss_inorg_nitro)","text":"

Concentration of dissolved inorganic nitrogen

URI: MIXS:0000698

"},{"location":"diss_inorg_nitro/#inheritance","title":"Inheritance","text":""},{"location":"diss_inorg_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_inorg_nitro/#properties","title":"Properties","text":""},{"location":"diss_inorg_nitro/#aliases","title":"Aliases","text":""},{"location":"diss_inorg_nitro/#examples","title":"Examples","text":"Value 761 micromole per liter"},{"location":"diss_inorg_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_inorg_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_inorg_nitro/#schema-source","title":"Schema Source","text":""},{"location":"diss_inorg_nitro/#linkml-source","title":"LinkML Source","text":"
name: diss_inorg_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved inorganic nitrogen\ntitle: dissolved inorganic nitrogen\nexamples:\n- value: 761 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000698\nalias: diss_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_inorg_phosp/","title":"Slot: dissolved inorganic phosphorus (diss_inorg_phosp)","text":"

Concentration of dissolved inorganic phosphorus in the sample

URI: MIXS:0000106

"},{"location":"diss_inorg_phosp/#inheritance","title":"Inheritance","text":""},{"location":"diss_inorg_phosp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_inorg_phosp/#properties","title":"Properties","text":""},{"location":"diss_inorg_phosp/#aliases","title":"Aliases","text":""},{"location":"diss_inorg_phosp/#examples","title":"Examples","text":"Value 56.5 micromole per liter"},{"location":"diss_inorg_phosp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_inorg_phosp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_inorg_phosp/#schema-source","title":"Schema Source","text":""},{"location":"diss_inorg_phosp/#linkml-source","title":"LinkML Source","text":"
name: diss_inorg_phosp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved inorganic phosphorus in the sample\ntitle: dissolved inorganic phosphorus\nexamples:\n- value: 56.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000106\nalias: diss_inorg_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_iron/","title":"Slot: dissolved iron (diss_iron)","text":"

Concentration of dissolved iron in the sample

URI: MIXS:0000139

"},{"location":"diss_iron/#inheritance","title":"Inheritance","text":""},{"location":"diss_iron/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_iron/#properties","title":"Properties","text":""},{"location":"diss_iron/#aliases","title":"Aliases","text":""},{"location":"diss_iron/#examples","title":"Examples","text":"Value"},{"location":"diss_iron/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_iron/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_iron/#schema-source","title":"Schema Source","text":""},{"location":"diss_iron/#linkml-source","title":"LinkML Source","text":"
name: diss_iron\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved iron in the sample\ntitle: dissolved iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000139\nalias: diss_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_org_carb/","title":"Slot: dissolved organic carbon (diss_org_carb)","text":"

Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid

URI: MIXS:0000433

"},{"location":"diss_org_carb/#inheritance","title":"Inheritance","text":""},{"location":"diss_org_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_org_carb/#properties","title":"Properties","text":""},{"location":"diss_org_carb/#aliases","title":"Aliases","text":""},{"location":"diss_org_carb/#examples","title":"Examples","text":"Value 197 micromole per liter"},{"location":"diss_org_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_org_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_org_carb/#schema-source","title":"Schema Source","text":""},{"location":"diss_org_carb/#linkml-source","title":"LinkML Source","text":"
name: diss_org_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved organic carbon in the sample, liquid portion\n  of the sample, or aqueous phase of the fluid\ntitle: dissolved organic carbon\nexamples:\n- value: 197 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000433\nalias: diss_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_org_nitro/","title":"Slot: dissolved organic nitrogen (diss_org_nitro)","text":"

Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2

URI: MIXS:0000162

"},{"location":"diss_org_nitro/#inheritance","title":"Inheritance","text":""},{"location":"diss_org_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_org_nitro/#properties","title":"Properties","text":""},{"location":"diss_org_nitro/#aliases","title":"Aliases","text":""},{"location":"diss_org_nitro/#examples","title":"Examples","text":"Value 0.05 micromole per liter"},{"location":"diss_org_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_org_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_org_nitro/#schema-source","title":"Schema Source","text":""},{"location":"diss_org_nitro/#linkml-source","title":"LinkML Source","text":"
name: diss_org_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Dissolved organic nitrogen concentration measured as; total dissolved\n  nitrogen - NH4 - NO3 - NO2\ntitle: dissolved organic nitrogen\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000162\nalias: diss_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_oxygen/","title":"Slot: dissolved oxygen (diss_oxygen)","text":"

Concentration of dissolved oxygen

URI: MIXS:0000119

"},{"location":"diss_oxygen/#inheritance","title":"Inheritance","text":""},{"location":"diss_oxygen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_oxygen/#properties","title":"Properties","text":""},{"location":"diss_oxygen/#aliases","title":"Aliases","text":""},{"location":"diss_oxygen/#examples","title":"Examples","text":"Value 175 micromole per kilogram"},{"location":"diss_oxygen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_oxygen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_oxygen/#schema-source","title":"Schema Source","text":""},{"location":"diss_oxygen/#linkml-source","title":"LinkML Source","text":"
name: diss_oxygen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per kilogram, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved oxygen\ntitle: dissolved oxygen\nexamples:\n- value: 175 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000119\nalias: diss_oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_oxygen_fluid/","title":"Slot: dissolved oxygen in fluids (diss_oxygen_fluid)","text":"

Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).

URI: MIXS:0000438

"},{"location":"diss_oxygen_fluid/#inheritance","title":"Inheritance","text":""},{"location":"diss_oxygen_fluid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_oxygen_fluid/#properties","title":"Properties","text":""},{"location":"diss_oxygen_fluid/#aliases","title":"Aliases","text":""},{"location":"diss_oxygen_fluid/#examples","title":"Examples","text":"Value"},{"location":"diss_oxygen_fluid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_oxygen_fluid/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_oxygen_fluid/#schema-source","title":"Schema Source","text":""},{"location":"diss_oxygen_fluid/#linkml-source","title":"LinkML Source","text":"
name: diss_oxygen_fluid\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per kilogram, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved oxygen in the oil field produced fluids as\n  it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\ntitle: dissolved oxygen in fluids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen in fluids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000438\nalias: diss_oxygen_fluid\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"dna_absorb1/","title":"Slot: DNA absorbance 260/280 (dna_absorb1)","text":"

260/280 measurement of DNA sample purity

URI: nmdc:dna_absorb1

"},{"location":"dna_absorb1/#inheritance","title":"Inheritance","text":""},{"location":"dna_absorb1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no ProcessedSample no"},{"location":"dna_absorb1/#properties","title":"Properties","text":""},{"location":"dna_absorb1/#examples","title":"Examples","text":"Value 2.02"},{"location":"dna_absorb1/#comments","title":"Comments","text":""},{"location":"dna_absorb1/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_absorb1/#schema-source","title":"Schema Source","text":""},{"location":"dna_absorb1/#linkml-source","title":"LinkML Source","text":"
name: dna_absorb1\ndescription: 260/280 measurement of DNA sample purity\ntitle: DNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nis_a: biomaterial_purity\nalias: dna_absorb1\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\n
"},{"location":"dna_absorb2/","title":"Slot: DNA absorbance 260/230 (dna_absorb2)","text":"

260/230 measurement of DNA sample purity

URI: nmdc:dna_absorb2

"},{"location":"dna_absorb2/#inheritance","title":"Inheritance","text":""},{"location":"dna_absorb2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_absorb2/#properties","title":"Properties","text":""},{"location":"dna_absorb2/#examples","title":"Examples","text":"Value 2.02"},{"location":"dna_absorb2/#comments","title":"Comments","text":""},{"location":"dna_absorb2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_absorb2/#schema-source","title":"Schema Source","text":""},{"location":"dna_absorb2/#linkml-source","title":"LinkML Source","text":"
name: dna_absorb2\ndescription: 260/230 measurement of DNA sample purity\ntitle: DNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nis_a: biomaterial_purity\nalias: dna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\n
"},{"location":"dna_collect_site/","title":"Slot: DNA collection site (dna_collect_site)","text":"

Provide information on the site your DNA sample was collected from

URI: nmdc:dna_collect_site

"},{"location":"dna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_collect_site/#properties","title":"Properties","text":""},{"location":"dna_collect_site/#examples","title":"Examples","text":"Value untreated pond water"},{"location":"dna_collect_site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_collect_site/#schema-source","title":"Schema Source","text":""},{"location":"dna_collect_site/#linkml-source","title":"LinkML Source","text":"
name: dna_collect_site\ndescription: Provide information on the site your DNA sample was collected from\ntitle: DNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: dna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_concentration/","title":"Slot: DNA concentration in ng/ul (dna_concentration)","text":"

URI: nmdc:dna_concentration

"},{"location":"dna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no ProcessedSample no"},{"location":"dna_concentration/#properties","title":"Properties","text":""},{"location":"dna_concentration/#examples","title":"Examples","text":"Value 100"},{"location":"dna_concentration/#comments","title":"Comments","text":""},{"location":"dna_concentration/#see-also","title":"See Also","text":""},{"location":"dna_concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_concentration/#schema-source","title":"Schema Source","text":""},{"location":"dna_concentration/#linkml-source","title":"LinkML Source","text":"
name: dna_concentration\ntitle: DNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n  a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nalias: dna_concentration\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\n
"},{"location":"dna_cont_type/","title":"Slot: DNA container type (dna_cont_type)","text":"

Tube or plate (96-well)

URI: nmdc:dna_cont_type

"},{"location":"dna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_type/#properties","title":"Properties","text":""},{"location":"dna_cont_type/#examples","title":"Examples","text":"Value plate"},{"location":"dna_cont_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_cont_type/#schema-source","title":"Schema Source","text":""},{"location":"dna_cont_type/#linkml-source","title":"LinkML Source","text":"
name: dna_cont_type\ndescription: Tube or plate (96-well)\ntitle: DNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: dna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: JgiContTypeEnum\nrecommended: true\n\n
"},{"location":"dna_cont_well/","title":"Slot: DNA plate position (dna_cont_well)","text":"

URI: nmdc:dna_cont_well

"},{"location":"dna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_well/#properties","title":"Properties","text":""},{"location":"dna_cont_well/#examples","title":"Examples","text":"Value B2"},{"location":"dna_cont_well/#comments","title":"Comments","text":""},{"location":"dna_cont_well/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_cont_well/#schema-source","title":"Schema Source","text":""},{"location":"dna_cont_well/#linkml-source","title":"LinkML Source","text":"
name: dna_cont_well\ntitle: DNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n  validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: dna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\npattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n\n
"},{"location":"dna_container_id/","title":"Slot: DNA container label (dna_container_id)","text":"

URI: nmdc:dna_container_id

"},{"location":"dna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_container_id/#properties","title":"Properties","text":""},{"location":"dna_container_id/#examples","title":"Examples","text":"Value Pond_MT_041618"},{"location":"dna_container_id/#comments","title":"Comments","text":""},{"location":"dna_container_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_container_id/#schema-source","title":"Schema Source","text":""},{"location":"dna_container_id/#linkml-source","title":"LinkML Source","text":"
name: dna_container_id\ntitle: DNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n  plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: dna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_dnase/","title":"Slot: DNase treatment DNA (dna_dnase)","text":"

URI: nmdc:dna_dnase

"},{"location":"dna_dnase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_dnase/#properties","title":"Properties","text":""},{"location":"dna_dnase/#examples","title":"Examples","text":"Value no"},{"location":"dna_dnase/#comments","title":"Comments","text":""},{"location":"dna_dnase/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_dnase/#schema-source","title":"Schema Source","text":""},{"location":"dna_dnase/#linkml-source","title":"LinkML Source","text":"
name: dna_dnase\ntitle: DNase treatment DNA\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nalias: dna_dnase\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: YesNoEnum\nrecommended: true\n\n
"},{"location":"dna_isolate_meth/","title":"Slot: DNA isolation method (dna_isolate_meth)","text":"

Describe the method/protocol/kit used to extract DNA/RNA.

URI: nmdc:dna_isolate_meth

"},{"location":"dna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_isolate_meth/#properties","title":"Properties","text":""},{"location":"dna_isolate_meth/#aliases","title":"Aliases","text":""},{"location":"dna_isolate_meth/#examples","title":"Examples","text":"Value phenol/chloroform extraction"},{"location":"dna_isolate_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_isolate_meth/#schema-source","title":"Schema Source","text":""},{"location":"dna_isolate_meth/#linkml-source","title":"LinkML Source","text":"
name: dna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: DNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Sample Isolation Method\nrank: 16\nstring_serialization: '{text}'\nalias: dna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_organisms/","title":"Slot: DNA expected organisms (dna_organisms)","text":"

List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.

URI: nmdc:dna_organisms

"},{"location":"dna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_organisms/#properties","title":"Properties","text":""},{"location":"dna_organisms/#examples","title":"Examples","text":"Value expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)"},{"location":"dna_organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_organisms/#schema-source","title":"Schema Source","text":""},{"location":"dna_organisms/#linkml-source","title":"LinkML Source","text":"
name: dna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n  as estimated % of the organism in that culture.\ntitle: DNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: dna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_project_contact/","title":"Slot: DNA seq project contact (dna_project_contact)","text":"

URI: nmdc:dna_project_contact

"},{"location":"dna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_project_contact/#properties","title":"Properties","text":""},{"location":"dna_project_contact/#examples","title":"Examples","text":"Value John Jones"},{"location":"dna_project_contact/#comments","title":"Comments","text":""},{"location":"dna_project_contact/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_project_contact/#schema-source","title":"Schema Source","text":""},{"location":"dna_project_contact/#linkml-source","title":"LinkML Source","text":"
name: dna_project_contact\ntitle: DNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: dna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_samp_id/","title":"Slot: DNA sample ID (dna_samp_id)","text":"

URI: nmdc:dna_samp_id

"},{"location":"dna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_samp_id/#properties","title":"Properties","text":""},{"location":"dna_samp_id/#examples","title":"Examples","text":"Value 187654"},{"location":"dna_samp_id/#comments","title":"Comments","text":""},{"location":"dna_samp_id/#todos","title":"TODOs","text":""},{"location":"dna_samp_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_samp_id/#schema-source","title":"Schema Source","text":""},{"location":"dna_samp_id/#linkml-source","title":"LinkML Source","text":"
name: dna_samp_id\ntitle: DNA sample ID\ntodos:\n- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n  have two identifiers. How to force uniqueness? Moot because that column will be\n  prefilled?\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: dna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_sample_format/","title":"Slot: DNA sample format (dna_sample_format)","text":"

Solution in which the DNA sample has been suspended

URI: nmdc:dna_sample_format

"},{"location":"dna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_format/#properties","title":"Properties","text":""},{"location":"dna_sample_format/#examples","title":"Examples","text":"Value Water"},{"location":"dna_sample_format/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_sample_format/#schema-source","title":"Schema Source","text":""},{"location":"dna_sample_format/#linkml-source","title":"LinkML Source","text":"
name: dna_sample_format\ndescription: Solution in which the DNA sample has been suspended\ntitle: DNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: dna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: DNASampleFormatEnum\nrecommended: true\n\n
"},{"location":"dna_sample_name/","title":"Slot: DNA sample name (dna_sample_name)","text":"

Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.

URI: nmdc:dna_sample_name

"},{"location":"dna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_name/#properties","title":"Properties","text":""},{"location":"dna_sample_name/#examples","title":"Examples","text":"Value JGI_pond_041618"},{"location":"dna_sample_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_sample_name/#schema-source","title":"Schema Source","text":""},{"location":"dna_sample_name/#linkml-source","title":"LinkML Source","text":"
name: dna_sample_name\ndescription: Give the DNA sample a name that is meaningful to you. Sample names must\n  be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: DNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: dna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_seq_project/","title":"Slot: DNA seq project ID (dna_seq_project)","text":"

URI: nmdc:dna_seq_project

"},{"location":"dna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project/#properties","title":"Properties","text":""},{"location":"dna_seq_project/#aliases","title":"Aliases","text":""},{"location":"dna_seq_project/#examples","title":"Examples","text":"Value 1191234"},{"location":"dna_seq_project/#comments","title":"Comments","text":""},{"location":"dna_seq_project/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_seq_project/#schema-source","title":"Schema Source","text":""},{"location":"dna_seq_project/#linkml-source","title":"LinkML Source","text":"
name: dna_seq_project\ntitle: DNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Seq Project ID\nrank: 1\nstring_serialization: '{text}'\nalias: dna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_seq_project_name/","title":"Slot: DNA seq project name (dna_seq_project_name)","text":"

URI: nmdc:dna_seq_project_name

"},{"location":"dna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_name/#properties","title":"Properties","text":""},{"location":"dna_seq_project_name/#examples","title":"Examples","text":"Value JGI Pond metagenomics"},{"location":"dna_seq_project_name/#comments","title":"Comments","text":""},{"location":"dna_seq_project_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_seq_project_name/#schema-source","title":"Schema Source","text":""},{"location":"dna_seq_project_name/#linkml-source","title":"LinkML Source","text":"
name: dna_seq_project_name\ntitle: DNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: JGI Pond metagenomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: dna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_seq_project_pi/","title":"Slot: DNA seq project PI (dna_seq_project_pi)","text":"

URI: nmdc:dna_seq_project_pi

"},{"location":"dna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_pi/#properties","title":"Properties","text":""},{"location":"dna_seq_project_pi/#examples","title":"Examples","text":"Value Jane Johnson"},{"location":"dna_seq_project_pi/#comments","title":"Comments","text":""},{"location":"dna_seq_project_pi/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_seq_project_pi/#schema-source","title":"Schema Source","text":""},{"location":"dna_seq_project_pi/#linkml-source","title":"LinkML Source","text":"
name: dna_seq_project_pi\ntitle: DNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: dna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_volume/","title":"Slot: DNA volume in ul (dna_volume)","text":"

URI: nmdc:dna_volume

"},{"location":"dna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_volume/#properties","title":"Properties","text":""},{"location":"dna_volume/#examples","title":"Examples","text":"Value 25"},{"location":"dna_volume/#comments","title":"Comments","text":""},{"location":"dna_volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_volume/#schema-source","title":"Schema Source","text":""},{"location":"dna_volume/#linkml-source","title":"LinkML Source","text":"
name: dna_volume\ntitle: DNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n  accepts values < 25, but JGI may refuse to process them unless permission has been\n  granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: dna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\n
"},{"location":"dnase_rna/","title":"Slot: DNase treated (dnase_rna)","text":"

URI: nmdc:dnase_rna

"},{"location":"dnase_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dnase_rna/#properties","title":"Properties","text":""},{"location":"dnase_rna/#aliases","title":"Aliases","text":""},{"location":"dnase_rna/#examples","title":"Examples","text":"Value no"},{"location":"dnase_rna/#comments","title":"Comments","text":""},{"location":"dnase_rna/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dnase_rna/#schema-source","title":"Schema Source","text":""},{"location":"dnase_rna/#linkml-source","title":"LinkML Source","text":"
name: dnase_rna\ntitle: DNase treated\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Was Sample DNAse treated?\nrank: 13\nalias: dnase_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: YesNoEnum\nrecommended: true\n\n
"},{"location":"doi_category/","title":"Slot: doi_category","text":"

The resource type the corresponding doi resolves to.

URI: nmdc:doi_category

"},{"location":"doi_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_category/#properties","title":"Properties","text":""},{"location":"doi_category/#examples","title":"Examples","text":"Value dataset_doi"},{"location":"doi_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"doi_category/#schema-source","title":"Schema Source","text":""},{"location":"doi_category/#linkml-source","title":"LinkML Source","text":"
name: doi_category\ndescription: The resource type the corresponding doi resolves to.\nexamples:\n- value: dataset_doi\n  description: The corresponding DOI is a dataset resource type.\nin_subset:\n- data_portal_subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: doi_category\ndomain_of:\n- Doi\nrange: DoiCategoryEnum\nrequired: true\n\n
"},{"location":"doi_provider/","title":"Slot: doi_provider","text":"

The authority, or organization, the DOI is associated with.

URI: nmdc:doi_provider

"},{"location":"doi_provider/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_provider/#properties","title":"Properties","text":""},{"location":"doi_provider/#examples","title":"Examples","text":"Value ess_dive"},{"location":"doi_provider/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"doi_provider/#schema-source","title":"Schema Source","text":""},{"location":"doi_provider/#linkml-source","title":"LinkML Source","text":"
name: doi_provider\ndescription: The authority, or organization, the DOI is associated with.\nexamples:\n- value: ess_dive\n  description: The corresponding DOI is associated with ESS-DIVE.\nin_subset:\n- data_portal_subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C74932\nrank: 1000\nalias: doi_provider\ndomain_of:\n- Doi\nrange: DoiProviderEnum\n\n
"},{"location":"doi_value/","title":"Slot: doi_value","text":"

A digital object identifier, which is intended to persistantly identify some resource on the web.

URI: nmdc:doi_value

"},{"location":"doi_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_value/#properties","title":"Properties","text":""},{"location":"doi_value/#aliases","title":"Aliases","text":""},{"location":"doi_value/#examples","title":"Examples","text":"Value doi:10.46936/10.25585/60000880"},{"location":"doi_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"doi_value/#schema-source","title":"Schema Source","text":""},{"location":"doi_value/#linkml-source","title":"LinkML Source","text":"
name: doi_value\ndescription: A digital object identifier, which is intended to persistantly identify\n  some resource on the web.\nexamples:\n- value: doi:10.46936/10.25585/60000880\n  description: The DOI links to an electronic document.\nin_subset:\n- data_portal_subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOI\n- digital object identifier\nexact_mappings:\n- OBI:0002110\nnarrow_mappings:\n- edam.data:1188\nrank: 1000\nalias: doi_value\ndomain_of:\n- Doi\nrange: uriorcurie\nrequired: true\npattern: ^doi:10.\\d{2,9}/.*$\n\n
"},{"location":"door_comp_type/","title":"Slot: door type, composite (door_comp_type)","text":"

The composite type of the door

URI: MIXS:0000795

"},{"location":"door_comp_type/#inheritance","title":"Inheritance","text":""},{"location":"door_comp_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_comp_type/#properties","title":"Properties","text":""},{"location":"door_comp_type/#aliases","title":"Aliases","text":""},{"location":"door_comp_type/#examples","title":"Examples","text":"Value revolving"},{"location":"door_comp_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_comp_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_comp_type/#schema-source","title":"Schema Source","text":""},{"location":"door_comp_type/#linkml-source","title":"LinkML Source","text":"
name: door_comp_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The composite type of the door\ntitle: door type, composite\nexamples:\n- value: revolving\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, composite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000795\nalias: door_comp_type\ndomain_of:\n- Biosample\nrange: door_comp_type_enum\nmultivalued: false\n\n
"},{"location":"door_cond/","title":"Slot: door condition (door_cond)","text":"

The phsical condition of the door

URI: MIXS:0000788

"},{"location":"door_cond/#inheritance","title":"Inheritance","text":""},{"location":"door_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_cond/#properties","title":"Properties","text":""},{"location":"door_cond/#aliases","title":"Aliases","text":""},{"location":"door_cond/#examples","title":"Examples","text":"Value new"},{"location":"door_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_cond/#schema-source","title":"Schema Source","text":""},{"location":"door_cond/#linkml-source","title":"LinkML Source","text":"
name: door_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The phsical condition of the door\ntitle: door condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000788\nalias: door_cond\ndomain_of:\n- Biosample\nrange: door_cond_enum\nmultivalued: false\n\n
"},{"location":"door_direct/","title":"Slot: door direction of opening (door_direct)","text":"

The direction the door opens

URI: MIXS:0000789

"},{"location":"door_direct/#inheritance","title":"Inheritance","text":""},{"location":"door_direct/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_direct/#properties","title":"Properties","text":""},{"location":"door_direct/#aliases","title":"Aliases","text":""},{"location":"door_direct/#examples","title":"Examples","text":"Value inward"},{"location":"door_direct/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_direct/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_direct/#schema-source","title":"Schema Source","text":""},{"location":"door_direct/#linkml-source","title":"LinkML Source","text":"
name: door_direct\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The direction the door opens\ntitle: door direction of opening\nexamples:\n- value: inward\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door direction of opening\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000789\nalias: door_direct\ndomain_of:\n- Biosample\nrange: door_direct_enum\nmultivalued: false\n\n
"},{"location":"door_loc/","title":"Slot: door location (door_loc)","text":"

The relative location of the door in the room

URI: MIXS:0000790

"},{"location":"door_loc/#inheritance","title":"Inheritance","text":""},{"location":"door_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_loc/#properties","title":"Properties","text":""},{"location":"door_loc/#aliases","title":"Aliases","text":""},{"location":"door_loc/#examples","title":"Examples","text":"Value north"},{"location":"door_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_loc/#schema-source","title":"Schema Source","text":""},{"location":"door_loc/#linkml-source","title":"LinkML Source","text":"
name: door_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The relative location of the door in the room\ntitle: door location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000790\nalias: door_loc\ndomain_of:\n- Biosample\nrange: door_loc_enum\nmultivalued: false\n\n
"},{"location":"door_mat/","title":"Slot: door material (door_mat)","text":"

The material the door is composed of

URI: MIXS:0000791

"},{"location":"door_mat/#inheritance","title":"Inheritance","text":""},{"location":"door_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_mat/#properties","title":"Properties","text":""},{"location":"door_mat/#aliases","title":"Aliases","text":""},{"location":"door_mat/#examples","title":"Examples","text":"Value wood"},{"location":"door_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_mat/#schema-source","title":"Schema Source","text":""},{"location":"door_mat/#linkml-source","title":"LinkML Source","text":"
name: door_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The material the door is composed of\ntitle: door material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000791\nalias: door_mat\ndomain_of:\n- Biosample\nrange: door_mat_enum\nmultivalued: false\n\n
"},{"location":"door_move/","title":"Slot: door movement (door_move)","text":"

The type of movement of the door

URI: MIXS:0000792

"},{"location":"door_move/#inheritance","title":"Inheritance","text":""},{"location":"door_move/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_move/#properties","title":"Properties","text":""},{"location":"door_move/#aliases","title":"Aliases","text":""},{"location":"door_move/#examples","title":"Examples","text":"Value swinging"},{"location":"door_move/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_move/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_move/#schema-source","title":"Schema Source","text":""},{"location":"door_move/#linkml-source","title":"LinkML Source","text":"
name: door_move\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of movement of the door\ntitle: door movement\nexamples:\n- value: swinging\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door movement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000792\nalias: door_move\ndomain_of:\n- Biosample\nrange: door_move_enum\nmultivalued: false\n\n
"},{"location":"door_size/","title":"Slot: door area or size (door_size)","text":"

The size of the door

URI: MIXS:0000158

"},{"location":"door_size/#inheritance","title":"Inheritance","text":""},{"location":"door_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_size/#properties","title":"Properties","text":""},{"location":"door_size/#aliases","title":"Aliases","text":""},{"location":"door_size/#examples","title":"Examples","text":"Value 2.5 square meter"},{"location":"door_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_size/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"door_size/#schema-source","title":"Schema Source","text":""},{"location":"door_size/#linkml-source","title":"LinkML Source","text":"
name: door_size\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The size of the door\ntitle: door area or size\nexamples:\n- value: 2.5 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door area or size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000158\nalias: door_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"door_type/","title":"Slot: door type (door_type)","text":"

The type of door material

URI: MIXS:0000794

"},{"location":"door_type/#inheritance","title":"Inheritance","text":""},{"location":"door_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_type/#properties","title":"Properties","text":""},{"location":"door_type/#aliases","title":"Aliases","text":""},{"location":"door_type/#examples","title":"Examples","text":"Value wooden"},{"location":"door_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_type/#schema-source","title":"Schema Source","text":""},{"location":"door_type/#linkml-source","title":"LinkML Source","text":"
name: door_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of door material\ntitle: door type\nexamples:\n- value: wooden\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000794\nalias: door_type\ndomain_of:\n- Biosample\nrange: door_type_enum\nmultivalued: false\n\n
"},{"location":"door_type_metal/","title":"Slot: door type, metal (door_type_metal)","text":"

The type of metal door

URI: MIXS:0000796

"},{"location":"door_type_metal/#inheritance","title":"Inheritance","text":""},{"location":"door_type_metal/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_type_metal/#properties","title":"Properties","text":""},{"location":"door_type_metal/#aliases","title":"Aliases","text":""},{"location":"door_type_metal/#examples","title":"Examples","text":"Value hollow"},{"location":"door_type_metal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_type_metal/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_type_metal/#schema-source","title":"Schema Source","text":""},{"location":"door_type_metal/#linkml-source","title":"LinkML Source","text":"
name: door_type_metal\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of metal door\ntitle: door type, metal\nexamples:\n- value: hollow\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, metal\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000796\nalias: door_type_metal\ndomain_of:\n- Biosample\nrange: door_type_metal_enum\nmultivalued: false\n\n
"},{"location":"door_type_wood/","title":"Slot: door type, wood (door_type_wood)","text":"

The type of wood door

URI: MIXS:0000797

"},{"location":"door_type_wood/#inheritance","title":"Inheritance","text":""},{"location":"door_type_wood/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_type_wood/#properties","title":"Properties","text":""},{"location":"door_type_wood/#aliases","title":"Aliases","text":""},{"location":"door_type_wood/#examples","title":"Examples","text":"Value battened"},{"location":"door_type_wood/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_type_wood/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_type_wood/#schema-source","title":"Schema Source","text":""},{"location":"door_type_wood/#linkml-source","title":"LinkML Source","text":"
name: door_type_wood\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of wood door\ntitle: door type, wood\nexamples:\n- value: battened\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, wood\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000797\nalias: door_type_wood\ndomain_of:\n- Biosample\nrange: door_type_wood_enum\nmultivalued: false\n\n
"},{"location":"door_water_mold/","title":"Slot: door signs of water/mold (door_water_mold)","text":"

Signs of the presence of mold or mildew on a door

URI: MIXS:0000793

"},{"location":"door_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"door_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_water_mold/#properties","title":"Properties","text":""},{"location":"door_water_mold/#aliases","title":"Aliases","text":""},{"location":"door_water_mold/#examples","title":"Examples","text":"Value presence of mold visible"},{"location":"door_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"door_water_mold/#linkml-source","title":"LinkML Source","text":"
name: door_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on a door\ntitle: door signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000793\nalias: door_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"down_par/","title":"Slot: downward PAR (down_par)","text":"

Visible waveband radiance and irradiance measurements in the water column

URI: MIXS:0000703

"},{"location":"down_par/#inheritance","title":"Inheritance","text":""},{"location":"down_par/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"down_par/#properties","title":"Properties","text":""},{"location":"down_par/#aliases","title":"Aliases","text":""},{"location":"down_par/#examples","title":"Examples","text":"Value 28.71 microEinstein per square meter per second"},{"location":"down_par/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"down_par/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"down_par/#schema-source","title":"Schema Source","text":""},{"location":"down_par/#linkml-source","title":"LinkML Source","text":"
name: down_par\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microEinstein per square meter per second, microEinstein per square centimeter\n      per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Visible waveband radiance and irradiance measurements in the water column\ntitle: downward PAR\nexamples:\n- value: 28.71 microEinstein per square meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- downward PAR\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000703\nalias: down_par\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"drainage_class/","title":"Slot: drainage classification (drainage_class)","text":"

Drainage classification from a standard system such as the USDA system

URI: MIXS:0001085

"},{"location":"drainage_class/#inheritance","title":"Inheritance","text":""},{"location":"drainage_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"drainage_class/#properties","title":"Properties","text":""},{"location":"drainage_class/#aliases","title":"Aliases","text":""},{"location":"drainage_class/#examples","title":"Examples","text":"Value well"},{"location":"drainage_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drainage_class/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"drainage_class/#schema-source","title":"Schema Source","text":""},{"location":"drainage_class/#linkml-source","title":"LinkML Source","text":"
name: drainage_class\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Drainage classification from a standard system such as the USDA system\ntitle: drainage classification\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drainage classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001085\nalias: drainage_class\ndomain_of:\n- Biosample\nrange: drainage_class_enum\nmultivalued: false\n\n
"},{"location":"drawings/","title":"Slot: drawings (drawings)","text":"

The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents

URI: MIXS:0000798

"},{"location":"drawings/#inheritance","title":"Inheritance","text":""},{"location":"drawings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"drawings/#properties","title":"Properties","text":""},{"location":"drawings/#aliases","title":"Aliases","text":""},{"location":"drawings/#examples","title":"Examples","text":"Value sketch"},{"location":"drawings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drawings/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"drawings/#schema-source","title":"Schema Source","text":""},{"location":"drawings/#linkml-source","title":"LinkML Source","text":"
name: drawings\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The buildings architectural drawings; if design is chosen, indicate phase-conceptual,\n  schematic, design development, and construction documents\ntitle: drawings\nexamples:\n- value: sketch\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drawings\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000798\nalias: drawings\ndomain_of:\n- Biosample\nrange: drawings_enum\nmultivalued: false\n\n
"},{"location":"duration/","title":"Slot: duration","text":"

The elapsed time of an activity.

URI: nmdc:duration

"},{"location":"duration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no"},{"location":"duration/#properties","title":"Properties","text":""},{"location":"duration/#examples","title":"Examples","text":"Value JsonObj(has_numeric_value=2, has_unit='hours')"},{"location":"duration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"duration/#schema-source","title":"Schema Source","text":""},{"location":"duration/#linkml-source","title":"LinkML Source","text":"
name: duration\ndescription: The elapsed time of an activity.\nexamples:\n- value: JsonObj(has_numeric_value=2, has_unit='hours')\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: duration\ndomain_of:\n- MixingProcess\n- DissolvingProcess\n- ChemicalConversionProcess\n- MobilePhaseSegment\nrange: QuantityValue\n\n
"},{"location":"ecosystem/","title":"Slot: ecosystem","text":"

An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.

URI: nmdc:ecosystem

"},{"location":"ecosystem/#inheritance","title":"Inheritance","text":""},{"location":"ecosystem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ecosystem/#properties","title":"Properties","text":""},{"location":"ecosystem/#comments","title":"Comments","text":""},{"location":"ecosystem/#see-also","title":"See Also","text":""},{"location":"ecosystem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem/#linkml-source","title":"LinkML Source","text":"
name: ecosystem\ndescription: An ecosystem is a combination of a physical environment (abiotic factors)\n  and all the organisms (biotic factors) that interact with this environment. Ecosystem\n  is in position 1/5 in a GOLD path.\ncomments:\n- The abiotic factors play a profound role on the type and composition of organisms\n  in a given environment. The GOLD Ecosystem at the top of the five-level classification\n  system is aimed at capturing the broader environment from which an organism or environmental\n  sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated,\n  and Engineered. They represent samples collected from a natural environment or from\n  another organism or from engineered environments like bioreactors respectively.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"ecosystem_category/","title":"Slot: ecosystem_category","text":"

Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.

URI: nmdc:ecosystem_category

"},{"location":"ecosystem_category/#inheritance","title":"Inheritance","text":""},{"location":"ecosystem_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ecosystem_category/#properties","title":"Properties","text":""},{"location":"ecosystem_category/#comments","title":"Comments","text":""},{"location":"ecosystem_category/#see-also","title":"See Also","text":""},{"location":"ecosystem_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem_category/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem_category/#linkml-source","title":"LinkML Source","text":"
name: ecosystem_category\ndescription: Ecosystem categories represent divisions within the ecosystem based on\n  specific characteristics of the environment from where an organism or sample is\n  isolated. Ecosystem category is in position 2/5 in a GOLD path.\ncomments:\n- The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n  Ecosystem categories for Host-associated samples can be individual hosts or phyla\n  and for engineered samples it may be manipulated environments like bioreactors,\n  solid waste etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_category\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"ecosystem_path_id/","title":"Slot: ecosystem_path_id","text":"

A unique id representing the GOLD classifiers associated with a sample.

URI: nmdc:ecosystem_path_id

"},{"location":"ecosystem_path_id/#properties","title":"Properties","text":""},{"location":"ecosystem_path_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem_path_id/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem_path_id/#linkml-source","title":"LinkML Source","text":"
name: ecosystem_path_id\ndescription: A unique id representing the GOLD classifiers associated with a sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ecosystem_path_id\nrange: string\n\n
"},{"location":"ecosystem_subtype/","title":"Slot: ecosystem_subtype","text":"

Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.

URI: nmdc:ecosystem_subtype

"},{"location":"ecosystem_subtype/#inheritance","title":"Inheritance","text":""},{"location":"ecosystem_subtype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ecosystem_subtype/#properties","title":"Properties","text":""},{"location":"ecosystem_subtype/#comments","title":"Comments","text":""},{"location":"ecosystem_subtype/#see-also","title":"See Also","text":""},{"location":"ecosystem_subtype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem_subtype/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem_subtype/#linkml-source","title":"LinkML Source","text":"
name: ecosystem_subtype\ndescription: Ecosystem subtypes represent further subdivision of Ecosystem types into\n  more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.\ncomments:\n- Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for\n  example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem\n  subtype category.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_subtype\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"ecosystem_type/","title":"Slot: ecosystem_type","text":"

Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.

URI: nmdc:ecosystem_type

"},{"location":"ecosystem_type/#inheritance","title":"Inheritance","text":""},{"location":"ecosystem_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ecosystem_type/#properties","title":"Properties","text":""},{"location":"ecosystem_type/#comments","title":"Comments","text":""},{"location":"ecosystem_type/#see-also","title":"See Also","text":""},{"location":"ecosystem_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem_type/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem_type/#linkml-source","title":"LinkML Source","text":"
name: ecosystem_type\ndescription: Ecosystem types represent things having common characteristics within\n  the Ecosystem Category. These common characteristics based grouping is still broad\n  but specific to the characteristics of a given environment. Ecosystem type is in\n  position 3/5 in a GOLD path.\ncomments:\n- The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n  or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air\n  as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n  type can represent Respiratory system, Digestive system, Roots etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_type\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"efficiency_percent/","title":"Slot: efficiency percent (efficiency_percent)","text":"

Percentage of volatile solids removed from the anaerobic digestor

URI: MIXS:0000657

"},{"location":"efficiency_percent/#inheritance","title":"Inheritance","text":""},{"location":"efficiency_percent/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"efficiency_percent/#properties","title":"Properties","text":""},{"location":"efficiency_percent/#aliases","title":"Aliases","text":""},{"location":"efficiency_percent/#examples","title":"Examples","text":"Value"},{"location":"efficiency_percent/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"efficiency_percent/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"efficiency_percent/#schema-source","title":"Schema Source","text":""},{"location":"efficiency_percent/#linkml-source","title":"LinkML Source","text":"
name: efficiency_percent\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Percentage of volatile solids removed from the anaerobic digestor\ntitle: efficiency percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- efficiency percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000657\nalias: efficiency_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"elev/","title":"Slot: elevation (elev)","text":"

Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.

URI: MIXS:0000093

"},{"location":"elev/#inheritance","title":"Inheritance","text":""},{"location":"elev/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment yes"},{"location":"elev/#properties","title":"Properties","text":""},{"location":"elev/#aliases","title":"Aliases","text":""},{"location":"elev/#examples","title":"Examples","text":"Value 100 meter"},{"location":"elev/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"elev/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"elev/#schema-source","title":"Schema Source","text":""},{"location":"elev/#linkml-source","title":"LinkML Source","text":"
name: elev\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\ndescription: Elevation of the sampling site is its height above a fixed reference\n  point, most commonly the mean sea level. Elevation is mainly used when referring\n  to points on the earth's surface, while altitude is used for points above the surface,\n  such as an aircraft in flight or a spacecraft in orbit.\ntitle: elevation\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevation\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000093\nalias: elev\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: float\nmultivalued: false\n\n
"},{"location":"elevator/","title":"Slot: elevator count (elevator)","text":"

The number of elevators within the built structure

URI: MIXS:0000799

"},{"location":"elevator/#inheritance","title":"Inheritance","text":""},{"location":"elevator/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"elevator/#properties","title":"Properties","text":""},{"location":"elevator/#aliases","title":"Aliases","text":""},{"location":"elevator/#examples","title":"Examples","text":"Value 2"},{"location":"elevator/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"elevator/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"elevator/#schema-source","title":"Schema Source","text":""},{"location":"elevator/#linkml-source","title":"LinkML Source","text":"
name: elevator\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of elevators within the built structure\ntitle: elevator count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000799\nalias: elevator\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"eluent_introduction_category/","title":"Slot: eluent_introduction_category","text":"

A high-level categorization for how the processed sample is introduced into a mass spectrometer.

URI: nmdc:eluent_introduction_category

"},{"location":"eluent_introduction_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"eluent_introduction_category/#properties","title":"Properties","text":""},{"location":"eluent_introduction_category/#examples","title":"Examples","text":"Value liquid_chromatography direct_infusion_syringe"},{"location":"eluent_introduction_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"eluent_introduction_category/#schema-source","title":"Schema Source","text":""},{"location":"eluent_introduction_category/#linkml-source","title":"LinkML Source","text":"
name: eluent_introduction_category\ndescription: A high-level categorization for how the processed sample is introduced\n  into a mass spectrometer.\nexamples:\n- value: liquid_chromatography\n- value: direct_infusion_syringe\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: eluent_introduction_category\ndomain_of:\n- MassSpectrometry\nrange: EluentIntroductionCategoryEnum\n\n
"},{"location":"email/","title":"Slot: email","text":"

An email address for an entity such as a person. This should be the primary email address used.

URI: schema:email

"},{"location":"email/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"email/#properties","title":"Properties","text":""},{"location":"email/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"email/#schema-source","title":"Schema Source","text":""},{"location":"email/#linkml-source","title":"LinkML Source","text":"
name: email\ndescription: An email address for an entity such as a person. This should be the primary\n  email address used.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: schema:email\nalias: email\ndomain_of:\n- PersonValue\nrange: string\n\n
"},{"location":"embargoed/","title":"Slot: embargoed","text":"

If true, the data are embargoed and not available for public access.

URI: nmdc:embargoed

"},{"location":"embargoed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"embargoed/#properties","title":"Properties","text":""},{"location":"embargoed/#todos","title":"TODOs","text":""},{"location":"embargoed/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"embargoed/#schema-source","title":"Schema Source","text":""},{"location":"embargoed/#linkml-source","title":"LinkML Source","text":"
name: embargoed\ndescription: If true, the data are embargoed and not available for public access.\ntodos:\n- make this required?\n- first apply to Biosample\n- try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n- applying to a Study may not be granular enough\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: embargoed\ndomain_of:\n- Biosample\nrange: boolean\nrecommended: true\n\n
"},{"location":"emsl_biosample_identifiers/","title":"Slot: EMSL Biosample Identifiers (emsl_biosample_identifiers)","text":"

A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.

URI: nmdc:emsl_biosample_identifiers

"},{"location":"emsl_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"emsl_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"emsl_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"emsl_biosample_identifiers/#todos","title":"TODOs","text":""},{"location":"emsl_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emsl_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"emsl_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: emsl_biosample_identifiers\ndescription: A list of identifiers for the biosample from the EMSL database.  This\n  is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n  EMSL NEXUS database.\ntitle: EMSL Biosample Identifiers\ntodos:\n- removed \"planned\" once NEXUS is online\n- determine real expansion for emsl prefix\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- emsl_identifiers\nalias: emsl_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"emsl_identifiers/","title":"Slot: emsl_identifiers","text":"

URI: nmdc:emsl_identifiers

"},{"location":"emsl_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain emsl_project_identifiers Identifiers that link a NMDC study to the EMSL user facility website hosting ... None Study emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database None Biosample"},{"location":"emsl_identifiers/#properties","title":"Properties","text":""},{"location":"emsl_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emsl_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"emsl_identifiers/#linkml-source","title":"LinkML Source","text":"
name: emsl_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: emsl_identifiers\nrange: string\n\n
"},{"location":"emsl_project_identifiers/","title":"Slot: EMSL Project Identifiers (emsl_project_identifiers)","text":"

Identifiers that link a NMDC study to the EMSL user facility website hosting the project description of an EMSL user project

URI: nmdc:emsl_project_identifiers

"},{"location":"emsl_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"emsl_project_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"emsl_project_identifiers/#properties","title":"Properties","text":""},{"location":"emsl_project_identifiers/#examples","title":"Examples","text":"Value emsl.project:60141"},{"location":"emsl_project_identifiers/#todos","title":"TODOs","text":""},{"location":"emsl_project_identifiers/#see-also","title":"See Also","text":""},{"location":"emsl_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emsl_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"emsl_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: emsl_project_identifiers\ndescription: Identifiers that link a NMDC study to the EMSL user facility website\n  hosting the project description of an EMSL user project\ntitle: EMSL Project Identifiers\ntodos:\n- elaborate on description\nnotes:\n- these identifiers are all currently 5 digits long but that could change in the future\nexamples:\n- value: emsl.project:60141\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-schema/issues/927#issuecomment-1802136437\nrank: 1000\nis_a: study_identifiers\nmixins:\n- emsl_identifiers\nalias: emsl_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^emsl\\.project:[0-9]{5}$\n\n
"},{"location":"emsl_store_temp/","title":"Slot: EMSL sample storage temperature, deg. C (emsl_store_temp)","text":"

The temperature at which the sample should be stored upon delivery to EMSL

URI: nmdc:emsl_store_temp

"},{"location":"emsl_store_temp/#properties","title":"Properties","text":""},{"location":"emsl_store_temp/#examples","title":"Examples","text":"Value -80"},{"location":"emsl_store_temp/#comments","title":"Comments","text":""},{"location":"emsl_store_temp/#todos","title":"TODOs","text":""},{"location":"emsl_store_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emsl_store_temp/#schema-source","title":"Schema Source","text":""},{"location":"emsl_store_temp/#linkml-source","title":"LinkML Source","text":"
name: emsl_store_temp\ndescription: The temperature at which the sample should be stored upon delivery to\n  EMSL\ntitle: EMSL sample storage temperature, deg. C\ntodos:\n- add 'see_alsos' with link to NEXUS info\ncomments:\n- Enter a temperature in celsius. Numeric portion only.\nexamples:\n- value: '-80'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{float}'\nalias: emsl_store_temp\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"emulsions/","title":"Slot: emulsions (emulsions)","text":"

Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types

URI: MIXS:0000660

"},{"location":"emulsions/#inheritance","title":"Inheritance","text":""},{"location":"emulsions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"emulsions/#properties","title":"Properties","text":""},{"location":"emulsions/#aliases","title":"Aliases","text":""},{"location":"emulsions/#examples","title":"Examples","text":"Value"},{"location":"emulsions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emulsions/#annotations","title":"Annotations","text":"property value expected_value emulsion name;measurement value"},{"location":"emulsions/#schema-source","title":"Schema Source","text":""},{"location":"emulsions/#linkml-source","title":"LinkML Source","text":"
name: emulsions\nannotations:\n  expected_value:\n    tag: expected_value\n    value: emulsion name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Amount or concentration of substances such as paints, adhesives, mayonnaise,\n  hair colorants, emulsified oils, etc.; can include multiple emulsion types\ntitle: emulsions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- emulsions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000660\nalias: emulsions\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"encodes/","title":"Slot: encodes","text":"

The gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA

URI: nmdc:encodes

"},{"location":"encodes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"encodes/#properties","title":"Properties","text":""},{"location":"encodes/#todos","title":"TODOs","text":""},{"location":"encodes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"encodes/#schema-source","title":"Schema Source","text":""},{"location":"encodes/#linkml-source","title":"LinkML Source","text":"
name: encodes\ndescription: The gene product encoded by this feature. Typically this is used for\n  a CDS feature or gene feature which will encode a protein. It can also be used by\n  a nc transcript ot gene feature that encoded a ncRNA\ntodos:\n- If we revert Reaction back into the schema, that would be a reasonable domain for\n  this slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: encodes\ndomain_of:\n- GenomeFeature\nrange: GeneProduct\n\n
"},{"location":"end/","title":"Slot: end","text":"

The end of the feature in positive 1-based integer coordinates

URI: nmdc:end

"},{"location":"end/#inheritance","title":"Inheritance","text":""},{"location":"end/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"end/#properties","title":"Properties","text":""},{"location":"end/#comments","title":"Comments","text":""},{"location":"end/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"end/#schema-source","title":"Schema Source","text":""},{"location":"end/#linkml-source","title":"LinkML Source","text":"
name: end\ndescription: The end of the feature in positive 1-based integer coordinates\ncomments:\n- '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n  feature,  end = the position of the end + the length of the landmark feature.\"'\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:end_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: end\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\n
"},{"location":"end_date/","title":"Slot: end_date","text":"

The date on which any process or activity was ended

URI: nmdc:end_date

"},{"location":"end_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... no WorkflowExecution Represents an instance of an execution of a particular workflow no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetabolomicsAnalysis no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAssembly no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no LibraryPreparation no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"end_date/#properties","title":"Properties","text":""},{"location":"end_date/#comments","title":"Comments","text":""},{"location":"end_date/#todos","title":"TODOs","text":""},{"location":"end_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"end_date/#schema-source","title":"Schema Source","text":""},{"location":"end_date/#linkml-source","title":"LinkML Source","text":"
name: end_date\ndescription: The date on which any process or activity was ended\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n  can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: end_date\ndomain_of:\n- PlannedProcess\nrange: string\n\n
"},{"location":"ended_at_time/","title":"Slot: ended_at_time","text":"

URI: nmdc:ended_at_time

"},{"location":"ended_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetaproteomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetatranscriptomeAnnotation no MetatranscriptomeAssembly no"},{"location":"ended_at_time/#properties","title":"Properties","text":""},{"location":"ended_at_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ended_at_time/#schema-source","title":"Schema Source","text":""},{"location":"ended_at_time/#linkml-source","title":"LinkML Source","text":"
name: ended_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n  It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:endedAtTime\nrank: 1000\nalias: ended_at_time\ndomain_of:\n- WorkflowExecution\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\n
"},{"location":"env_broad_scale/","title":"Slot: broad-scale environmental context (env_broad_scale)","text":"

Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS

URI: MIXS:0000012

"},{"location":"env_broad_scale/#inheritance","title":"Inheritance","text":""},{"location":"env_broad_scale/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"env_broad_scale/#properties","title":"Properties","text":""},{"location":"env_broad_scale/#aliases","title":"Aliases","text":""},{"location":"env_broad_scale/#examples","title":"Examples","text":"Value oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean"},{"location":"env_broad_scale/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"env_broad_scale/#annotations","title":"Annotations","text":"property value expected_value The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes."},{"location":"env_broad_scale/#schema-source","title":"Schema Source","text":""},{"location":"env_broad_scale/#linkml-source","title":"LinkML Source","text":"
name: env_broad_scale\nannotations:\n  expected_value:\n    tag: expected_value\n    value: The major environment type(s) where the sample was collected. Recommend\n      subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one\n      or more pipes.\n  tooltip:\n    tag: tooltip\n    value: The biome or major environmental system where the sample or specimen originated.\n      Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment\n      Ontology (ENVO). For host-associated or plant-associated samples, use terms\n      from the UBERON or Plant Ontology to describe the broad anatomical or morphological\n      context\ndescription: 'Report the major environmental system the sample or specimen came from.\n  The system(s) identified should have a coarse spatial grain, to provide the general\n  environmental context of where the sampling was done (e.g. in the desert or a rainforest).\n  We recommend using subclasses of EnvO\u2019s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.\n  EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\ntitle: broad-scale environmental context\nexamples:\n- value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample\n    from the photic zone in middle of the Atlantic Ocean\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- broad-scale environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000012\nalias: env_broad_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"env_local_scale/","title":"Slot: local environmental context (env_local_scale)","text":"

Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.

URI: MIXS:0000013

"},{"location":"env_local_scale/#inheritance","title":"Inheritance","text":""},{"location":"env_local_scale/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"env_local_scale/#properties","title":"Properties","text":""},{"location":"env_local_scale/#aliases","title":"Aliases","text":""},{"location":"env_local_scale/#examples","title":"Examples","text":"Value litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]"},{"location":"env_local_scale/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"env_local_scale/#annotations","title":"Annotations","text":"property value expected_value Environmental entities having causal influences upon the entity at time of sampling."},{"location":"env_local_scale/#schema-source","title":"Schema Source","text":""},{"location":"env_local_scale/#linkml-source","title":"LinkML Source","text":"
name: env_local_scale\nannotations:\n  expected_value:\n    tag: expected_value\n    value: Environmental entities having causal influences upon the entity at time\n      of sampling.\n  tooltip:\n    tag: tooltip\n    value: The specific environmental entities or features near the sample or specimen\n      that significantly influence its characteristics or composition. These entities\n      are typically smaller in scale than the broad environmental context. Values\n      for this field should be countable, material nouns and must be chosen from subclasses\n      of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO).\n      For host-associated or plant-associated samples, use terms from the UBERON or\n      Plant Ontology to describe specific anatomical structures or plant parts.\ndescription: 'Report the entity or entities which are in the sample or specimen\u2019s\n  local vicinity and which you believe have significant causal influences on your\n  sample or specimen. We recommend using EnvO terms which are of smaller spatial grain\n  than your entry for env_broad_scale. Terms, such as anatomical sites, from other\n  OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in\n  this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\ntitle: local environmental context\nexamples:\n- value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from various\n    vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer\n    [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer\n    [ENVO:01000336].'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- local environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000013\nalias: env_local_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"env_medium/","title":"Slot: environmental medium (env_medium)","text":"

Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).

URI: MIXS:0000014

"},{"location":"env_medium/#inheritance","title":"Inheritance","text":""},{"location":"env_medium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"env_medium/#properties","title":"Properties","text":""},{"location":"env_medium/#aliases","title":"Aliases","text":""},{"location":"env_medium/#examples","title":"Examples","text":"Value soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]"},{"location":"env_medium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"env_medium/#annotations","title":"Annotations","text":"property value expected_value The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]."},{"location":"env_medium/#schema-source","title":"Schema Source","text":""},{"location":"env_medium/#linkml-source","title":"LinkML Source","text":"
name: env_medium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: The material displaced by the entity at time of sampling. Recommend subclasses\n      of environmental material [ENVO:00010483].\n  tooltip:\n    tag: tooltip\n    value: The predominant environmental material or substrate that directly surrounds\n      or hosts the sample or specimen at the time of sampling. Choose values from\n      subclasses of the 'environmental material' class [ENVO:00010483] in the Environment\n      Ontology (ENVO). Values for this field should be measurable or mass material\n      nouns, representing continuous environmental materials. For host-associated\n      or plant-associated samples, use terms from the UBERON or Plant Ontology to\n      indicate a tissue, organ, or plant structure\ndescription: 'Report the environmental material(s) immediately surrounding the sample\n  or specimen at the time of sampling. We recommend using subclasses of ''environmental\n  material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about\n  how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n  . Terms from other OBO ontologies are permissible as long as they reference mass/volume\n  nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree,\n  a leaf, a table top).'\ntitle: environmental medium\nexamples:\n- value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the\n    Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck\n    on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental medium\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000014\nalias: env_medium\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"env_package/","title":"Slot: env_package","text":"

MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported

URI: nmdc:env_package

"},{"location":"env_package/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"env_package/#properties","title":"Properties","text":""},{"location":"env_package/#aliases","title":"Aliases","text":""},{"location":"env_package/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"env_package/#schema-source","title":"Schema Source","text":""},{"location":"env_package/#linkml-source","title":"LinkML Source","text":"
name: env_package\ndescription: MIxS extension for reporting of measurements and observations obtained\n  from one or more of the environments where the sample was obtained. All environmental\n  packages listed here are further defined in separate subtables. By giving the name\n  of the environmental package, a selection of fields can be made from the subtables\n  and can be reported\nnotes:\n- no longer in MIxS as of 6.0?\nin_subset:\n- mixs extension\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental package\nrank: 1000\nalias: env_package\ndomain_of:\n- Biosample\nrange: TextValue\n\n
"},{"location":"environment_field/","title":"Slot: environment_field","text":"

field describing environmental aspect of a sample

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:environment_field

"},{"location":"environment_field/#inheritance","title":"Inheritance","text":""},{"location":"environment_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"environment_field/#properties","title":"Properties","text":""},{"location":"environment_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environment_field/#schema-source","title":"Schema Source","text":""},{"location":"environment_field/#linkml-source","title":"LinkML Source","text":"
name: environment field\ndescription: field describing environmental aspect of a sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: environment_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"escalator/","title":"Slot: escalator count (escalator)","text":"

The number of escalators within the built structure

URI: MIXS:0000800

"},{"location":"escalator/#inheritance","title":"Inheritance","text":""},{"location":"escalator/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"escalator/#properties","title":"Properties","text":""},{"location":"escalator/#aliases","title":"Aliases","text":""},{"location":"escalator/#examples","title":"Examples","text":"Value 4"},{"location":"escalator/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"escalator/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"escalator/#schema-source","title":"Schema Source","text":""},{"location":"escalator/#linkml-source","title":"LinkML Source","text":"
name: escalator\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of escalators within the built structure\ntitle: escalator count\nexamples:\n- value: '4'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- escalator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000800\nalias: escalator\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ethylbenzene/","title":"Slot: ethylbenzene (ethylbenzene)","text":"

Concentration of ethylbenzene in the sample

URI: MIXS:0000155

"},{"location":"ethylbenzene/#inheritance","title":"Inheritance","text":""},{"location":"ethylbenzene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ethylbenzene/#properties","title":"Properties","text":""},{"location":"ethylbenzene/#aliases","title":"Aliases","text":""},{"location":"ethylbenzene/#examples","title":"Examples","text":"Value"},{"location":"ethylbenzene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ethylbenzene/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ethylbenzene/#schema-source","title":"Schema Source","text":""},{"location":"ethylbenzene/#linkml-source","title":"LinkML Source","text":"
name: ethylbenzene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of ethylbenzene in the sample\ntitle: ethylbenzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ethylbenzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000155\nalias: ethylbenzene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"etl_software_version/","title":"Slot: etl_software_version","text":"

from database class

URI: nmdc:etl_software_version

"},{"location":"etl_software_version/#properties","title":"Properties","text":""},{"location":"etl_software_version/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"etl_software_version/#schema-source","title":"Schema Source","text":""},{"location":"etl_software_version/#linkml-source","title":"LinkML Source","text":"
name: etl_software_version\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: etl_software_version\nrange: string\n\n
"},{"location":"eukaryotic_evaluation/","title":"Slot: eukaryotic_evaluation","text":"

Contains results from evaluating if a Metagenome-Assembled Genome is of eukaryotic lineage.

URI: nmdc:eukaryotic_evaluation

"},{"location":"eukaryotic_evaluation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"eukaryotic_evaluation/#properties","title":"Properties","text":""},{"location":"eukaryotic_evaluation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"eukaryotic_evaluation/#schema-source","title":"Schema Source","text":""},{"location":"eukaryotic_evaluation/#linkml-source","title":"LinkML Source","text":"
name: eukaryotic_evaluation\ndescription: Contains results from evaluating if a Metagenome-Assembled Genome is\n  of eukaryotic lineage.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: eukaryotic_evaluation\ndomain_of:\n- MagBin\nrange: EukEval\n\n
"},{"location":"execution_resource/","title":"Slot: execution_resource","text":"

The computing resource or facility where the workflow was executed.

URI: nmdc:execution_resource

"},{"location":"execution_resource/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetaproteomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetatranscriptomeAnnotation no MetatranscriptomeAssembly no"},{"location":"execution_resource/#properties","title":"Properties","text":""},{"location":"execution_resource/#examples","title":"Examples","text":"Value NERSC-Cori"},{"location":"execution_resource/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"execution_resource/#schema-source","title":"Schema Source","text":""},{"location":"execution_resource/#linkml-source","title":"LinkML Source","text":"
name: execution_resource\ndescription: The computing resource or facility where the workflow was executed.\nexamples:\n- value: NERSC-Cori\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: execution_resource\ndomain_of:\n- WorkflowExecution\nrange: ExecutionResourceEnum\n\n
"},{"location":"exp_duct/","title":"Slot: exposed ductwork (exp_duct)","text":"

The amount of exposed ductwork in the room

URI: MIXS:0000144

"},{"location":"exp_duct/#inheritance","title":"Inheritance","text":""},{"location":"exp_duct/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"exp_duct/#properties","title":"Properties","text":""},{"location":"exp_duct/#aliases","title":"Aliases","text":""},{"location":"exp_duct/#examples","title":"Examples","text":"Value"},{"location":"exp_duct/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"exp_duct/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"exp_duct/#schema-source","title":"Schema Source","text":""},{"location":"exp_duct/#linkml-source","title":"LinkML Source","text":"
name: exp_duct\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The amount of exposed ductwork in the room\ntitle: exposed ductwork\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed ductwork\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000144\nalias: exp_duct\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"exp_pipe/","title":"Slot: exposed pipes (exp_pipe)","text":"

The number of exposed pipes in the room

URI: MIXS:0000220

"},{"location":"exp_pipe/#inheritance","title":"Inheritance","text":""},{"location":"exp_pipe/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"exp_pipe/#properties","title":"Properties","text":""},{"location":"exp_pipe/#aliases","title":"Aliases","text":""},{"location":"exp_pipe/#examples","title":"Examples","text":"Value"},{"location":"exp_pipe/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"exp_pipe/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"exp_pipe/#schema-source","title":"Schema Source","text":""},{"location":"exp_pipe/#linkml-source","title":"LinkML Source","text":"
name: exp_pipe\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of exposed pipes in the room\ntitle: exposed pipes\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed pipes\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000220\nalias: exp_pipe\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"experimental_factor/","title":"Slot: experimental factor (experimental_factor)","text":"

Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI

URI: MIXS:0000008

"},{"location":"experimental_factor/#inheritance","title":"Inheritance","text":""},{"location":"experimental_factor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"experimental_factor/#properties","title":"Properties","text":""},{"location":"experimental_factor/#aliases","title":"Aliases","text":""},{"location":"experimental_factor/#examples","title":"Examples","text":"Value time series design [EFO:EFO_0001779]"},{"location":"experimental_factor/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"experimental_factor/#annotations","title":"Annotations","text":"property value expected_value text or EFO and/or OBI"},{"location":"experimental_factor/#schema-source","title":"Schema Source","text":""},{"location":"experimental_factor/#linkml-source","title":"LinkML Source","text":"
name: experimental_factor\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text or EFO and/or OBI\ndescription: Experimental factors are essentially the variable aspects of an experiment\n  design which can be used to describe an experiment, or set of experiments, in an\n  increasingly detailed manner. This field accepts ontology terms from Experimental\n  Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a\n  browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n  for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\ntitle: experimental factor\nexamples:\n- value: time series design [EFO:EFO_0001779]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- experimental factor\nrank: 1000\nis_a: investigation field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000008\nalias: experimental_factor\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"experimental_factor_other/","title":"Slot: experimental factor- other (experimental_factor_other)","text":"

Other details about your sample that you feel can't be accurately represented in the available columns.

URI: nmdc:experimental_factor_other

"},{"location":"experimental_factor_other/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"experimental_factor_other/#properties","title":"Properties","text":""},{"location":"experimental_factor_other/#examples","title":"Examples","text":"Value experimental treatment: value"},{"location":"experimental_factor_other/#comments","title":"Comments","text":""},{"location":"experimental_factor_other/#see-also","title":"See Also","text":""},{"location":"experimental_factor_other/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"experimental_factor_other/#schema-source","title":"Schema Source","text":""},{"location":"experimental_factor_other/#linkml-source","title":"LinkML Source","text":"
name: experimental_factor_other\ndescription: Other details about your sample that you feel can't be accurately represented\n  in the available columns.\ntitle: experimental factor- other\ncomments:\n- This slot accepts open-ended text about your sample.\n- We recommend using key:value pairs.\n- Provided pairs will be considered for inclusion as future slots/terms in this data\n  collection template.\nexamples:\n- value: 'experimental treatment: value'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000008\n- MIXS:0000300\nrank: 7\nstring_serialization: '{text}'\nalias: experimental_factor_other\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"ext_door/","title":"Slot: exterior door count (ext_door)","text":"

The number of exterior doors in the built structure

URI: MIXS:0000170

"},{"location":"ext_door/#inheritance","title":"Inheritance","text":""},{"location":"ext_door/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ext_door/#properties","title":"Properties","text":""},{"location":"ext_door/#aliases","title":"Aliases","text":""},{"location":"ext_door/#examples","title":"Examples","text":"Value"},{"location":"ext_door/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ext_door/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"ext_door/#schema-source","title":"Schema Source","text":""},{"location":"ext_door/#linkml-source","title":"LinkML Source","text":"
name: ext_door\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of exterior doors in the built structure\ntitle: exterior door count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exterior door count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000170\nalias: ext_door\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ext_wall_orient/","title":"Slot: orientations of exterior wall (ext_wall_orient)","text":"

The orientation of the exterior wall

URI: MIXS:0000817

"},{"location":"ext_wall_orient/#inheritance","title":"Inheritance","text":""},{"location":"ext_wall_orient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ext_wall_orient/#properties","title":"Properties","text":""},{"location":"ext_wall_orient/#aliases","title":"Aliases","text":""},{"location":"ext_wall_orient/#examples","title":"Examples","text":"Value northwest"},{"location":"ext_wall_orient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ext_wall_orient/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ext_wall_orient/#schema-source","title":"Schema Source","text":""},{"location":"ext_wall_orient/#linkml-source","title":"LinkML Source","text":"
name: ext_wall_orient\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The orientation of the exterior wall\ntitle: orientations of exterior wall\nexamples:\n- value: northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior wall\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000817\nalias: ext_wall_orient\ndomain_of:\n- Biosample\nrange: ext_wall_orient_enum\nmultivalued: false\n\n
"},{"location":"ext_window_orient/","title":"Slot: orientations of exterior window (ext_window_orient)","text":"

The compass direction the exterior window of the room is facing

URI: MIXS:0000818

"},{"location":"ext_window_orient/#inheritance","title":"Inheritance","text":""},{"location":"ext_window_orient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ext_window_orient/#properties","title":"Properties","text":""},{"location":"ext_window_orient/#aliases","title":"Aliases","text":""},{"location":"ext_window_orient/#examples","title":"Examples","text":"Value southwest"},{"location":"ext_window_orient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ext_window_orient/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ext_window_orient/#schema-source","title":"Schema Source","text":""},{"location":"ext_window_orient/#linkml-source","title":"LinkML Source","text":"
name: ext_window_orient\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The compass direction the exterior window of the room is facing\ntitle: orientations of exterior window\nexamples:\n- value: southwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior window\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000818\nalias: ext_window_orient\ndomain_of:\n- Biosample\nrange: ext_window_orient_enum\nmultivalued: false\n\n
"},{"location":"external_database_identifiers/","title":"Slot: external_database_identifiers","text":"

Link to corresponding identifier in external database

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:external_database_identifiers

"},{"location":"external_database_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"external_database_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProcessedSample no"},{"location":"external_database_identifiers/#properties","title":"Properties","text":""},{"location":"external_database_identifiers/#comments","title":"Comments","text":""},{"location":"external_database_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"external_database_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"external_database_identifiers/#linkml-source","title":"LinkML Source","text":"
name: external_database_identifiers\ndescription: Link to corresponding identifier in external database\nnotes:\n- had tried ranges of external identifier and string\ncomments:\n- The value of this field is always a registered CURIE\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- skos:closeMatch\nrank: 1000\nis_a: alternative_identifiers\nabstract: true\nalias: external_database_identifiers\ndomain_of:\n- ProcessedSample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"extraction_targets/","title":"Slot: extraction_targets","text":"

Provides the target biomolecule that has been separated from a sample during an extraction process.

URI: nmdc:extraction_targets

"},{"location":"extraction_targets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"extraction_targets/#properties","title":"Properties","text":""},{"location":"extraction_targets/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"extraction_targets/#schema-source","title":"Schema Source","text":""},{"location":"extraction_targets/#linkml-source","title":"LinkML Source","text":"
name: extraction_targets\ndescription: Provides the target biomolecule that has been separated from a sample\n  during an extraction process.\nnotes:\n- todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)\nfrom_schema: https://w3id.org/nmdc/nmdc\nnarrow_mappings:\n- NCIT:C177560\n- MIXS:0000037\nrank: 1000\nalias: extraction_targets\ndomain_of:\n- Extraction\nrange: ExtractionTargetEnum\nmultivalued: true\n\n
"},{"location":"extreme_event/","title":"Slot: history/extreme events (extreme_event)","text":"

Unusual physical events that may have affected microbial populations

URI: MIXS:0000320

"},{"location":"extreme_event/#inheritance","title":"Inheritance","text":""},{"location":"extreme_event/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"extreme_event/#properties","title":"Properties","text":""},{"location":"extreme_event/#aliases","title":"Aliases","text":""},{"location":"extreme_event/#examples","title":"Examples","text":"Value"},{"location":"extreme_event/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"extreme_event/#annotations","title":"Annotations","text":"property value expected_value date"},{"location":"extreme_event/#schema-source","title":"Schema Source","text":""},{"location":"extreme_event/#linkml-source","title":"LinkML Source","text":"
name: extreme_event\nannotations:\n  expected_value:\n    tag: expected_value\n    value: date\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Unusual physical events that may have affected microbial populations\ntitle: history/extreme events\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/extreme events\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000320\nalias: extreme_event\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"fao_class/","title":"Slot: soil_taxonomic/FAO classification (fao_class)","text":"

Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups

URI: MIXS:0001083

"},{"location":"fao_class/#inheritance","title":"Inheritance","text":""},{"location":"fao_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fao_class/#properties","title":"Properties","text":""},{"location":"fao_class/#aliases","title":"Aliases","text":""},{"location":"fao_class/#examples","title":"Examples","text":"Value Luvisols"},{"location":"fao_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fao_class/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"fao_class/#schema-source","title":"Schema Source","text":""},{"location":"fao_class/#linkml-source","title":"LinkML Source","text":"
name: fao_class\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Soil classification from the FAO World Reference Database for Soil Resources.\n  The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\ntitle: soil_taxonomic/FAO classification\nexamples:\n- value: Luvisols\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/FAO classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001083\nalias: fao_class\ndomain_of:\n- Biosample\nrange: fao_class_enum\nmultivalued: false\n\n
"},{"location":"feature_category/","title":"Slot: feature_category","text":"

A Sequence Ontology term that describes the category of a feature

URI: nmdc:feature_category

"},{"location":"feature_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e no GenomeFeature A feature localized to an interval along a genome no"},{"location":"feature_category/#properties","title":"Properties","text":""},{"location":"feature_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"feature_category/#schema-source","title":"Schema Source","text":""},{"location":"feature_category/#linkml-source","title":"LinkML Source","text":"
name: feature_category\ndescription: A Sequence Ontology term that describes the category of a feature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_category\ndomain_of:\n- GenomeFeature\n- FunctionalAnnotation\nrange: ControlledIdentifiedTermValue\n\n
"},{"location":"feature_type/","title":"Slot: feature_type","text":"

TODO: Yuri to write

URI: nmdc:feature_type

"},{"location":"feature_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"feature_type/#properties","title":"Properties","text":""},{"location":"feature_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"feature_type/#schema-source","title":"Schema Source","text":""},{"location":"feature_type/#linkml-source","title":"LinkML Source","text":"
name: feature_type\ndescription: 'TODO: Yuri to write'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_type\ndomain_of:\n- GenomeFeature\nrange: string\n\n
"},{"location":"fertilizer_regm/","title":"Slot: fertilizer regimen (fertilizer_regm)","text":"

Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens

URI: MIXS:0000556

"},{"location":"fertilizer_regm/#inheritance","title":"Inheritance","text":""},{"location":"fertilizer_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fertilizer_regm/#properties","title":"Properties","text":""},{"location":"fertilizer_regm/#aliases","title":"Aliases","text":""},{"location":"fertilizer_regm/#examples","title":"Examples","text":"Value urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M"},{"location":"fertilizer_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fertilizer_regm/#annotations","title":"Annotations","text":"property value expected_value fertilizer name;fertilizer amount;treatment interval and duration"},{"location":"fertilizer_regm/#schema-source","title":"Schema Source","text":""},{"location":"fertilizer_regm/#linkml-source","title":"LinkML Source","text":"
name: fertilizer_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: fertilizer name;fertilizer amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving the use of fertilizers; should\n  include the name of fertilizer, amount administered, treatment regimen including\n  how many times the treatment was repeated, how long each treatment lasted, and the\n  start and end time of the entire treatment; can include multiple fertilizer regimens\ntitle: fertilizer regimen\nexamples:\n- value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fertilizer regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000556\nalias: fertilizer_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"field/","title":"Slot: field name (field)","text":"

Name of the hydrocarbon field (e.g. Albacora)

URI: MIXS:0000291

"},{"location":"field/#inheritance","title":"Inheritance","text":""},{"location":"field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"field/#properties","title":"Properties","text":""},{"location":"field/#aliases","title":"Aliases","text":""},{"location":"field/#examples","title":"Examples","text":"Value"},{"location":"field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"field/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"field/#schema-source","title":"Schema Source","text":""},{"location":"field/#linkml-source","title":"LinkML Source","text":"
name: field\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of the hydrocarbon field (e.g. Albacora)\ntitle: field name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- field name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000291\nalias: field\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"field_research_site_set/","title":"Slot: field_research_site_set","text":"

URI: nmdc:field_research_site_set

"},{"location":"field_research_site_set/#inheritance","title":"Inheritance","text":""},{"location":"field_research_site_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"field_research_site_set/#properties","title":"Properties","text":""},{"location":"field_research_site_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"field_research_site_set/#schema-source","title":"Schema Source","text":""},{"location":"field_research_site_set/#linkml-source","title":"LinkML Source","text":"
name: field_research_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: field_research_site_set\ndomain_of:\n- Database\nrange: FieldResearchSite\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"file_size_bytes/","title":"Slot: file_size_bytes","text":"

Size of the file in bytes

URI: nmdc:file_size_bytes

"},{"location":"file_size_bytes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"file_size_bytes/#properties","title":"Properties","text":""},{"location":"file_size_bytes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"file_size_bytes/#schema-source","title":"Schema Source","text":""},{"location":"file_size_bytes/#linkml-source","title":"LinkML Source","text":"
name: file_size_bytes\ndescription: Size of the file in bytes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: file_size_bytes\ndomain_of:\n- DataObject\nrange: bytes\n\n
"},{"location":"filter_material/","title":"Slot: filter_material","text":"

A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained.

URI: nmdc:filter_material

"},{"location":"filter_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filter_material/#properties","title":"Properties","text":""},{"location":"filter_material/#comments","title":"Comments","text":""},{"location":"filter_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filter_material/#schema-source","title":"Schema Source","text":""},{"location":"filter_material/#linkml-source","title":"LinkML Source","text":"
name: filter_material\ndescription: A porous material on which solid particles present in air or other fluid\n  which flows through it are largely caught and retained.\ncomments:\n- 'Filters are made with a variety of materials: cellulose and derivatives, glass\n  fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous or\n  be made so by mechanical or other means. Membrane/ceramic filters are prepared with\n  highly controlled pore size in a sheet of suitable material such as polyfluoroethylene,\n  polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement.\n  The pores constitute 80\u201385% of the filter volume commonly and several pore sizes\n  are available for air sampling (0.45\u22120.8 \u03bcm are commonly employed).'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filter_material\ndomain_of:\n- FiltrationProcess\nrange: string\n\n
"},{"location":"filter_method/","title":"Slot: filter method (filter_method)","text":"

Type of filter used or how the sample was filtered

URI: nmdc:filter_method

"},{"location":"filter_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"filter_method/#properties","title":"Properties","text":""},{"location":"filter_method/#examples","title":"Examples","text":"Value C18 Basix PES, 13-100-106 FisherSci"},{"location":"filter_method/#comments","title":"Comments","text":""},{"location":"filter_method/#see-also","title":"See Also","text":""},{"location":"filter_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filter_method/#schema-source","title":"Schema Source","text":""},{"location":"filter_method/#linkml-source","title":"LinkML Source","text":"
name: filter_method\ndescription: Type of filter used or how the sample was filtered\ntitle: filter method\ncomments:\n- describe the filter or provide a catalog number and manufacturer\nexamples:\n- value: C18\n- value: Basix PES, 13-100-106 FisherSci\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000765\nrank: 6\nstring_serialization: '{text}'\nalias: filter_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"filter_pore_size/","title":"Slot: filter_pore_size","text":"

A quantitative or qualitative measurement of the physical dimensions of the pores in a material.

URI: nmdc:filter_pore_size

"},{"location":"filter_pore_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filter_pore_size/#properties","title":"Properties","text":""},{"location":"filter_pore_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filter_pore_size/#schema-source","title":"Schema Source","text":""},{"location":"filter_pore_size/#linkml-source","title":"LinkML Source","text":"
name: filter_pore_size\ndescription: A quantitative or qualitative measurement of the physical dimensions\n  of the pores in a material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filter_pore_size\ndomain_of:\n- FiltrationProcess\nrange: QuantityValue\n\n
"},{"location":"filter_type/","title":"Slot: filter type (filter_type)","text":"

A device which removes solid particulates or airborne molecular contaminants

URI: MIXS:0000765

"},{"location":"filter_type/#inheritance","title":"Inheritance","text":""},{"location":"filter_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"filter_type/#properties","title":"Properties","text":""},{"location":"filter_type/#aliases","title":"Aliases","text":""},{"location":"filter_type/#examples","title":"Examples","text":"Value HEPA"},{"location":"filter_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filter_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"filter_type/#schema-source","title":"Schema Source","text":""},{"location":"filter_type/#linkml-source","title":"LinkML Source","text":"
name: filter_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: A device which removes solid particulates or airborne molecular contaminants\ntitle: filter type\nexamples:\n- value: HEPA\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- filter type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000765\nalias: filter_type\ndomain_of:\n- Biosample\nrange: filter_type_enum\nmultivalued: true\n\n
"},{"location":"filtration_category/","title":"Slot: filtration_category","text":"

The type of conditioning applied to a filter, device, etc.

URI: nmdc:filtration_category

"},{"location":"filtration_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filtration_category/#properties","title":"Properties","text":""},{"location":"filtration_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filtration_category/#schema-source","title":"Schema Source","text":""},{"location":"filtration_category/#linkml-source","title":"LinkML Source","text":"
name: filtration_category\ndescription: The type of conditioning applied to a filter, device, etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filtration_category\ndomain_of:\n- FiltrationProcess\nrange: string\n\n
"},{"location":"final_concentration/","title":"Slot: final_concentration","text":"

When solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in the combination

URI: nmdc:final_concentration

"},{"location":"final_concentration/#inheritance","title":"Inheritance","text":""},{"location":"final_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"final_concentration/#properties","title":"Properties","text":""},{"location":"final_concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"final_concentration/#schema-source","title":"Schema Source","text":""},{"location":"final_concentration/#linkml-source","title":"LinkML Source","text":"
name: final_concentration\ndescription: When solutions A (containing substance X) and B are combined together,\n  this slot captures the concentration of X in the combination\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: concentration\nalias: final_concentration\ndomain_of:\n- PortionOfSubstance\nrange: QuantityValue\n\n
"},{"location":"fire/","title":"Slot: history/fire (fire)","text":"

Historical and/or physical evidence of fire

URI: MIXS:0001086

"},{"location":"fire/#inheritance","title":"Inheritance","text":""},{"location":"fire/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"fire/#properties","title":"Properties","text":""},{"location":"fire/#aliases","title":"Aliases","text":""},{"location":"fire/#examples","title":"Examples","text":"Value"},{"location":"fire/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fire/#annotations","title":"Annotations","text":"property value expected_value date"},{"location":"fire/#schema-source","title":"Schema Source","text":""},{"location":"fire/#linkml-source","title":"LinkML Source","text":"
name: fire\nannotations:\n  expected_value:\n    tag: expected_value\n    value: date\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Historical and/or physical evidence of fire\ntitle: history/fire\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/fire\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001086\nalias: fire\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"fireplace_type/","title":"Slot: fireplace type (fireplace_type)","text":"

A firebox with chimney

URI: MIXS:0000802

"},{"location":"fireplace_type/#inheritance","title":"Inheritance","text":""},{"location":"fireplace_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fireplace_type/#properties","title":"Properties","text":""},{"location":"fireplace_type/#aliases","title":"Aliases","text":""},{"location":"fireplace_type/#examples","title":"Examples","text":"Value wood burning"},{"location":"fireplace_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fireplace_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"fireplace_type/#schema-source","title":"Schema Source","text":""},{"location":"fireplace_type/#linkml-source","title":"LinkML Source","text":"
name: fireplace_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A firebox with chimney\ntitle: fireplace type\nexamples:\n- value: wood burning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fireplace type\nrank: 1000\nis_a: core field\nstring_serialization: '[gas burning|wood burning]'\nslot_uri: MIXS:0000802\nalias: fireplace_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"flooding/","title":"Slot: history/flooding (flooding)","text":"

Historical and/or physical evidence of flooding

URI: MIXS:0000319

"},{"location":"flooding/#inheritance","title":"Inheritance","text":""},{"location":"flooding/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"flooding/#properties","title":"Properties","text":""},{"location":"flooding/#aliases","title":"Aliases","text":""},{"location":"flooding/#examples","title":"Examples","text":"Value"},{"location":"flooding/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"flooding/#annotations","title":"Annotations","text":"property value expected_value date"},{"location":"flooding/#schema-source","title":"Schema Source","text":""},{"location":"flooding/#linkml-source","title":"LinkML Source","text":"
name: flooding\nannotations:\n  expected_value:\n    tag: expected_value\n    value: date\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Historical and/or physical evidence of flooding\ntitle: history/flooding\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/flooding\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000319\nalias: flooding\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"floor_age/","title":"Slot: floor age (floor_age)","text":"

The time period since installment of the carpet or flooring

URI: MIXS:0000164

"},{"location":"floor_age/#inheritance","title":"Inheritance","text":""},{"location":"floor_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_age/#properties","title":"Properties","text":""},{"location":"floor_age/#aliases","title":"Aliases","text":""},{"location":"floor_age/#examples","title":"Examples","text":"Value"},{"location":"floor_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_age/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"floor_age/#schema-source","title":"Schema Source","text":""},{"location":"floor_age/#linkml-source","title":"LinkML Source","text":"
name: floor_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: years, weeks, days\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The time period since installment of the carpet or flooring\ntitle: floor age\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000164\nalias: floor_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"floor_area/","title":"Slot: floor area (floor_area)","text":"

The area of the floor space within the room

URI: MIXS:0000165

"},{"location":"floor_area/#inheritance","title":"Inheritance","text":""},{"location":"floor_area/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_area/#properties","title":"Properties","text":""},{"location":"floor_area/#aliases","title":"Aliases","text":""},{"location":"floor_area/#examples","title":"Examples","text":"Value"},{"location":"floor_area/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_area/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"floor_area/#schema-source","title":"Schema Source","text":""},{"location":"floor_area/#linkml-source","title":"LinkML Source","text":"
name: floor_area\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The area of the floor space within the room\ntitle: floor area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000165\nalias: floor_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"floor_cond/","title":"Slot: floor condition (floor_cond)","text":"

The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas

URI: MIXS:0000803

"},{"location":"floor_cond/#inheritance","title":"Inheritance","text":""},{"location":"floor_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_cond/#properties","title":"Properties","text":""},{"location":"floor_cond/#aliases","title":"Aliases","text":""},{"location":"floor_cond/#examples","title":"Examples","text":"Value new"},{"location":"floor_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"floor_cond/#schema-source","title":"Schema Source","text":""},{"location":"floor_cond/#linkml-source","title":"LinkML Source","text":"
name: floor_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the floor at the time of sampling; photos or\n  video preferred; use drawings to indicate location of damaged areas\ntitle: floor condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000803\nalias: floor_cond\ndomain_of:\n- Biosample\nrange: floor_cond_enum\nmultivalued: false\n\n
"},{"location":"floor_count/","title":"Slot: floor count (floor_count)","text":"

The number of floors in the building, including basements and mechanical penthouse

URI: MIXS:0000225

"},{"location":"floor_count/#inheritance","title":"Inheritance","text":""},{"location":"floor_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_count/#properties","title":"Properties","text":""},{"location":"floor_count/#aliases","title":"Aliases","text":""},{"location":"floor_count/#examples","title":"Examples","text":"Value"},{"location":"floor_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"floor_count/#schema-source","title":"Schema Source","text":""},{"location":"floor_count/#linkml-source","title":"LinkML Source","text":"
name: floor_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of floors in the building, including basements and mechanical\n  penthouse\ntitle: floor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000225\nalias: floor_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"floor_finish_mat/","title":"Slot: floor finish material (floor_finish_mat)","text":"

The floor covering type; the finished surface that is walked on

URI: MIXS:0000804

"},{"location":"floor_finish_mat/#inheritance","title":"Inheritance","text":""},{"location":"floor_finish_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_finish_mat/#properties","title":"Properties","text":""},{"location":"floor_finish_mat/#aliases","title":"Aliases","text":""},{"location":"floor_finish_mat/#examples","title":"Examples","text":"Value carpet"},{"location":"floor_finish_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_finish_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"floor_finish_mat/#schema-source","title":"Schema Source","text":""},{"location":"floor_finish_mat/#linkml-source","title":"LinkML Source","text":"
name: floor_finish_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The floor covering type; the finished surface that is walked on\ntitle: floor finish material\nexamples:\n- value: carpet\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000804\nalias: floor_finish_mat\ndomain_of:\n- Biosample\nrange: floor_finish_mat_enum\nmultivalued: false\n\n
"},{"location":"floor_struc/","title":"Slot: floor structure (floor_struc)","text":"

Refers to the structural elements and subfloor upon which the finish flooring is installed

URI: MIXS:0000806

"},{"location":"floor_struc/#inheritance","title":"Inheritance","text":""},{"location":"floor_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_struc/#properties","title":"Properties","text":""},{"location":"floor_struc/#aliases","title":"Aliases","text":""},{"location":"floor_struc/#examples","title":"Examples","text":"Value concrete"},{"location":"floor_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"floor_struc/#schema-source","title":"Schema Source","text":""},{"location":"floor_struc/#linkml-source","title":"LinkML Source","text":"
name: floor_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Refers to the structural elements and subfloor upon which the finish\n  flooring is installed\ntitle: floor structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000806\nalias: floor_struc\ndomain_of:\n- Biosample\nrange: floor_struc_enum\nmultivalued: false\n\n
"},{"location":"floor_thermal_mass/","title":"Slot: floor thermal mass (floor_thermal_mass)","text":"

The ability of the floor to provide inertia against temperature fluctuations

URI: MIXS:0000166

"},{"location":"floor_thermal_mass/#inheritance","title":"Inheritance","text":""},{"location":"floor_thermal_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_thermal_mass/#properties","title":"Properties","text":""},{"location":"floor_thermal_mass/#aliases","title":"Aliases","text":""},{"location":"floor_thermal_mass/#examples","title":"Examples","text":"Value"},{"location":"floor_thermal_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_thermal_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"floor_thermal_mass/#schema-source","title":"Schema Source","text":""},{"location":"floor_thermal_mass/#linkml-source","title":"LinkML Source","text":"
name: floor_thermal_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: joule per degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The ability of the floor to provide inertia against temperature fluctuations\ntitle: floor thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000166\nalias: floor_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"floor_water_mold/","title":"Slot: floor signs of water/mold (floor_water_mold)","text":"

Signs of the presence of mold or mildew in a room

URI: MIXS:0000805

"},{"location":"floor_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"floor_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_water_mold/#properties","title":"Properties","text":""},{"location":"floor_water_mold/#aliases","title":"Aliases","text":""},{"location":"floor_water_mold/#examples","title":"Examples","text":"Value ceiling discoloration"},{"location":"floor_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"floor_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"floor_water_mold/#linkml-source","title":"LinkML Source","text":"
name: floor_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew in a room\ntitle: floor signs of water/mold\nexamples:\n- value: ceiling discoloration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor signs of water/mold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000805\nalias: floor_water_mold\ndomain_of:\n- Biosample\nrange: floor_water_mold_enum\nmultivalued: false\n\n
"},{"location":"fluor/","title":"Slot: fluorescence (fluor)","text":"

Raw or converted fluorescence of water

URI: MIXS:0000704

"},{"location":"fluor/#inheritance","title":"Inheritance","text":""},{"location":"fluor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fluor/#properties","title":"Properties","text":""},{"location":"fluor/#aliases","title":"Aliases","text":""},{"location":"fluor/#examples","title":"Examples","text":"Value 2.5 volts"},{"location":"fluor/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fluor/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"fluor/#schema-source","title":"Schema Source","text":""},{"location":"fluor/#linkml-source","title":"LinkML Source","text":"
name: fluor\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram chlorophyll a per cubic meter, volts\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Raw or converted fluorescence of water\ntitle: fluorescence\nexamples:\n- value: 2.5 volts\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fluorescence\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000704\nalias: fluor\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"freq_clean/","title":"Slot: frequency of cleaning (freq_clean)","text":"

The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.

URI: MIXS:0000226

"},{"location":"freq_clean/#inheritance","title":"Inheritance","text":""},{"location":"freq_clean/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"freq_clean/#properties","title":"Properties","text":""},{"location":"freq_clean/#aliases","title":"Aliases","text":""},{"location":"freq_clean/#examples","title":"Examples","text":"Value"},{"location":"freq_clean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"freq_clean/#annotations","title":"Annotations","text":"property value expected_value enumeration or {text}"},{"location":"freq_clean/#schema-source","title":"Schema Source","text":""},{"location":"freq_clean/#linkml-source","title":"LinkML Source","text":"
name: freq_clean\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration or {text}\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of times the sample location is cleaned. Frequency of cleaning\n  might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\ntitle: frequency of cleaning\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cleaning\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000226\nalias: freq_clean\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"freq_cook/","title":"Slot: frequency of cooking (freq_cook)","text":"

The number of times a meal is cooked per week

URI: MIXS:0000227

"},{"location":"freq_cook/#inheritance","title":"Inheritance","text":""},{"location":"freq_cook/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"freq_cook/#properties","title":"Properties","text":""},{"location":"freq_cook/#aliases","title":"Aliases","text":""},{"location":"freq_cook/#examples","title":"Examples","text":"Value"},{"location":"freq_cook/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"freq_cook/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"freq_cook/#schema-source","title":"Schema Source","text":""},{"location":"freq_cook/#linkml-source","title":"LinkML Source","text":"
name: freq_cook\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of times a meal is cooked per week\ntitle: frequency of cooking\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cooking\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000227\nalias: freq_cook\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"functional_annotation_agg/","title":"Slot: functional_annotation_agg","text":"

URI: nmdc:functional_annotation_agg

"},{"location":"functional_annotation_agg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"functional_annotation_agg/#properties","title":"Properties","text":""},{"location":"functional_annotation_agg/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"functional_annotation_agg/#schema-source","title":"Schema Source","text":""},{"location":"functional_annotation_agg/#linkml-source","title":"LinkML Source","text":"
name: functional_annotation_agg\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: functional_annotation_agg\ndomain_of:\n- Database\nrange: FunctionalAnnotationAggMember\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"functional_annotation_set/","title":"Slot: functional_annotation_set","text":"

This property links a database object to the set of all functional annotations

URI: nmdc:functional_annotation_set

"},{"location":"functional_annotation_set/#inheritance","title":"Inheritance","text":""},{"location":"functional_annotation_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"functional_annotation_set/#properties","title":"Properties","text":""},{"location":"functional_annotation_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"functional_annotation_set/#schema-source","title":"Schema Source","text":""},{"location":"functional_annotation_set/#linkml-source","title":"LinkML Source","text":"
name: functional_annotation_set\ndescription: This property links a database object to the set of all functional annotations\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: functional_annotation_set\ndomain_of:\n- Database\nrange: FunctionalAnnotation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"funding_sources/","title":"Slot: funding_sources","text":"

A list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants.

URI: nmdc:funding_sources

"},{"location":"funding_sources/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"funding_sources/#properties","title":"Properties","text":""},{"location":"funding_sources/#examples","title":"Examples","text":"Value National Sciences Foundation Dimensions of Biodiversity (award no. 1342701) U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract DE-AC05-00OR2275"},{"location":"funding_sources/#comments","title":"Comments","text":""},{"location":"funding_sources/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"funding_sources/#schema-source","title":"Schema Source","text":""},{"location":"funding_sources/#linkml-source","title":"LinkML Source","text":"
name: funding_sources\ndescription: A list of organizations, along with the award numbers, that underwrite\n  financial support for projects of a particular type. Typically, they process applications\n  and award funds to the chosen qualified applicants.\ncomments:\n- Include only the name of the funding organization and the award or contract number.\nexamples:\n- value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n- value: U.S. Department of Energy, Office of Science, Office of Biological and Environmental\n    Research (BER) under contract DE-AC05-00OR2275\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C39409\nrank: 1000\nalias: funding_sources\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\n
"},{"location":"fungicide_regm/","title":"Slot: fungicide regimen (fungicide_regm)","text":"

Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens

URI: MIXS:0000557

"},{"location":"fungicide_regm/#inheritance","title":"Inheritance","text":""},{"location":"fungicide_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fungicide_regm/#properties","title":"Properties","text":""},{"location":"fungicide_regm/#aliases","title":"Aliases","text":""},{"location":"fungicide_regm/#examples","title":"Examples","text":"Value bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"fungicide_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fungicide_regm/#annotations","title":"Annotations","text":"property value expected_value fungicide name;fungicide amount;treatment interval and duration"},{"location":"fungicide_regm/#schema-source","title":"Schema Source","text":""},{"location":"fungicide_regm/#linkml-source","title":"LinkML Source","text":"
name: fungicide_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: fungicide name;fungicide amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of fungicides; should include\n  the name of fungicide, amount administered, treatment regimen including how many\n  times the treatment was repeated, how long each treatment lasted, and the start\n  and end time of the entire treatment; can include multiple fungicide regimens\ntitle: fungicide regimen\nexamples:\n- value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fungicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000557\nalias: fungicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"furniture/","title":"Slot: furniture (furniture)","text":"

The types of furniture present in the sampled room

URI: MIXS:0000807

"},{"location":"furniture/#inheritance","title":"Inheritance","text":""},{"location":"furniture/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"furniture/#properties","title":"Properties","text":""},{"location":"furniture/#aliases","title":"Aliases","text":""},{"location":"furniture/#examples","title":"Examples","text":"Value chair"},{"location":"furniture/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"furniture/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"furniture/#schema-source","title":"Schema Source","text":""},{"location":"furniture/#linkml-source","title":"LinkML Source","text":"
name: furniture\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The types of furniture present in the sampled room\ntitle: furniture\nexamples:\n- value: chair\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- furniture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000807\nalias: furniture\ndomain_of:\n- Biosample\nrange: furniture_enum\nmultivalued: false\n\n
"},{"location":"gap_pct/","title":"Slot: gap_pct","text":"

The gap size percentage of all scaffolds.

URI: nmdc:gap_pct

"},{"location":"gap_pct/#inheritance","title":"Inheritance","text":""},{"location":"gap_pct/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"gap_pct/#properties","title":"Properties","text":""},{"location":"gap_pct/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gap_pct/#schema-source","title":"Schema Source","text":""},{"location":"gap_pct/#linkml-source","title":"LinkML Source","text":"
name: gap_pct\ndescription: The gap size percentage of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gap_pct\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"gaseous_environment/","title":"Slot: gaseous environment (gaseous_environment)","text":"

Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens

URI: MIXS:0000558

"},{"location":"gaseous_environment/#inheritance","title":"Inheritance","text":""},{"location":"gaseous_environment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"gaseous_environment/#properties","title":"Properties","text":""},{"location":"gaseous_environment/#aliases","title":"Aliases","text":""},{"location":"gaseous_environment/#examples","title":"Examples","text":"Value nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"gaseous_environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gaseous_environment/#annotations","title":"Annotations","text":"property value expected_value gaseous compound name;gaseous compound amount;treatment interval and duration"},{"location":"gaseous_environment/#schema-source","title":"Schema Source","text":""},{"location":"gaseous_environment/#linkml-source","title":"LinkML Source","text":"
name: gaseous_environment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gaseous compound name;gaseous compound amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Use of conditions with differing gaseous environments; should include\n  the name of gaseous compound, amount administered, treatment duration, interval\n  and total experimental duration; can include multiple gaseous environment regimens\ntitle: gaseous environment\nexamples:\n- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000558\nalias: gaseous_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gaseous_substances/","title":"Slot: gaseous substances (gaseous_substances)","text":"

Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances

URI: MIXS:0000661

"},{"location":"gaseous_substances/#inheritance","title":"Inheritance","text":""},{"location":"gaseous_substances/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"gaseous_substances/#properties","title":"Properties","text":""},{"location":"gaseous_substances/#aliases","title":"Aliases","text":""},{"location":"gaseous_substances/#examples","title":"Examples","text":"Value"},{"location":"gaseous_substances/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gaseous_substances/#annotations","title":"Annotations","text":"property value expected_value gaseous substance name;measurement value"},{"location":"gaseous_substances/#schema-source","title":"Schema Source","text":""},{"location":"gaseous_substances/#linkml-source","title":"LinkML Source","text":"
name: gaseous_substances\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gaseous substance name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Amount or concentration of substances such as hydrogen sulfide, carbon\n  dioxide, methane, etc.; can include multiple substances\ntitle: gaseous substances\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous substances\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000661\nalias: gaseous_substances\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gc_avg/","title":"Slot: gc_avg","text":"

Average of GC content of all contigs.

URI: nmdc:gc_avg

"},{"location":"gc_avg/#inheritance","title":"Inheritance","text":""},{"location":"gc_avg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"gc_avg/#properties","title":"Properties","text":""},{"location":"gc_avg/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gc_avg/#schema-source","title":"Schema Source","text":""},{"location":"gc_avg/#linkml-source","title":"LinkML Source","text":"
name: gc_avg\ndescription: Average of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_avg\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"gc_std/","title":"Slot: gc_std","text":"

Standard deviation of GC content of all contigs.

URI: nmdc:gc_std

"},{"location":"gc_std/#inheritance","title":"Inheritance","text":""},{"location":"gc_std/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"gc_std/#properties","title":"Properties","text":""},{"location":"gc_std/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gc_std/#schema-source","title":"Schema Source","text":""},{"location":"gc_std/#linkml-source","title":"LinkML Source","text":"
name: gc_std\ndescription: Standard deviation of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_std\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"gender_restroom/","title":"Slot: gender of restroom (gender_restroom)","text":"

The gender type of the restroom

URI: MIXS:0000808

"},{"location":"gender_restroom/#inheritance","title":"Inheritance","text":""},{"location":"gender_restroom/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"gender_restroom/#properties","title":"Properties","text":""},{"location":"gender_restroom/#aliases","title":"Aliases","text":""},{"location":"gender_restroom/#examples","title":"Examples","text":"Value male"},{"location":"gender_restroom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gender_restroom/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"gender_restroom/#schema-source","title":"Schema Source","text":""},{"location":"gender_restroom/#linkml-source","title":"LinkML Source","text":"
name: gender_restroom\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The gender type of the restroom\ntitle: gender of restroom\nexamples:\n- value: male\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gender of restroom\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000808\nalias: gender_restroom\ndomain_of:\n- Biosample\nrange: gender_restroom_enum\nmultivalued: false\n\n
"},{"location":"gene_count/","title":"Slot: gene_count","text":"

URI: nmdc:gene_count

"},{"location":"gene_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gene_count/#properties","title":"Properties","text":""},{"location":"gene_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_count/#schema-source","title":"Schema Source","text":""},{"location":"gene_count/#linkml-source","title":"LinkML Source","text":"
name: gene_count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_count\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"gene_function_id/","title":"Slot: gene_function_id","text":"

The identifier for the gene function.

URI: nmdc:gene_function_id

"},{"location":"gene_function_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"gene_function_id/#properties","title":"Properties","text":""},{"location":"gene_function_id/#examples","title":"Examples","text":"Value KEGG.ORTHOLOGY:K00627"},{"location":"gene_function_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_function_id/#schema-source","title":"Schema Source","text":""},{"location":"gene_function_id/#linkml-source","title":"LinkML Source","text":"
name: gene_function_id\ndescription: The identifier for the gene function.\nexamples:\n- value: KEGG.ORTHOLOGY:K00627\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_function_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: uriorcurie\nrequired: true\n\n
"},{"location":"genetic_mod/","title":"Slot: genetic modification (genetic_mod)","text":"

Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection

URI: MIXS:0000859

"},{"location":"genetic_mod/#inheritance","title":"Inheritance","text":""},{"location":"genetic_mod/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"genetic_mod/#properties","title":"Properties","text":""},{"location":"genetic_mod/#aliases","title":"Aliases","text":""},{"location":"genetic_mod/#examples","title":"Examples","text":"Value aox1A transgenic"},{"location":"genetic_mod/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"genetic_mod/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url or free text"},{"location":"genetic_mod/#schema-source","title":"Schema Source","text":""},{"location":"genetic_mod/#linkml-source","title":"LinkML Source","text":"
name: genetic_mod\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url or free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Genetic modifications of the genome of an organism, which may occur naturally\n  by spontaneous mutation, or be introduced by some experimental means, e.g. specification\n  of a transgene or the gene knocked-out or details of transient transfection\ntitle: genetic modification\nexamples:\n- value: aox1A transgenic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- genetic modification\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000859\nalias: genetic_mod\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"genome_feature_set/","title":"Slot: genome_feature_set","text":"

This property links a database object to the set of all features

URI: nmdc:genome_feature_set

"},{"location":"genome_feature_set/#inheritance","title":"Inheritance","text":""},{"location":"genome_feature_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"genome_feature_set/#properties","title":"Properties","text":""},{"location":"genome_feature_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"genome_feature_set/#schema-source","title":"Schema Source","text":""},{"location":"genome_feature_set/#linkml-source","title":"LinkML Source","text":"
name: genome_feature_set\ndescription: This property links a database object to the set of all features\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: genome_feature_set\ndomain_of:\n- Database\nrange: GenomeFeature\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"geo_loc_name/","title":"Slot: geographic location (country and/or sea,region) (geo_loc_name)","text":"

The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)

URI: MIXS:0000010

"},{"location":"geo_loc_name/#inheritance","title":"Inheritance","text":""},{"location":"geo_loc_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment no"},{"location":"geo_loc_name/#properties","title":"Properties","text":""},{"location":"geo_loc_name/#aliases","title":"Aliases","text":""},{"location":"geo_loc_name/#examples","title":"Examples","text":"Value USA: Maryland, Bethesda"},{"location":"geo_loc_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"geo_loc_name/#annotations","title":"Annotations","text":"property value expected_value country or sea name (INSDC or GAZ): region(GAZ), specific location name"},{"location":"geo_loc_name/#schema-source","title":"Schema Source","text":""},{"location":"geo_loc_name/#linkml-source","title":"LinkML Source","text":"
name: geo_loc_name\nannotations:\n  expected_value:\n    tag: expected_value\n    value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location name'\ndescription: The geographical origin of the sample as defined by the country or sea\n  name followed by specific region name. Country or sea names should be chosen from\n  the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)\ntitle: geographic location (country and/or sea,region)\nexamples:\n- value: 'USA: Maryland, Bethesda'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (country and/or sea,region)\nrank: 1000\nis_a: environment field\nstring_serialization: '{term}: {term}, {text}'\nslot_uri: MIXS:0000010\nalias: geo_loc_name\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"gff_coordinate/","title":"Slot: gff_coordinate","text":"

A positive 1-based integer coordinate indicating start or end

URI: nmdc:gff_coordinate

"},{"location":"gff_coordinate/#inheritance","title":"Inheritance","text":""},{"location":"gff_coordinate/#properties","title":"Properties","text":""},{"location":"gff_coordinate/#comments","title":"Comments","text":""},{"location":"gff_coordinate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gff_coordinate/#schema-source","title":"Schema Source","text":""},{"location":"gff_coordinate/#linkml-source","title":"LinkML Source","text":"
name: gff_coordinate\ndescription: A positive 1-based integer coordinate indicating start or end\ncomments:\n- For features that cross the origin of a circular feature (e.g. most bacterial genomes,\n  plasmids, and some viral genomes), the requirement for start to be less than or\n  equal to end is satisfied by making end = the position of the end + the length of\n  the landmark feature.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gff_coordinate\nrange: integer\nminimum_value: 1\n\n
"},{"location":"git_url/","title":"Slot: git_url","text":"

The url that points to the exact github location of a workflow.

URI: nmdc:git_url

"},{"location":"git_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetaproteomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetatranscriptomeAnnotation no MetatranscriptomeAssembly no"},{"location":"git_url/#properties","title":"Properties","text":""},{"location":"git_url/#examples","title":"Examples","text":"Value https://github.com/microbiomedata/mg_annotation/releases/tag/0.1 https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py"},{"location":"git_url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"git_url/#schema-source","title":"Schema Source","text":""},{"location":"git_url/#linkml-source","title":"LinkML Source","text":"
name: git_url\ndescription: The url that points to the exact github location of a workflow.\nexamples:\n- value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n- value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: git_url\ndomain_of:\n- WorkflowExecution\nrange: string\n\n
"},{"location":"glucosidase_act/","title":"Slot: glucosidase activity (glucosidase_act)","text":"

Measurement of glucosidase activity

URI: MIXS:0000137

"},{"location":"glucosidase_act/#inheritance","title":"Inheritance","text":""},{"location":"glucosidase_act/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"glucosidase_act/#properties","title":"Properties","text":""},{"location":"glucosidase_act/#aliases","title":"Aliases","text":""},{"location":"glucosidase_act/#examples","title":"Examples","text":"Value 5 mol per liter per hour"},{"location":"glucosidase_act/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"glucosidase_act/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"glucosidase_act/#schema-source","title":"Schema Source","text":""},{"location":"glucosidase_act/#linkml-source","title":"LinkML Source","text":"
name: glucosidase_act\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mol per liter per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of glucosidase activity\ntitle: glucosidase activity\nexamples:\n- value: 5 mol per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- glucosidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000137\nalias: glucosidase_act\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"gnps_identifiers/","title":"Slot: gnps_identifiers","text":"

URI: nmdc:gnps_identifiers

"},{"location":"gnps_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... None Study"},{"location":"gnps_identifiers/#properties","title":"Properties","text":""},{"location":"gnps_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gnps_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gnps_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gnps_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: gnps_identifiers\nrange: string\n\n
"},{"location":"gnps_task_identifiers/","title":"Slot: GNPS task identifiers (gnps_task_identifiers)","text":"

identifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results

URI: nmdc:gnps_task_identifiers

"},{"location":"gnps_task_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gnps_task_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"gnps_task_identifiers/#properties","title":"Properties","text":""},{"location":"gnps_task_identifiers/#examples","title":"Examples","text":"Value gnps.task:4b848c342a4f4abc871bdf8a09a60807"},{"location":"gnps_task_identifiers/#comments","title":"Comments","text":""},{"location":"gnps_task_identifiers/#see-also","title":"See Also","text":""},{"location":"gnps_task_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gnps_task_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gnps_task_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gnps_task_identifiers\ndescription: identifiers that link a NMDC study to a web-based report about metabolomics\n  analysis progress and results\ntitle: GNPS task identifiers\ncomments:\n- this could be considered a related identifier, as the metabolomics progress and\n  results aren't a study per se\n- this identifier was registered with bioregistry but not identifiers.org\nexamples:\n- value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysis/\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gnps_identifiers\nalias: gnps_task_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^gnps\\.task:[a-f0-9]+$\n\n
"},{"location":"gold_analysis_project_identifiers/","title":"Slot: gold_analysis_project_identifiers","text":"

identifiers for corresponding analysis projects in GOLD

URI: nmdc:gold_analysis_project_identifiers

"},{"location":"gold_analysis_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gold_analysis_project_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes MetatranscriptomeAnnotation yes"},{"location":"gold_analysis_project_identifiers/#properties","title":"Properties","text":""},{"location":"gold_analysis_project_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/gold:Ga0526289"},{"location":"gold_analysis_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_analysis_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_analysis_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_analysis_project_identifiers\ndescription: identifiers for corresponding analysis projects in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Ga0526289\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- gold_identifiers\nalias: gold_analysis_project_identifiers\ndomain_of:\n- MetagenomeAnnotation\n- MetatranscriptomeAnnotation\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Ga[0-9]+$\n\n
"},{"location":"gold_biosample_identifiers/","title":"Slot: gold_biosample_identifiers","text":"

identifiers for corresponding sample in GOLD

URI: nmdc:gold_biosample_identifiers

"},{"location":"gold_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gold_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"gold_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"gold_biosample_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/gold:Gb0312930"},{"location":"gold_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_biosample_identifiers\ndescription: identifiers for corresponding sample in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gb0312930\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- gold_identifiers\nalias: gold_biosample_identifiers\ndomain_of:\n- Biosample\nrange: uriorcurie\nmultivalued: true\npattern: ^gold:Gb[0-9]+$\n\n
"},{"location":"gold_identifiers/","title":"Slot: gold_identifiers","text":"

URI: nmdc:gold_identifiers

"},{"location":"gold_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gold_study_identifiers identifiers for corresponding project(s) in GOLD None Study gold_biosample_identifiers identifiers for corresponding sample in GOLD uriorcurie Biosample gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD None NucleotideSequencing gold_analysis_project_identifiers identifiers for corresponding analysis projects in GOLD None MetagenomeAnnotation, MetatranscriptomeAnnotation"},{"location":"gold_identifiers/#properties","title":"Properties","text":""},{"location":"gold_identifiers/#see-also","title":"See Also","text":""},{"location":"gold_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: gold_identifiers\nrange: string\n\n
"},{"location":"gold_path_field/","title":"Slot: gold_path_field","text":"

This is a grouping for any of the gold path fields

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:gold_path_field

"},{"location":"gold_path_field/#inheritance","title":"Inheritance","text":""},{"location":"gold_path_field/#properties","title":"Properties","text":""},{"location":"gold_path_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_path_field/#annotations","title":"Annotations","text":"property value tooltip GOLD Ecosystem Classification paths describe the surroundings from which an environmental sample or an organism is collected."},{"location":"gold_path_field/#schema-source","title":"Schema Source","text":""},{"location":"gold_path_field/#linkml-source","title":"LinkML Source","text":"
name: gold_path_field\nannotations:\n  tooltip:\n    tag: tooltip\n    value: GOLD Ecosystem Classification paths describe the surroundings from which\n      an environmental sample or an organism is collected.\n    annotations:\n      source:\n        tag: source\n        value: https://gold.jgi.doe.gov/ecosystem_classification\ndescription: This is a grouping for any of the gold path fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: gold_path_field\nrange: string\n\n
"},{"location":"gold_sequencing_project_identifiers/","title":"Slot: gold_sequencing_project_identifiers","text":"

identifiers for corresponding sequencing project in GOLD

URI: nmdc:gold_sequencing_project_identifiers

"},{"location":"gold_sequencing_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gold_sequencing_project_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"gold_sequencing_project_identifiers/#properties","title":"Properties","text":""},{"location":"gold_sequencing_project_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/gold:Gp0108335"},{"location":"gold_sequencing_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_sequencing_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_sequencing_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_sequencing_project_identifiers\ndescription: identifiers for corresponding sequencing project in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gp0108335\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: omics_processing_identifiers\nmixins:\n- gold_identifiers\nalias: gold_sequencing_project_identifiers\ndomain_of:\n- NucleotideSequencing\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Gp[0-9]+$\n\n
"},{"location":"gold_study_identifiers/","title":"Slot: GOLD Study Identifiers (gold_study_identifiers)","text":"

identifiers for corresponding project(s) in GOLD

URI: nmdc:gold_study_identifiers

"},{"location":"gold_study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gold_study_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"gold_study_identifiers/#properties","title":"Properties","text":""},{"location":"gold_study_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/gold:Gs0110115"},{"location":"gold_study_identifiers/#comments","title":"Comments","text":""},{"location":"gold_study_identifiers/#see-also","title":"See Also","text":""},{"location":"gold_study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_study_identifiers\ndescription: identifiers for corresponding project(s) in GOLD\ntitle: GOLD Study Identifiers\ncomments:\n- uses the prefix GS (but possibly in a different case)\nexamples:\n- value: https://bioregistry.io/gold:Gs0110115\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/studies\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gold_identifiers\nalias: gold_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Gs[0-9]+$\n\n
"},{"location":"gravidity/","title":"Slot: gravidity (gravidity)","text":"

Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used

URI: MIXS:0000875

"},{"location":"gravidity/#inheritance","title":"Inheritance","text":""},{"location":"gravidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"gravidity/#properties","title":"Properties","text":""},{"location":"gravidity/#aliases","title":"Aliases","text":""},{"location":"gravidity/#examples","title":"Examples","text":"Value yes;due date:2018-05-11"},{"location":"gravidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gravidity/#annotations","title":"Annotations","text":"property value expected_value gravidity status;timestamp"},{"location":"gravidity/#schema-source","title":"Schema Source","text":""},{"location":"gravidity/#linkml-source","title":"LinkML Source","text":"
name: gravidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gravidity status;timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Whether or not subject is gravid, and if yes date due or date post-conception,\n  specifying which is used\ntitle: gravidity\nexamples:\n- value: yes;due date:2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravidity\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{timestamp}'\nslot_uri: MIXS:0000875\nalias: gravidity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"gravity/","title":"Slot: gravity (gravity)","text":"

Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments

URI: MIXS:0000559

"},{"location":"gravity/#inheritance","title":"Inheritance","text":""},{"location":"gravity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"gravity/#properties","title":"Properties","text":""},{"location":"gravity/#aliases","title":"Aliases","text":""},{"location":"gravity/#examples","title":"Examples","text":"Value 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"gravity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gravity/#annotations","title":"Annotations","text":"property value expected_value gravity factor value;treatment interval and duration"},{"location":"gravity/#schema-source","title":"Schema Source","text":""},{"location":"gravity/#linkml-source","title":"LinkML Source","text":"
name: gravity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gravity factor value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: meter per square second, g\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of gravity factor to study\n  various types of responses in presence, absence or modified levels of gravity; treatment\n  regimen including how many times the treatment was repeated, how long each treatment\n  lasted, and the start and end time of the entire treatment; can include multiple\n  treatments\ntitle: gravity\nexamples:\n- value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000559\nalias: gravity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"growth_facil/","title":"Slot: growth facility (growth_facil)","text":"

Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research

URI: MIXS:0001043

"},{"location":"growth_facil/#inheritance","title":"Inheritance","text":""},{"location":"growth_facil/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"growth_facil/#properties","title":"Properties","text":""},{"location":"growth_facil/#aliases","title":"Aliases","text":""},{"location":"growth_facil/#examples","title":"Examples","text":"Value Growth chamber [CO_715:0000189]"},{"location":"growth_facil/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"growth_facil/#annotations","title":"Annotations","text":"property value expected_value free text or CO"},{"location":"growth_facil/#schema-source","title":"Schema Source","text":""},{"location":"growth_facil/#linkml-source","title":"LinkML Source","text":"
name: growth_facil\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text or CO\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n  growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n  use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\ntitle: growth facility\nexamples:\n- value: Growth chamber [CO_715:0000189]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth facility\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{termLabel} {[termID]}'\nslot_uri: MIXS:0001043\nalias: growth_facil\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"growth_habit/","title":"Slot: growth habit (growth_habit)","text":"

Characteristic shape, appearance or growth form of a plant species

URI: MIXS:0001044

"},{"location":"growth_habit/#inheritance","title":"Inheritance","text":""},{"location":"growth_habit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"growth_habit/#properties","title":"Properties","text":""},{"location":"growth_habit/#aliases","title":"Aliases","text":""},{"location":"growth_habit/#examples","title":"Examples","text":"Value spreading"},{"location":"growth_habit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"growth_habit/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"growth_habit/#schema-source","title":"Schema Source","text":""},{"location":"growth_habit/#linkml-source","title":"LinkML Source","text":"
name: growth_habit\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Characteristic shape, appearance or growth form of a plant species\ntitle: growth habit\nexamples:\n- value: spreading\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth habit\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001044\nalias: growth_habit\ndomain_of:\n- Biosample\nrange: growth_habit_enum\nmultivalued: false\n\n
"},{"location":"growth_hormone_regm/","title":"Slot: growth hormone regimen (growth_hormone_regm)","text":"

Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens

URI: MIXS:0000560

"},{"location":"growth_hormone_regm/#inheritance","title":"Inheritance","text":""},{"location":"growth_hormone_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"growth_hormone_regm/#properties","title":"Properties","text":""},{"location":"growth_hormone_regm/#aliases","title":"Aliases","text":""},{"location":"growth_hormone_regm/#examples","title":"Examples","text":"Value abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"growth_hormone_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"growth_hormone_regm/#annotations","title":"Annotations","text":"property value expected_value growth hormone name;growth hormone amount;treatment interval and duration"},{"location":"growth_hormone_regm/#schema-source","title":"Schema Source","text":""},{"location":"growth_hormone_regm/#linkml-source","title":"LinkML Source","text":"
name: growth_hormone_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: growth hormone name;growth hormone amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of growth hormones; should\n  include the name of growth hormone, amount administered, treatment regimen including\n  how many times the treatment was repeated, how long each treatment lasted, and the\n  start and end time of the entire treatment; can include multiple growth hormone\n  regimens\ntitle: growth hormone regimen\nexamples:\n- value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth hormone regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000560\nalias: growth_hormone_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gtdbtk_class/","title":"Slot: gtdbtk_class","text":"

URI: nmdc:gtdbtk_class

"},{"location":"gtdbtk_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_class/#properties","title":"Properties","text":""},{"location":"gtdbtk_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_class/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_class/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_class\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_domain/","title":"Slot: gtdbtk_domain","text":"

URI: nmdc:gtdbtk_domain

"},{"location":"gtdbtk_domain/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_domain/#properties","title":"Properties","text":""},{"location":"gtdbtk_domain/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_domain/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_domain/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_domain\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_domain\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_family/","title":"Slot: gtdbtk_family","text":"

URI: nmdc:gtdbtk_family

"},{"location":"gtdbtk_family/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_family/#properties","title":"Properties","text":""},{"location":"gtdbtk_family/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_family/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_family/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_family\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_family\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_genus/","title":"Slot: gtdbtk_genus","text":"

URI: nmdc:gtdbtk_genus

"},{"location":"gtdbtk_genus/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_genus/#properties","title":"Properties","text":""},{"location":"gtdbtk_genus/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_genus/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_genus/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_genus\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_genus\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_order/","title":"Slot: gtdbtk_order","text":"

URI: nmdc:gtdbtk_order

"},{"location":"gtdbtk_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_order/#properties","title":"Properties","text":""},{"location":"gtdbtk_order/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_order/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_order/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_order\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_order\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_phylum/","title":"Slot: gtdbtk_phylum","text":"

URI: nmdc:gtdbtk_phylum

"},{"location":"gtdbtk_phylum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_phylum/#properties","title":"Properties","text":""},{"location":"gtdbtk_phylum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_phylum/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_phylum/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_phylum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_phylum\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_species/","title":"Slot: gtdbtk_species","text":"

URI: nmdc:gtdbtk_species

"},{"location":"gtdbtk_species/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_species/#properties","title":"Properties","text":""},{"location":"gtdbtk_species/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_species/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_species/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_species\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_species\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"habitat/","title":"Slot: habitat","text":"

URI: nmdc:habitat

"},{"location":"habitat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment no"},{"location":"habitat/#properties","title":"Properties","text":""},{"location":"habitat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"habitat/#schema-source","title":"Schema Source","text":""},{"location":"habitat/#linkml-source","title":"LinkML Source","text":"
name: habitat\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: habitat\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: string\n\n
"},{"location":"hall_count/","title":"Slot: hallway/corridor count (hall_count)","text":"

The total count of hallways and cooridors in the built structure

URI: MIXS:0000228

"},{"location":"hall_count/#inheritance","title":"Inheritance","text":""},{"location":"hall_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hall_count/#properties","title":"Properties","text":""},{"location":"hall_count/#aliases","title":"Aliases","text":""},{"location":"hall_count/#examples","title":"Examples","text":"Value"},{"location":"hall_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hall_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"hall_count/#schema-source","title":"Schema Source","text":""},{"location":"hall_count/#linkml-source","title":"LinkML Source","text":"
name: hall_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The total count of hallways and cooridors in the built structure\ntitle: hallway/corridor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hallway/corridor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000228\nalias: hall_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"handidness/","title":"Slot: handidness (handidness)","text":"

The handidness of the individual sampled

URI: MIXS:0000809

"},{"location":"handidness/#inheritance","title":"Inheritance","text":""},{"location":"handidness/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"handidness/#properties","title":"Properties","text":""},{"location":"handidness/#aliases","title":"Aliases","text":""},{"location":"handidness/#examples","title":"Examples","text":"Value right handedness"},{"location":"handidness/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"handidness/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"handidness/#schema-source","title":"Schema Source","text":""},{"location":"handidness/#linkml-source","title":"LinkML Source","text":"
name: handidness\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The handidness of the individual sampled\ntitle: handidness\nexamples:\n- value: right handedness\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- handidness\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000809\nalias: handidness\ndomain_of:\n- Biosample\nrange: handidness_enum\nmultivalued: false\n\n
"},{"location":"has_boolean_value/","title":"Slot: has_boolean_value","text":"

Links a quantity value to a boolean

URI: nmdc:has_boolean_value

"},{"location":"has_boolean_value/#properties","title":"Properties","text":""},{"location":"has_boolean_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_boolean_value/#schema-source","title":"Schema Source","text":""},{"location":"has_boolean_value/#linkml-source","title":"LinkML Source","text":"
name: has_boolean_value\ndescription: Links a quantity value to a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_boolean_value\nrange: boolean\n\n
"},{"location":"has_calibration/","title":"Slot: has_calibration","text":"

a calibration instance associated with a process

URI: nmdc:has_calibration

"},{"location":"has_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NomAnalysis no MetabolomicsAnalysis no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"has_calibration/#properties","title":"Properties","text":""},{"location":"has_calibration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_calibration/#schema-source","title":"Schema Source","text":""},{"location":"has_calibration/#linkml-source","title":"LinkML Source","text":"
name: has_calibration\ndescription: a calibration instance associated with a process\nnotes:\n- 'has_calibration slot will be removed from all WorkflowExecution classes but remain\n  on the MassSpectrometry class after an ingest of the appropriate set has occurred.  Once\n  this has occurred, this slot''s range can be updated to CalibrationInformation and\n  class/slot definitions can move to nmdc.yaml.   See PR #29 in Berkeley schema.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_calibration\ndomain_of:\n- MassSpectrometry\n- MetabolomicsAnalysis\n- NomAnalysis\nrange: string\nany_of:\n- range: CalibrationInformation\n- range: string\n\n
"},{"location":"has_chromatography_configuration/","title":"Slot: has_chromatography_configuration","text":"

The identifier of the associated ChromatographyConfiguration, providing information about how a sample was introduced into the mass spectrometer.

URI: nmdc:has_chromatography_configuration

"},{"location":"has_chromatography_configuration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"has_chromatography_configuration/#properties","title":"Properties","text":""},{"location":"has_chromatography_configuration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_chromatography_configuration/#schema-source","title":"Schema Source","text":""},{"location":"has_chromatography_configuration/#linkml-source","title":"LinkML Source","text":"
name: has_chromatography_configuration\ndescription: The identifier of the associated ChromatographyConfiguration, providing\n  information about how a sample was introduced into the mass spectrometer.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_chromatography_configuration\ndomain_of:\n- MassSpectrometry\nrange: ChromatographyConfiguration\n\n
"},{"location":"has_credit_associations/","title":"Slot: has_credit_associations","text":"

This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study

URI: prov:qualifiedAssociation

"},{"location":"has_credit_associations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"has_credit_associations/#properties","title":"Properties","text":""},{"location":"has_credit_associations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_credit_associations/#annotations","title":"Annotations","text":"property value tooltip Other researchers associated with this study."},{"location":"has_credit_associations/#schema-source","title":"Schema Source","text":""},{"location":"has_credit_associations/#linkml-source","title":"LinkML Source","text":"
name: has_credit_associations\nannotations:\n  tooltip:\n    tag: tooltip\n    value: Other researchers associated with this study.\ndescription: 'This slot links a study to a credit association.  The credit association\n  will be linked to a person value and to a CRediT Contributor Roles term. Overall\n  semantics: person should get credit X for their participation in the study'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: prov:qualifiedAssociation\nalias: has_credit_associations\ndomain_of:\n- Study\nrange: CreditAssociation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"has_failure_categorization/","title":"Slot: has_failure_categorization","text":"

URI: nmdc:has_failure_categorization

"},{"location":"has_failure_categorization/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... no WorkflowExecution Represents an instance of an execution of a particular workflow no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetabolomicsAnalysis no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAssembly no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no LibraryPreparation no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"has_failure_categorization/#properties","title":"Properties","text":""},{"location":"has_failure_categorization/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_failure_categorization/#schema-source","title":"Schema Source","text":""},{"location":"has_failure_categorization/#linkml-source","title":"LinkML Source","text":"
name: has_failure_categorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_failure_categorization\ndomain_of:\n- PlannedProcess\nrange: FailureCategorization\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"has_function/","title":"Slot: has_function","text":"

URI: nmdc:has_function

"},{"location":"has_function/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e yes"},{"location":"has_function/#properties","title":"Properties","text":""},{"location":"has_function/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_function/#schema-source","title":"Schema Source","text":""},{"location":"has_function/#linkml-source","title":"LinkML Source","text":"
name: has_function\nnotes:\n- the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm,\n- but is actually taking string arguments in MongoDB,\n- and those are frequently fulltext, not CURIEs. MAM 2021-06-23\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_function\ndomain_of:\n- FunctionalAnnotation\nrange: string\npattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n\n
"},{"location":"has_input/","title":"Slot: has_input","text":"

An input to a process.

URI: nmdc:has_input

"},{"location":"has_input/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... yes WorkflowExecution Represents an instance of an execution of a particular workflow yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts yes ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotation yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes NomAnalysis no CollectingBiosamplesFromSite yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes MetabolomicsAnalysis no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAssembly no MetagenomeSequencing Initial sequencing activity that precedes any analysis yes FiltrationProcess The process of segregation of phases; e yes LibraryPreparation yes Pooling physical combination of several instances of like material yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... yes StorageProcess A planned process with the objective to preserve and protect material entitie... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no DataGeneration The methods and processes used to generate omics data from a biosample or org... yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"has_input/#properties","title":"Properties","text":""},{"location":"has_input/#aliases","title":"Aliases","text":""},{"location":"has_input/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_input/#schema-source","title":"Schema Source","text":""},{"location":"has_input/#linkml-source","title":"LinkML Source","text":"
name: has_input\ndescription: An input to a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- input\nrank: 1000\nalias: has_input\ndomain_of:\n- PlannedProcess\nrange: NamedThing\nmultivalued: true\n\n
"},{"location":"has_mass_spectrometry_configuration/","title":"Slot: has_mass_spectrometry_configuration","text":"

The identifier of the associated MassSpectrometryConfiguration.

URI: nmdc:has_mass_spectrometry_configuration

"},{"location":"has_mass_spectrometry_configuration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"has_mass_spectrometry_configuration/#properties","title":"Properties","text":""},{"location":"has_mass_spectrometry_configuration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_mass_spectrometry_configuration/#schema-source","title":"Schema Source","text":""},{"location":"has_mass_spectrometry_configuration/#linkml-source","title":"LinkML Source","text":"
name: has_mass_spectrometry_configuration\ndescription: The identifier of the associated MassSpectrometryConfiguration.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_mass_spectrometry_configuration\ndomain_of:\n- MassSpectrometry\nrange: MassSpectrometryConfiguration\n\n
"},{"location":"has_maximum_numeric_value/","title":"Slot: has_maximum_numeric_value","text":"

The maximum value part, expressed as number, of the quantity value when the value covers a range.

URI: nmdc:has_maximum_numeric_value

"},{"location":"has_maximum_numeric_value/#inheritance","title":"Inheritance","text":""},{"location":"has_maximum_numeric_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e no"},{"location":"has_maximum_numeric_value/#properties","title":"Properties","text":""},{"location":"has_maximum_numeric_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_maximum_numeric_value/#schema-source","title":"Schema Source","text":""},{"location":"has_maximum_numeric_value/#linkml-source","title":"LinkML Source","text":"
name: has_maximum_numeric_value\ndescription: The maximum value part, expressed as number, of the quantity value when\n  the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_maximum_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\n
"},{"location":"has_metabolite_identifications/","title":"Slot: has_metabolite_identifications","text":"

URI: nmdc:has_metabolite_identifications

"},{"location":"has_metabolite_identifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysis no"},{"location":"has_metabolite_identifications/#properties","title":"Properties","text":""},{"location":"has_metabolite_identifications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_metabolite_identifications/#schema-source","title":"Schema Source","text":""},{"location":"has_metabolite_identifications/#linkml-source","title":"LinkML Source","text":"
name: has_metabolite_identifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_metabolite_identifications\ndomain_of:\n- MetabolomicsAnalysis\nrange: MetaboliteIdentification\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"has_minimum_numeric_value/","title":"Slot: has_minimum_numeric_value","text":"

The minimum value part, expressed as number, of the quantity value when the value covers a range.

URI: nmdc:has_minimum_numeric_value

"},{"location":"has_minimum_numeric_value/#inheritance","title":"Inheritance","text":""},{"location":"has_minimum_numeric_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e no"},{"location":"has_minimum_numeric_value/#properties","title":"Properties","text":""},{"location":"has_minimum_numeric_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_minimum_numeric_value/#schema-source","title":"Schema Source","text":""},{"location":"has_minimum_numeric_value/#linkml-source","title":"LinkML Source","text":"
name: has_minimum_numeric_value\ndescription: The minimum value part, expressed as number, of the quantity value when\n  the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_minimum_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\n
"},{"location":"has_numeric_value/","title":"Slot: has_numeric_value","text":"

Links a quantity value to a number

URI: nmdc:has_numeric_value

"},{"location":"has_numeric_value/#inheritance","title":"Inheritance","text":""},{"location":"has_numeric_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e yes"},{"location":"has_numeric_value/#properties","title":"Properties","text":""},{"location":"has_numeric_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_numeric_value/#schema-source","title":"Schema Source","text":""},{"location":"has_numeric_value/#linkml-source","title":"LinkML Source","text":"
name: has_numeric_value\ndescription: Links a quantity value to a number\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- qud:quantityValue\n- schema:value\nrank: 1000\nalias: has_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\n
"},{"location":"has_output/","title":"Slot: has_output","text":"

An output from a process.

URI: nmdc:has_output

"},{"location":"has_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... yes WorkflowExecution Represents an instance of an execution of a particular workflow yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts yes ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotation yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes NomAnalysis no CollectingBiosamplesFromSite yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes MetabolomicsAnalysis no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAssembly no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e yes LibraryPreparation yes Pooling physical combination of several instances of like material yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... yes StorageProcess A planned process with the objective to preserve and protect material entitie... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no DataGeneration The methods and processes used to generate omics data from a biosample or org... yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"has_output/#properties","title":"Properties","text":""},{"location":"has_output/#aliases","title":"Aliases","text":""},{"location":"has_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_output/#schema-source","title":"Schema Source","text":""},{"location":"has_output/#linkml-source","title":"LinkML Source","text":"
name: has_output\ndescription: An output from a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- output\nrank: 1000\nalias: has_output\ndomain_of:\n- PlannedProcess\nrange: NamedThing\nmultivalued: true\n\n
"},{"location":"has_peptide_quantifications/","title":"Slot: has_peptide_quantifications","text":"

URI: nmdc:has_peptide_quantifications

"},{"location":"has_peptide_quantifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no"},{"location":"has_peptide_quantifications/#properties","title":"Properties","text":""},{"location":"has_peptide_quantifications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_peptide_quantifications/#schema-source","title":"Schema Source","text":""},{"location":"has_peptide_quantifications/#linkml-source","title":"LinkML Source","text":"
name: has_peptide_quantifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_peptide_quantifications\ndomain_of:\n- MetaproteomicsAnalysis\nrange: PeptideQuantification\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"has_process_parts/","title":"Slot: has_process_parts","text":"

A list of process parts that make up a protocol.

URI: nmdc:has_process_parts

"},{"location":"has_process_parts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProtocolExecution A PlannedProces that has PlannedProcess parts yes"},{"location":"has_process_parts/#properties","title":"Properties","text":""},{"location":"has_process_parts/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_process_parts/#schema-source","title":"Schema Source","text":""},{"location":"has_process_parts/#linkml-source","title":"LinkML Source","text":"
name: has_process_parts\ndescription: A list of process parts that make up a protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: has_process_parts\ndomain_of:\n- ProtocolExecution\nrange: PlannedProcess\nrequired: true\nmultivalued: true\n\n
"},{"location":"has_raw_value/","title":"Slot: has_raw_value","text":"

The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"

URI: nmdc:has_raw_value

"},{"location":"has_raw_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TimestampValue A value that is a timestamp no TextValue A basic string value no ImageValue An attribute value representing an image no GeolocationValue A normalized value for a location on the earth's surface yes ControlledTermValue A controlled term or class from an ontology no AttributeValue The value for any value of a attribute for a sample no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no PersonValue An attribute value representing a person yes QuantityValue A simple quantity, e yes"},{"location":"has_raw_value/#properties","title":"Properties","text":""},{"location":"has_raw_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_raw_value/#schema-source","title":"Schema Source","text":""},{"location":"has_raw_value/#linkml-source","title":"LinkML Source","text":"
name: has_raw_value\ndescription: The value that was specified for an annotation in raw form, i.e. a string.\n  E.g. \"2 cm\" or \"2-4 cm\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_raw_value\ndomain_of:\n- AttributeValue\nrange: string\n\n
"},{"location":"has_unit/","title":"Slot: has_unit","text":"

Links a QuantityValue to a unit

URI: nmdc:has_unit

"},{"location":"has_unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e yes"},{"location":"has_unit/#properties","title":"Properties","text":""},{"location":"has_unit/#aliases","title":"Aliases","text":""},{"location":"has_unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_unit/#schema-source","title":"Schema Source","text":""},{"location":"has_unit/#linkml-source","title":"LinkML Source","text":"
name: has_unit\ndescription: Links a QuantityValue to a unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- scale\nmappings:\n- qud:unit\n- schema:unitCode\nrank: 1000\nalias: has_unit\ndomain_of:\n- QuantityValue\nrange: unit\n\n
"},{"location":"hc_produced/","title":"Slot: hydrocarbon type produced (hc_produced)","text":"

Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000989

"},{"location":"hc_produced/#inheritance","title":"Inheritance","text":""},{"location":"hc_produced/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hc_produced/#properties","title":"Properties","text":""},{"location":"hc_produced/#aliases","title":"Aliases","text":""},{"location":"hc_produced/#examples","title":"Examples","text":"Value Gas"},{"location":"hc_produced/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hc_produced/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"hc_produced/#schema-source","title":"Schema Source","text":""},{"location":"hc_produced/#linkml-source","title":"LinkML Source","text":"
name: hc_produced\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n  etc). If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: hydrocarbon type produced\nexamples:\n- value: Gas\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon type produced\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000989\nalias: hc_produced\ndomain_of:\n- Biosample\nrange: hc_produced_enum\nmultivalued: false\n\n
"},{"location":"hcr/","title":"Slot: hydrocarbon resource type (hcr)","text":"

Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000988

"},{"location":"hcr/#inheritance","title":"Inheritance","text":""},{"location":"hcr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr/#properties","title":"Properties","text":""},{"location":"hcr/#aliases","title":"Aliases","text":""},{"location":"hcr/#examples","title":"Examples","text":"Value Oil Sand"},{"location":"hcr/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"hcr/#schema-source","title":"Schema Source","text":""},{"location":"hcr/#linkml-source","title":"LinkML Source","text":"
name: hcr\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined\n  as a natural environmental feature containing large amounts of hydrocarbons at high\n  concentrations potentially suitable for commercial exploitation. This term should\n  not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich\n  environments with currently limited commercial interest such as seeps, outcrops,\n  gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\"\n  field\ntitle: hydrocarbon resource type\nexamples:\n- value: Oil Sand\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000988\nalias: hcr\ndomain_of:\n- Biosample\nrange: hcr_enum\nmultivalued: false\n\n
"},{"location":"hcr_fw_salinity/","title":"Slot: formation water salinity (hcr_fw_salinity)","text":"

Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS

URI: MIXS:0000406

"},{"location":"hcr_fw_salinity/#inheritance","title":"Inheritance","text":""},{"location":"hcr_fw_salinity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr_fw_salinity/#properties","title":"Properties","text":""},{"location":"hcr_fw_salinity/#aliases","title":"Aliases","text":""},{"location":"hcr_fw_salinity/#examples","title":"Examples","text":"Value"},{"location":"hcr_fw_salinity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr_fw_salinity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"hcr_fw_salinity/#schema-source","title":"Schema Source","text":""},{"location":"hcr_fw_salinity/#linkml-source","title":"LinkML Source","text":"
name: hcr_fw_salinity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original formation water salinity (prior to secondary recovery e.g. Waterflooding)\n  expressed as TDS\ntitle: formation water salinity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- formation water salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000406\nalias: hcr_fw_salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"hcr_geol_age/","title":"Slot: hydrocarbon resource geological age (hcr_geol_age)","text":"

Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000993

"},{"location":"hcr_geol_age/#inheritance","title":"Inheritance","text":""},{"location":"hcr_geol_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr_geol_age/#properties","title":"Properties","text":""},{"location":"hcr_geol_age/#aliases","title":"Aliases","text":""},{"location":"hcr_geol_age/#examples","title":"Examples","text":"Value Silurian"},{"location":"hcr_geol_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr_geol_age/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"hcr_geol_age/#schema-source","title":"Schema Source","text":""},{"location":"hcr_geol_age/#linkml-source","title":"LinkML Source","text":"
name: hcr_geol_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n  If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: hydrocarbon resource geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000993\nalias: hcr_geol_age\ndomain_of:\n- Biosample\nrange: hcr_geol_age_enum\nmultivalued: false\n\n
"},{"location":"hcr_pressure/","title":"Slot: hydrocarbon resource original pressure (hcr_pressure)","text":"

Original pressure of the hydrocarbon resource

URI: MIXS:0000395

"},{"location":"hcr_pressure/#inheritance","title":"Inheritance","text":""},{"location":"hcr_pressure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr_pressure/#properties","title":"Properties","text":""},{"location":"hcr_pressure/#aliases","title":"Aliases","text":""},{"location":"hcr_pressure/#examples","title":"Examples","text":"Value"},{"location":"hcr_pressure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr_pressure/#annotations","title":"Annotations","text":"property value expected_value measurement value range"},{"location":"hcr_pressure/#schema-source","title":"Schema Source","text":""},{"location":"hcr_pressure/#linkml-source","title":"LinkML Source","text":"
name: hcr_pressure\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: atmosphere, kilopascal\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original pressure of the hydrocarbon resource\ntitle: hydrocarbon resource original pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original pressure\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000395\nalias: hcr_pressure\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"hcr_temp/","title":"Slot: hydrocarbon resource original temperature (hcr_temp)","text":"

Original temperature of the hydrocarbon resource

URI: MIXS:0000393

"},{"location":"hcr_temp/#inheritance","title":"Inheritance","text":""},{"location":"hcr_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr_temp/#properties","title":"Properties","text":""},{"location":"hcr_temp/#aliases","title":"Aliases","text":""},{"location":"hcr_temp/#examples","title":"Examples","text":"Value 150-295 degree Celsius"},{"location":"hcr_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value range"},{"location":"hcr_temp/#schema-source","title":"Schema Source","text":""},{"location":"hcr_temp/#linkml-source","title":"LinkML Source","text":"
name: hcr_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original temperature of the hydrocarbon resource\ntitle: hydrocarbon resource original temperature\nexamples:\n- value: 150-295 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original temperature\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000393\nalias: hcr_temp\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"heat_cool_type/","title":"Slot: heating and cooling system type (heat_cool_type)","text":"

Methods of conditioning or heating a room or building

URI: MIXS:0000766

"},{"location":"heat_cool_type/#inheritance","title":"Inheritance","text":""},{"location":"heat_cool_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"heat_cool_type/#properties","title":"Properties","text":""},{"location":"heat_cool_type/#aliases","title":"Aliases","text":""},{"location":"heat_cool_type/#examples","title":"Examples","text":"Value heat pump"},{"location":"heat_cool_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heat_cool_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"heat_cool_type/#schema-source","title":"Schema Source","text":""},{"location":"heat_cool_type/#linkml-source","title":"LinkML Source","text":"
name: heat_cool_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Methods of conditioning or heating a room or building\ntitle: heating and cooling system type\nexamples:\n- value: heat pump\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating and cooling system type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000766\nalias: heat_cool_type\ndomain_of:\n- Biosample\nrange: heat_cool_type_enum\nmultivalued: true\n\n
"},{"location":"heat_deliv_loc/","title":"Slot: heating delivery locations (heat_deliv_loc)","text":"

The location of heat delivery within the room

URI: MIXS:0000810

"},{"location":"heat_deliv_loc/#inheritance","title":"Inheritance","text":""},{"location":"heat_deliv_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"heat_deliv_loc/#properties","title":"Properties","text":""},{"location":"heat_deliv_loc/#aliases","title":"Aliases","text":""},{"location":"heat_deliv_loc/#examples","title":"Examples","text":"Value north"},{"location":"heat_deliv_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heat_deliv_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"heat_deliv_loc/#schema-source","title":"Schema Source","text":""},{"location":"heat_deliv_loc/#linkml-source","title":"LinkML Source","text":"
name: heat_deliv_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The location of heat delivery within the room\ntitle: heating delivery locations\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating delivery locations\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000810\nalias: heat_deliv_loc\ndomain_of:\n- Biosample\nrange: heat_deliv_loc_enum\nmultivalued: false\n\n
"},{"location":"heat_sys_deliv_meth/","title":"Slot: heating system delivery method (heat_sys_deliv_meth)","text":"

The method by which the heat is delivered through the system

URI: MIXS:0000812

"},{"location":"heat_sys_deliv_meth/#inheritance","title":"Inheritance","text":""},{"location":"heat_sys_deliv_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"heat_sys_deliv_meth/#properties","title":"Properties","text":""},{"location":"heat_sys_deliv_meth/#aliases","title":"Aliases","text":""},{"location":"heat_sys_deliv_meth/#examples","title":"Examples","text":"Value radiant"},{"location":"heat_sys_deliv_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heat_sys_deliv_meth/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"heat_sys_deliv_meth/#schema-source","title":"Schema Source","text":""},{"location":"heat_sys_deliv_meth/#linkml-source","title":"LinkML Source","text":"
name: heat_sys_deliv_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The method by which the heat is delivered through the system\ntitle: heating system delivery method\nexamples:\n- value: radiant\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system delivery method\nrank: 1000\nis_a: core field\nstring_serialization: '[conductive|radiant]'\nslot_uri: MIXS:0000812\nalias: heat_sys_deliv_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"heat_system_id/","title":"Slot: heating system identifier (heat_system_id)","text":"

The heating system identifier

URI: MIXS:0000833

"},{"location":"heat_system_id/#inheritance","title":"Inheritance","text":""},{"location":"heat_system_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"heat_system_id/#properties","title":"Properties","text":""},{"location":"heat_system_id/#aliases","title":"Aliases","text":""},{"location":"heat_system_id/#examples","title":"Examples","text":"Value"},{"location":"heat_system_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heat_system_id/#annotations","title":"Annotations","text":"property value expected_value unique identifier"},{"location":"heat_system_id/#schema-source","title":"Schema Source","text":""},{"location":"heat_system_id/#linkml-source","title":"LinkML Source","text":"
name: heat_system_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: unique identifier\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The heating system identifier\ntitle: heating system identifier\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000833\nalias: heat_system_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"heavy_metals/","title":"Slot: extreme_unusual_properties/heavy metals (heavy_metals)","text":"

Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.

URI: MIXS:0000652

"},{"location":"heavy_metals/#inheritance","title":"Inheritance","text":""},{"location":"heavy_metals/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"heavy_metals/#properties","title":"Properties","text":""},{"location":"heavy_metals/#aliases","title":"Aliases","text":""},{"location":"heavy_metals/#examples","title":"Examples","text":"Value mercury;0.09 micrograms per gram"},{"location":"heavy_metals/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heavy_metals/#annotations","title":"Annotations","text":"property value expected_value heavy metal name;measurement value unit"},{"location":"heavy_metals/#schema-source","title":"Schema Source","text":""},{"location":"heavy_metals/#linkml-source","title":"LinkML Source","text":"
name: heavy_metals\nannotations:\n  expected_value:\n    tag: expected_value\n    value: heavy metal name;measurement value unit\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per gram\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Heavy metals present in the sequenced sample and their concentrations.\n  For multiple heavy metals and concentrations, add multiple copies of this field.\ntitle: extreme_unusual_properties/heavy metals\nexamples:\n- value: mercury;0.09 micrograms per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000652\nalias: heavy_metals\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"heavy_metals_meth/","title":"Slot: extreme_unusual_properties/heavy metals method (heavy_metals_meth)","text":"

Reference or method used in determining heavy metals

URI: MIXS:0000343

"},{"location":"heavy_metals_meth/#inheritance","title":"Inheritance","text":""},{"location":"heavy_metals_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"heavy_metals_meth/#properties","title":"Properties","text":""},{"location":"heavy_metals_meth/#aliases","title":"Aliases","text":""},{"location":"heavy_metals_meth/#examples","title":"Examples","text":"Value"},{"location":"heavy_metals_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heavy_metals_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"heavy_metals_meth/#schema-source","title":"Schema Source","text":""},{"location":"heavy_metals_meth/#linkml-source","title":"LinkML Source","text":"
name: heavy_metals_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining heavy metals\ntitle: extreme_unusual_properties/heavy metals method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000343\nalias: heavy_metals_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"height_carper_fiber/","title":"Slot: height carpet fiber mat (height_carper_fiber)","text":"

The average carpet fiber height in the indoor environment

URI: MIXS:0000167

"},{"location":"height_carper_fiber/#inheritance","title":"Inheritance","text":""},{"location":"height_carper_fiber/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"height_carper_fiber/#properties","title":"Properties","text":""},{"location":"height_carper_fiber/#aliases","title":"Aliases","text":""},{"location":"height_carper_fiber/#examples","title":"Examples","text":"Value"},{"location":"height_carper_fiber/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"height_carper_fiber/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"height_carper_fiber/#schema-source","title":"Schema Source","text":""},{"location":"height_carper_fiber/#linkml-source","title":"LinkML Source","text":"
name: height_carper_fiber\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average carpet fiber height in the indoor environment\ntitle: height carpet fiber mat\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- height carpet fiber mat\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000167\nalias: height_carper_fiber\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"herbicide_regm/","title":"Slot: herbicide regimen (herbicide_regm)","text":"

Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000561

"},{"location":"herbicide_regm/#inheritance","title":"Inheritance","text":""},{"location":"herbicide_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"herbicide_regm/#properties","title":"Properties","text":""},{"location":"herbicide_regm/#aliases","title":"Aliases","text":""},{"location":"herbicide_regm/#examples","title":"Examples","text":"Value atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"herbicide_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"herbicide_regm/#annotations","title":"Annotations","text":"property value expected_value herbicide name;herbicide amount;treatment interval and duration"},{"location":"herbicide_regm/#schema-source","title":"Schema Source","text":""},{"location":"herbicide_regm/#linkml-source","title":"LinkML Source","text":"
name: herbicide_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: herbicide name;herbicide amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of herbicides; information\n  about treatment involving use of growth hormones; should include the name of herbicide,\n  amount administered, treatment regimen including how many times the treatment was\n  repeated, how long each treatment lasted, and the start and end time of the entire\n  treatment; can include multiple regimens\ntitle: herbicide regimen\nexamples:\n- value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- herbicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000561\nalias: herbicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"highest_similarity_score/","title":"Slot: highest_similarity_score","text":"

URI: nmdc:highest_similarity_score

"},{"location":"highest_similarity_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"highest_similarity_score/#properties","title":"Properties","text":""},{"location":"highest_similarity_score/#todos","title":"TODOs","text":""},{"location":"highest_similarity_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"highest_similarity_score/#schema-source","title":"Schema Source","text":""},{"location":"highest_similarity_score/#linkml-source","title":"LinkML Source","text":"
name: highest_similarity_score\ntodos:\n- Yuri to fill in description\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: highest_similarity_score\ndomain_of:\n- MetaboliteIdentification\nrange: float\n\n
"},{"location":"homepage_website/","title":"Slot: homepage_website","text":"

The website address (URL) of an entity's homepage.

URI: nmdc:homepage_website

"},{"location":"homepage_website/#inheritance","title":"Inheritance","text":""},{"location":"homepage_website/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"homepage_website/#properties","title":"Properties","text":""},{"location":"homepage_website/#examples","title":"Examples","text":"Value https://www.neonscience.org/"},{"location":"homepage_website/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"homepage_website/#schema-source","title":"Schema Source","text":""},{"location":"homepage_website/#linkml-source","title":"LinkML Source","text":"
name: homepage_website\ndescription: The website address (URL) of an entity's homepage.\nexamples:\n- value: https://www.neonscience.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: websites\nalias: homepage_website\ndomain_of:\n- Study\nrange: string\nmultivalued: true\npattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\nmaximum_cardinality: 1\n\n
"},{"location":"horizon_meth/","title":"Slot: soil horizon method (horizon_meth)","text":"

Reference or method used in determining the horizon

URI: MIXS:0000321

"},{"location":"horizon_meth/#inheritance","title":"Inheritance","text":""},{"location":"horizon_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"horizon_meth/#properties","title":"Properties","text":""},{"location":"horizon_meth/#aliases","title":"Aliases","text":""},{"location":"horizon_meth/#examples","title":"Examples","text":"Value"},{"location":"horizon_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"horizon_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"horizon_meth/#schema-source","title":"Schema Source","text":""},{"location":"horizon_meth/#linkml-source","title":"LinkML Source","text":"
name: horizon_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining the horizon\ntitle: soil horizon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000321\nalias: horizon_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_age/","title":"Slot: host age (host_age)","text":"

Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees

URI: MIXS:0000255

"},{"location":"host_age/#inheritance","title":"Inheritance","text":""},{"location":"host_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_age/#properties","title":"Properties","text":""},{"location":"host_age/#aliases","title":"Aliases","text":""},{"location":"host_age/#examples","title":"Examples","text":"Value 10 days"},{"location":"host_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_age/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"host_age/#schema-source","title":"Schema Source","text":""},{"location":"host_age/#linkml-source","title":"LinkML Source","text":"
name: host_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: year, day, hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Age of host at the time of sampling; relevant scale depends on species\n  and study, e.g. Could be seconds for amoebae or centuries for trees\ntitle: host age\nexamples:\n- value: 10 days\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000255\nalias: host_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_body_habitat/","title":"Slot: host body habitat (host_body_habitat)","text":"

Original body habitat where the sample was obtained from

URI: MIXS:0000866

"},{"location":"host_body_habitat/#inheritance","title":"Inheritance","text":""},{"location":"host_body_habitat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_body_habitat/#properties","title":"Properties","text":""},{"location":"host_body_habitat/#aliases","title":"Aliases","text":""},{"location":"host_body_habitat/#examples","title":"Examples","text":"Value nasopharynx"},{"location":"host_body_habitat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_body_habitat/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"host_body_habitat/#schema-source","title":"Schema Source","text":""},{"location":"host_body_habitat/#linkml-source","title":"LinkML Source","text":"
name: host_body_habitat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original body habitat where the sample was obtained from\ntitle: host body habitat\nexamples:\n- value: nasopharynx\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body habitat\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000866\nalias: host_body_habitat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_body_product/","title":"Slot: host body product (host_body_product)","text":"

Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon

URI: MIXS:0000888

"},{"location":"host_body_product/#inheritance","title":"Inheritance","text":""},{"location":"host_body_product/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_body_product/#properties","title":"Properties","text":""},{"location":"host_body_product/#aliases","title":"Aliases","text":""},{"location":"host_body_product/#examples","title":"Examples","text":"Value Portion of mucus [fma66938]"},{"location":"host_body_product/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_body_product/#annotations","title":"Annotations","text":"property value expected_value FMA or UBERON"},{"location":"host_body_product/#schema-source","title":"Schema Source","text":""},{"location":"host_body_product/#linkml-source","title":"LinkML Source","text":"
name: host_body_product\nannotations:\n  expected_value:\n    tag: expected_value\n    value: FMA or UBERON\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Substance produced by the body, e.g. Stool, mucus, where the sample was\n  obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n  ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or\n  https://www.ebi.ac.uk/ols/ontologies/uberon\ntitle: host body product\nexamples:\n- value: Portion of mucus [fma66938]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body product\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000888\nalias: host_body_product\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"host_body_site/","title":"Slot: host body site (host_body_site)","text":"

Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON

URI: MIXS:0000867

"},{"location":"host_body_site/#inheritance","title":"Inheritance","text":""},{"location":"host_body_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_body_site/#properties","title":"Properties","text":""},{"location":"host_body_site/#aliases","title":"Aliases","text":""},{"location":"host_body_site/#examples","title":"Examples","text":"Value gill [UBERON:0002535]"},{"location":"host_body_site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_body_site/#annotations","title":"Annotations","text":"property value expected_value FMA or UBERON"},{"location":"host_body_site/#schema-source","title":"Schema Source","text":""},{"location":"host_body_site/#linkml-source","title":"LinkML Source","text":"
name: host_body_site\nannotations:\n  expected_value:\n    tag: expected_value\n    value: FMA or UBERON\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of body site where the sample was obtained from, such as a specific\n  organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n  (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n  please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\ntitle: host body site\nexamples:\n- value: gill [UBERON:0002535]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body site\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000867\nalias: host_body_site\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"host_body_temp/","title":"Slot: host body temperature (host_body_temp)","text":"

Core body temperature of the host when sample was collected

URI: MIXS:0000274

"},{"location":"host_body_temp/#inheritance","title":"Inheritance","text":""},{"location":"host_body_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_body_temp/#properties","title":"Properties","text":""},{"location":"host_body_temp/#aliases","title":"Aliases","text":""},{"location":"host_body_temp/#examples","title":"Examples","text":"Value 15 degree Celsius"},{"location":"host_body_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_body_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_body_temp/#schema-source","title":"Schema Source","text":""},{"location":"host_body_temp/#linkml-source","title":"LinkML Source","text":"
name: host_body_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Core body temperature of the host when sample was collected\ntitle: host body temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000274\nalias: host_body_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_color/","title":"Slot: host color (host_color)","text":"

The color of host

URI: MIXS:0000260

"},{"location":"host_color/#inheritance","title":"Inheritance","text":""},{"location":"host_color/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_color/#properties","title":"Properties","text":""},{"location":"host_color/#aliases","title":"Aliases","text":""},{"location":"host_color/#examples","title":"Examples","text":"Value"},{"location":"host_color/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_color/#annotations","title":"Annotations","text":"property value expected_value color"},{"location":"host_color/#schema-source","title":"Schema Source","text":""},{"location":"host_color/#linkml-source","title":"LinkML Source","text":"
name: host_color\nannotations:\n  expected_value:\n    tag: expected_value\n    value: color\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The color of host\ntitle: host color\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host color\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000260\nalias: host_color\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_common_name/","title":"Slot: host common name (host_common_name)","text":"

Common name of the host.

URI: MIXS:0000248

"},{"location":"host_common_name/#inheritance","title":"Inheritance","text":""},{"location":"host_common_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_common_name/#properties","title":"Properties","text":""},{"location":"host_common_name/#aliases","title":"Aliases","text":""},{"location":"host_common_name/#examples","title":"Examples","text":"Value human"},{"location":"host_common_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_common_name/#annotations","title":"Annotations","text":"property value expected_value common name"},{"location":"host_common_name/#schema-source","title":"Schema Source","text":""},{"location":"host_common_name/#linkml-source","title":"LinkML Source","text":"
name: host_common_name\nannotations:\n  expected_value:\n    tag: expected_value\n    value: common name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Common name of the host.\ntitle: host common name\nexamples:\n- value: human\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host common name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000248\nalias: host_common_name\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_diet/","title":"Slot: host diet (host_diet)","text":"

Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types

URI: MIXS:0000869

"},{"location":"host_diet/#inheritance","title":"Inheritance","text":""},{"location":"host_diet/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_diet/#properties","title":"Properties","text":""},{"location":"host_diet/#aliases","title":"Aliases","text":""},{"location":"host_diet/#examples","title":"Examples","text":"Value herbivore"},{"location":"host_diet/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_diet/#annotations","title":"Annotations","text":"property value expected_value diet type"},{"location":"host_diet/#schema-source","title":"Schema Source","text":""},{"location":"host_diet/#linkml-source","title":"LinkML Source","text":"
name: host_diet\nannotations:\n  expected_value:\n    tag: expected_value\n    value: diet type\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Type of diet depending on the host, for animals omnivore, herbivore etc.,\n  for humans high-fat, meditteranean etc.; can include multiple diet types\ntitle: host diet\nexamples:\n- value: herbivore\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host diet\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000869\nalias: host_diet\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"host_disease_stat/","title":"Slot: host disease status (host_disease_stat)","text":"

List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text

URI: MIXS:0000031

"},{"location":"host_disease_stat/#inheritance","title":"Inheritance","text":""},{"location":"host_disease_stat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_disease_stat/#properties","title":"Properties","text":""},{"location":"host_disease_stat/#aliases","title":"Aliases","text":""},{"location":"host_disease_stat/#examples","title":"Examples","text":"Value rabies [DOID:11260]"},{"location":"host_disease_stat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_disease_stat/#annotations","title":"Annotations","text":"property value expected_value disease name or Disease Ontology term"},{"location":"host_disease_stat/#schema-source","title":"Schema Source","text":""},{"location":"host_disease_stat/#linkml-source","title":"LinkML Source","text":"
name: host_disease_stat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: disease name or Disease Ontology term\ndescription: List of diseases with which the host has been diagnosed; can include\n  multiple diagnoses. The value of the field depends on host; for humans the terms\n  should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,\n  non-human host diseases are free text\ntitle: host disease status\nexamples:\n- value: rabies [DOID:11260]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host disease status\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000031\nalias: host_disease_stat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_dry_mass/","title":"Slot: host dry mass (host_dry_mass)","text":"

Measurement of dry mass

URI: MIXS:0000257

"},{"location":"host_dry_mass/#inheritance","title":"Inheritance","text":""},{"location":"host_dry_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_dry_mass/#properties","title":"Properties","text":""},{"location":"host_dry_mass/#aliases","title":"Aliases","text":""},{"location":"host_dry_mass/#examples","title":"Examples","text":"Value 500 gram"},{"location":"host_dry_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_dry_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_dry_mass/#schema-source","title":"Schema Source","text":""},{"location":"host_dry_mass/#linkml-source","title":"LinkML Source","text":"
name: host_dry_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilogram, gram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of dry mass\ntitle: host dry mass\nexamples:\n- value: 500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host dry mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000257\nalias: host_dry_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_family_relation/","title":"Slot: host family relationship (host_family_relation)","text":"

Familial relationships to other hosts in the same study; can include multiple relationships

URI: MIXS:0000872

"},{"location":"host_family_relation/#inheritance","title":"Inheritance","text":""},{"location":"host_family_relation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_family_relation/#properties","title":"Properties","text":""},{"location":"host_family_relation/#aliases","title":"Aliases","text":""},{"location":"host_family_relation/#examples","title":"Examples","text":"Value offspring;Mussel25"},{"location":"host_family_relation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_family_relation/#annotations","title":"Annotations","text":"property value expected_value relationship type;arbitrary identifier"},{"location":"host_family_relation/#schema-source","title":"Schema Source","text":""},{"location":"host_family_relation/#linkml-source","title":"LinkML Source","text":"
name: host_family_relation\nannotations:\n  expected_value:\n    tag: expected_value\n    value: relationship type;arbitrary identifier\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Familial relationships to other hosts in the same study; can include\n  multiple relationships\ntitle: host family relationship\nexamples:\n- value: offspring;Mussel25\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host family relationship\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0000872\nalias: host_family_relation\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\n
"},{"location":"host_genotype/","title":"Slot: host genotype (host_genotype)","text":"

Observed genotype

URI: MIXS:0000365

"},{"location":"host_genotype/#inheritance","title":"Inheritance","text":""},{"location":"host_genotype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_genotype/#properties","title":"Properties","text":""},{"location":"host_genotype/#aliases","title":"Aliases","text":""},{"location":"host_genotype/#examples","title":"Examples","text":"Value C57BL/6"},{"location":"host_genotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_genotype/#annotations","title":"Annotations","text":"property value expected_value genotype"},{"location":"host_genotype/#schema-source","title":"Schema Source","text":""},{"location":"host_genotype/#linkml-source","title":"LinkML Source","text":"
name: host_genotype\nannotations:\n  expected_value:\n    tag: expected_value\n    value: genotype\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Observed genotype\ntitle: host genotype\nexamples:\n- value: C57BL/6\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host genotype\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000365\nalias: host_genotype\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_growth_cond/","title":"Slot: host growth conditions (host_growth_cond)","text":"

Literature reference giving growth conditions of the host

URI: MIXS:0000871

"},{"location":"host_growth_cond/#inheritance","title":"Inheritance","text":""},{"location":"host_growth_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_growth_cond/#properties","title":"Properties","text":""},{"location":"host_growth_cond/#aliases","title":"Aliases","text":""},{"location":"host_growth_cond/#examples","title":"Examples","text":"Value https://academic.oup.com/icesjms/article/68/2/349/617247"},{"location":"host_growth_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_growth_cond/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url or free text"},{"location":"host_growth_cond/#schema-source","title":"Schema Source","text":""},{"location":"host_growth_cond/#linkml-source","title":"LinkML Source","text":"
name: host_growth_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url or free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Literature reference giving growth conditions of the host\ntitle: host growth conditions\nexamples:\n- value: https://academic.oup.com/icesjms/article/68/2/349/617247\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host growth conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000871\nalias: host_growth_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_height/","title":"Slot: host height (host_height)","text":"

The height of subject

URI: MIXS:0000264

"},{"location":"host_height/#inheritance","title":"Inheritance","text":""},{"location":"host_height/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_height/#properties","title":"Properties","text":""},{"location":"host_height/#aliases","title":"Aliases","text":""},{"location":"host_height/#examples","title":"Examples","text":"Value 0.1 meter"},{"location":"host_height/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_height/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_height/#schema-source","title":"Schema Source","text":""},{"location":"host_height/#linkml-source","title":"LinkML Source","text":"
name: host_height\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: centimeter, millimeter, meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The height of subject\ntitle: host height\nexamples:\n- value: 0.1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000264\nalias: host_height\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_last_meal/","title":"Slot: host last meal (host_last_meal)","text":"

Content of last meal and time since feeding; can include multiple values

URI: MIXS:0000870

"},{"location":"host_last_meal/#inheritance","title":"Inheritance","text":""},{"location":"host_last_meal/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_last_meal/#properties","title":"Properties","text":""},{"location":"host_last_meal/#aliases","title":"Aliases","text":""},{"location":"host_last_meal/#examples","title":"Examples","text":"Value corn feed;P2H"},{"location":"host_last_meal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_last_meal/#annotations","title":"Annotations","text":"property value expected_value content;duration"},{"location":"host_last_meal/#schema-source","title":"Schema Source","text":""},{"location":"host_last_meal/#linkml-source","title":"LinkML Source","text":"
name: host_last_meal\nannotations:\n  expected_value:\n    tag: expected_value\n    value: content;duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Content of last meal and time since feeding; can include multiple values\ntitle: host last meal\nexamples:\n- value: corn feed;P2H\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host last meal\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000870\nalias: host_last_meal\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"host_length/","title":"Slot: host length (host_length)","text":"

The length of subject

URI: MIXS:0000256

"},{"location":"host_length/#inheritance","title":"Inheritance","text":""},{"location":"host_length/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_length/#properties","title":"Properties","text":""},{"location":"host_length/#aliases","title":"Aliases","text":""},{"location":"host_length/#examples","title":"Examples","text":"Value 1 meter"},{"location":"host_length/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_length/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_length/#schema-source","title":"Schema Source","text":""},{"location":"host_length/#linkml-source","title":"LinkML Source","text":"
name: host_length\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: centimeter, millimeter, meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The length of subject\ntitle: host length\nexamples:\n- value: 1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host length\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000256\nalias: host_length\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_life_stage/","title":"Slot: host life stage (host_life_stage)","text":"

Description of life stage of host

URI: MIXS:0000251

"},{"location":"host_life_stage/#inheritance","title":"Inheritance","text":""},{"location":"host_life_stage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_life_stage/#properties","title":"Properties","text":""},{"location":"host_life_stage/#aliases","title":"Aliases","text":""},{"location":"host_life_stage/#examples","title":"Examples","text":"Value adult"},{"location":"host_life_stage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_life_stage/#annotations","title":"Annotations","text":"property value expected_value stage"},{"location":"host_life_stage/#schema-source","title":"Schema Source","text":""},{"location":"host_life_stage/#linkml-source","title":"LinkML Source","text":"
name: host_life_stage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: stage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Description of life stage of host\ntitle: host life stage\nexamples:\n- value: adult\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host life stage\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000251\nalias: host_life_stage\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_name/","title":"Slot: host_name","text":"

URI: nmdc:host_name

"},{"location":"host_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_name/#properties","title":"Properties","text":""},{"location":"host_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_name/#schema-source","title":"Schema Source","text":""},{"location":"host_name/#linkml-source","title":"LinkML Source","text":"
name: host_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: host_name\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"host_phenotype/","title":"Slot: host phenotype (host_phenotype)","text":"

Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP

URI: MIXS:0000874

"},{"location":"host_phenotype/#inheritance","title":"Inheritance","text":""},{"location":"host_phenotype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_phenotype/#properties","title":"Properties","text":""},{"location":"host_phenotype/#aliases","title":"Aliases","text":""},{"location":"host_phenotype/#examples","title":"Examples","text":"Value elongated [PATO:0001154]"},{"location":"host_phenotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_phenotype/#annotations","title":"Annotations","text":"property value expected_value PATO or HP"},{"location":"host_phenotype/#schema-source","title":"Schema Source","text":""},{"location":"host_phenotype/#linkml-source","title":"LinkML Source","text":"
name: host_phenotype\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PATO or HP\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Phenotype of human or other host. For phenotypic quality ontology (pato)\n  (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For\n  Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\ntitle: host phenotype\nexamples:\n- value: elongated [PATO:0001154]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host phenotype\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000874\nalias: host_phenotype\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"host_sex/","title":"Slot: host sex (host_sex)","text":"

Gender or physical sex of the host.

URI: MIXS:0000811

"},{"location":"host_sex/#inheritance","title":"Inheritance","text":""},{"location":"host_sex/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_sex/#properties","title":"Properties","text":""},{"location":"host_sex/#aliases","title":"Aliases","text":""},{"location":"host_sex/#examples","title":"Examples","text":"Value non-binary"},{"location":"host_sex/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_sex/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"host_sex/#schema-source","title":"Schema Source","text":""},{"location":"host_sex/#linkml-source","title":"LinkML Source","text":"
name: host_sex\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Gender or physical sex of the host.\ntitle: host sex\nexamples:\n- value: non-binary\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000811\nalias: host_sex\ndomain_of:\n- Biosample\nrange: host_sex_enum\nmultivalued: false\n\n
"},{"location":"host_shape/","title":"Slot: host shape (host_shape)","text":"

Morphological shape of host

URI: MIXS:0000261

"},{"location":"host_shape/#inheritance","title":"Inheritance","text":""},{"location":"host_shape/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_shape/#properties","title":"Properties","text":""},{"location":"host_shape/#aliases","title":"Aliases","text":""},{"location":"host_shape/#examples","title":"Examples","text":"Value round"},{"location":"host_shape/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_shape/#annotations","title":"Annotations","text":"property value expected_value shape"},{"location":"host_shape/#schema-source","title":"Schema Source","text":""},{"location":"host_shape/#linkml-source","title":"LinkML Source","text":"
name: host_shape\nannotations:\n  expected_value:\n    tag: expected_value\n    value: shape\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Morphological shape of host\ntitle: host shape\nexamples:\n- value: round\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host shape\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000261\nalias: host_shape\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_subject_id/","title":"Slot: host subject id (host_subject_id)","text":"

A unique identifier by which each subject can be referred to, de-identified.

URI: MIXS:0000861

"},{"location":"host_subject_id/#inheritance","title":"Inheritance","text":""},{"location":"host_subject_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_subject_id/#properties","title":"Properties","text":""},{"location":"host_subject_id/#aliases","title":"Aliases","text":""},{"location":"host_subject_id/#examples","title":"Examples","text":"Value MPI123"},{"location":"host_subject_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_subject_id/#annotations","title":"Annotations","text":"property value expected_value unique identifier"},{"location":"host_subject_id/#schema-source","title":"Schema Source","text":""},{"location":"host_subject_id/#linkml-source","title":"LinkML Source","text":"
name: host_subject_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: unique identifier\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A unique identifier by which each subject can be referred to, de-identified.\ntitle: host subject id\nexamples:\n- value: MPI123\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subject id\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000861\nalias: host_subject_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_subspecf_genlin/","title":"Slot: host subspecific genetic lineage (host_subspecf_genlin)","text":"

Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.

URI: MIXS:0001318

"},{"location":"host_subspecf_genlin/#inheritance","title":"Inheritance","text":""},{"location":"host_subspecf_genlin/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_subspecf_genlin/#properties","title":"Properties","text":""},{"location":"host_subspecf_genlin/#aliases","title":"Aliases","text":""},{"location":"host_subspecf_genlin/#examples","title":"Examples","text":"Value serovar:Newport, variety:glabrum, cultivar: Red Delicious"},{"location":"host_subspecf_genlin/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_subspecf_genlin/#annotations","title":"Annotations","text":"property value expected_value Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar."},{"location":"host_subspecf_genlin/#schema-source","title":"Schema Source","text":""},{"location":"host_subspecf_genlin/#linkml-source","title":"LinkML Source","text":"
name: host_subspecf_genlin\nannotations:\n  expected_value:\n    tag: expected_value\n    value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n      e.g. serovar, biotype, ecotype, variety, cultivar.\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about the genetic distinctness of the host organism below\n  the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n  or any relevant genetic typing schemes like Group I plasmid. Subspecies should not\n  be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name\n  and the lineage rank separated by a colon, e.g., biovar:abc123.\ntitle: host subspecific genetic lineage\nexamples:\n- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subspecific genetic lineage\nrank: 1000\nis_a: core field\nstring_serialization: '{rank name}:{text}'\nslot_uri: MIXS:0001318\nalias: host_subspecf_genlin\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\n
"},{"location":"host_substrate/","title":"Slot: host substrate (host_substrate)","text":"

The growth substrate of the host.

URI: MIXS:0000252

"},{"location":"host_substrate/#inheritance","title":"Inheritance","text":""},{"location":"host_substrate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_substrate/#properties","title":"Properties","text":""},{"location":"host_substrate/#aliases","title":"Aliases","text":""},{"location":"host_substrate/#examples","title":"Examples","text":"Value rock"},{"location":"host_substrate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_substrate/#annotations","title":"Annotations","text":"property value expected_value substrate name"},{"location":"host_substrate/#schema-source","title":"Schema Source","text":""},{"location":"host_substrate/#linkml-source","title":"LinkML Source","text":"
name: host_substrate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: substrate name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The growth substrate of the host.\ntitle: host substrate\nexamples:\n- value: rock\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host substrate\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000252\nalias: host_substrate\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_symbiont/","title":"Slot: observed host symbionts (host_symbiont)","text":"

The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.

URI: MIXS:0001298

"},{"location":"host_symbiont/#inheritance","title":"Inheritance","text":""},{"location":"host_symbiont/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_symbiont/#properties","title":"Properties","text":""},{"location":"host_symbiont/#aliases","title":"Aliases","text":""},{"location":"host_symbiont/#examples","title":"Examples","text":"Value flukeworms"},{"location":"host_symbiont/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_symbiont/#annotations","title":"Annotations","text":"property value expected_value species name or common name"},{"location":"host_symbiont/#schema-source","title":"Schema Source","text":""},{"location":"host_symbiont/#linkml-source","title":"LinkML Source","text":"
name: host_symbiont\nannotations:\n  expected_value:\n    tag: expected_value\n    value: species name or common name\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: The taxonomic name of the organism(s) found living in mutualistic, commensalistic,\n  or parasitic symbiosis with the specific host.\ntitle: observed host symbionts\nexamples:\n- value: flukeworms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed host symbionts\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001298\nalias: host_symbiont\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\n
"},{"location":"host_taxid/","title":"Slot: host taxid (host_taxid)","text":"

NCBI taxon id of the host, e.g. 9606

URI: MIXS:0000250

"},{"location":"host_taxid/#inheritance","title":"Inheritance","text":""},{"location":"host_taxid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_taxid/#properties","title":"Properties","text":""},{"location":"host_taxid/#aliases","title":"Aliases","text":""},{"location":"host_taxid/#comments","title":"Comments","text":""},{"location":"host_taxid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_taxid/#annotations","title":"Annotations","text":"property value expected_value NCBI taxon identifier"},{"location":"host_taxid/#schema-source","title":"Schema Source","text":""},{"location":"host_taxid/#linkml-source","title":"LinkML Source","text":"
name: host_taxid\nannotations:\n  expected_value:\n    tag: expected_value\n    value: NCBI taxon identifier\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: NCBI taxon id of the host, e.g. 9606\ntitle: host taxid\ncomments:\n- Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host taxid\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000250\nalias: host_taxid\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"host_tot_mass/","title":"Slot: host total mass (host_tot_mass)","text":"

Total mass of the host at collection, the unit depends on host

URI: MIXS:0000263

"},{"location":"host_tot_mass/#inheritance","title":"Inheritance","text":""},{"location":"host_tot_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_tot_mass/#properties","title":"Properties","text":""},{"location":"host_tot_mass/#aliases","title":"Aliases","text":""},{"location":"host_tot_mass/#examples","title":"Examples","text":"Value 2500 gram"},{"location":"host_tot_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_tot_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_tot_mass/#schema-source","title":"Schema Source","text":""},{"location":"host_tot_mass/#linkml-source","title":"LinkML Source","text":"
name: host_tot_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilogram, gram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total mass of the host at collection, the unit depends on host\ntitle: host total mass\nexamples:\n- value: 2500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host total mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000263\nalias: host_tot_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_wet_mass/","title":"Slot: host wet mass (host_wet_mass)","text":"

Measurement of wet mass

URI: MIXS:0000567

"},{"location":"host_wet_mass/#inheritance","title":"Inheritance","text":""},{"location":"host_wet_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_wet_mass/#properties","title":"Properties","text":""},{"location":"host_wet_mass/#aliases","title":"Aliases","text":""},{"location":"host_wet_mass/#examples","title":"Examples","text":"Value 1500 gram"},{"location":"host_wet_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_wet_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_wet_mass/#schema-source","title":"Schema Source","text":""},{"location":"host_wet_mass/#linkml-source","title":"LinkML Source","text":"
name: host_wet_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilogram, gram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of wet mass\ntitle: host wet mass\nexamples:\n- value: 1500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host wet mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000567\nalias: host_wet_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"humidity/","title":"Slot: humidity (humidity)","text":"

Amount of water vapour in the air, at the time of sampling

URI: MIXS:0000100

"},{"location":"humidity/#inheritance","title":"Inheritance","text":""},{"location":"humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"humidity/#properties","title":"Properties","text":""},{"location":"humidity/#aliases","title":"Aliases","text":""},{"location":"humidity/#examples","title":"Examples","text":"Value 25 gram per cubic meter"},{"location":"humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"humidity/#schema-source","title":"Schema Source","text":""},{"location":"humidity/#linkml-source","title":"LinkML Source","text":"
name: humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per cubic meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Amount of water vapour in the air, at the time of sampling\ntitle: humidity\nexamples:\n- value: 25 gram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000100\nalias: humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"humidity_regm/","title":"Slot: humidity regimen (humidity_regm)","text":"

Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000568

"},{"location":"humidity_regm/#inheritance","title":"Inheritance","text":""},{"location":"humidity_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"humidity_regm/#properties","title":"Properties","text":""},{"location":"humidity_regm/#aliases","title":"Aliases","text":""},{"location":"humidity_regm/#examples","title":"Examples","text":"Value 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"humidity_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"humidity_regm/#annotations","title":"Annotations","text":"property value expected_value humidity value;treatment interval and duration"},{"location":"humidity_regm/#schema-source","title":"Schema Source","text":""},{"location":"humidity_regm/#linkml-source","title":"LinkML Source","text":"
name: humidity_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: humidity value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per cubic meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to varying degree of\n  humidity; information about treatment involving use of growth hormones; should include\n  amount of humidity administered, treatment regimen including how many times the\n  treatment was repeated, how long each treatment lasted, and the start and end time\n  of the entire treatment; can include multiple regimens\ntitle: humidity regimen\nexamples:\n- value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000568\nalias: humidity_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"id/","title":"Slot: id","text":"

A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI

URI: nmdc:id

"},{"location":"id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis yes Extraction A material separation in which a desired component of an input material is se... yes NamedThing a databased entity or concept/class no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes WorkflowExecution Represents an instance of an execution of a particular workflow no Biosample Biological source material which can be characterized by an experiment yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated yes ProtocolExecution A PlannedProces that has PlannedProcess parts yes ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes Configuration A set of parameters that define the actions of a process and is shared among ... no MetatranscriptomeAnnotation yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes NomAnalysis yes CollectingBiosamplesFromSite yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... yes MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes Site no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes MetabolomicsAnalysis yes ProcessedSample yes OntologyClass yes Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DataObject An object that primarily consists of symbols that represent information yes GeneProduct A molecule encoded by a gene that has an evolved function no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes Instrument A material entity that is designed to perform a function in a scientific inve... yes MetatranscriptomeAssembly yes ChemicalEntity An atom or molecule that can be represented with a chemical formula no FiltrationProcess The process of segregation of phases; e yes MetagenomeSequencing Initial sequencing activity that precedes any analysis yes EnvironmentalMaterialTerm no LibraryPreparation yes Pooling physical combination of several instances of like material yes MaterialEntity no CalibrationInformation A calibration object that is associated with a process yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component yes DataGeneration The methods and processes used to generate omics data from a biosample or org... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no OrthologyGroup A set of genes or gene products in which all members are orthologous no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... yes MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... yes Study A study summarizes the overall goal of a research initiative and outlines the... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... yes Manifest yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"id/#properties","title":"Properties","text":""},{"location":"id/#examples","title":"Examples","text":"Value nmdc:mgmag-00-x012.1_7_c1"},{"location":"id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"id/#schema-source","title":"Schema Source","text":""},{"location":"id/#linkml-source","title":"LinkML Source","text":"
name: id\ndescription: A unique identifier for a thing. Must be either a CURIE shorthand for\n  a URI or a complete URI\nnotes:\n- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n  will be accepted\n- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n  via per-class id slot usage assertions\n- minting authority shoulders should probably be enumerated and checked in the pattern\nexamples:\n- value: nmdc:mgmag-00-x012.1_7_c1\n  description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- NamedThing\nrange: uriorcurie\nrequired: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"identifiers/","title":"Identifiers in NMDC","text":"

Identifiers are crucial for the NMDC, both for any data objects created (aka minted) and for any external objects referenced

Examples of entities that require identifiers:

Identifiers should be:

See McMurry et al, PMID:28662064 for more desiderata.

"},{"location":"identifiers/#curies-prefixed-ids","title":"CURIEs - prefixed IDs","text":"

Following McMurry et al we adopt the use of prefixed identifiers

The syntax is:

Prefix:LocalId\n

Examples:

These prefixed identifiers are also known as CURIEs (Compact URIs). There is a W3C specification for these

All prefixes should be registered with a standard identifier prefix system. These include:

"},{"location":"identifiers/#examples","title":"Examples","text":""},{"location":"identifiers/#insdc-biosamples","title":"INSDC BioSamples","text":"

Registry entry: https://registry.identifiers.org/registry/biosample

Example ID/CURIE: BIOSAMPLE:SAMEA2397676

Resolving via identifiers.org: https://identifiers.org/BIOSAMPLE:SAMEA2397676

Resolving via nt2.net: http://n2t.net/BIOSAMPLE:SAMEA2397676

"},{"location":"identifiers/#gold-identifiers","title":"GOLD identifiers","text":"

https://registry.identifiers.org/registry/gold

Example ID: GOLD:Gp0119849

Resolving via identifiers.org: https://identifiers.org/GOLD:Gp0119849

"},{"location":"identifiers/#identifiers-for-ontology-terms-and-function-descriptors","title":"identifiers for ontology terms and function descriptors","text":"

Most of the ontologies we use are in OBO. All OBO IDs are prefixed using the ontology ID space. The list of ID spaces can be found on http://obofoundry.org

For example the ID/CURIE ENVO:00002007 represents the class sediment and is expanded to a URI of http://purl.obolibrary.org/obo/ENVO_00002007

"},{"location":"identifiers/#kegg","title":"KEGG","text":"

KEGG is actually a set of databases, each with its own prefix, usually of form KEGG.$database, e.g.

"},{"location":"identifiers/#recommended-ids-for-use-within-nmdc","title":"Recommended IDs for use within NMDC","text":"

The NMDC schema is annotated with the set of IDs that are allowed to act as primary keys for instances of each class.

For example the class OrthologyGroup has a description of the IDs allowed on the class web page, the first listed is KEGG.ORTHOLOGY

The underlying yaml looks like this:

  orthology group:\n    is_a: functional annotation term\n    description: >-\n      A set of genes or gene products in which all members are orthologous\n    id_prefixes:\n      - KEGG.ORTHOLOGY  ## KO number\n      - EGGNOG\n      - PFAM\n      - TIGRFAM\n      - SUPFAM\n      - PANTHER.FAMILY\n    exact_mappings:\n      - biolink:GeneFamily\n

The full URLs for each is in the jsonld context file

"},{"location":"identifiers/#ids-minted-for-use-within-nmdc","title":"IDs minted for use within NMDC","text":"

The NMDC schema specifies legal identifiers for all of its classes. All data instances/records that are intended for upload into the NMDC metadata store must have an id field that follows this specification, which is discussed below.

NMDC offers a central identifier minting endpoint in order to save data contributors the trouble of hand-crafting ids.

The possibility of decentralized (or offline) minting of ids by trusted organizations has also been anticipated. id component 3 below (the shoulder) is used to indicate the organization that minted an id. LBL, which hosts the id minting endpoint will use one shoulder value. If another organization, like JGI or EMSL, needs to bulk-create ids outside of the central identifier minting endpoint, they would use different shoulders, to be determined by the NMDC schema and metadata team.

No matter where they are minted, all NMDC id values must match this abstract pattern:

nmdc:<type-code>-<shoulder>-<blade><.version><_locus>\n

The abstract pattern has six parts, delimited by hyphens (unless otherwise specified):

  1. nmdc: All NMDC identifiers will begin with this static prefix.

  2. <typecode>: An alphabetical code with a 1:1 correspondence to a class from the NMDC schema. Answers the question \"of what class is the data record that bears this id\"? Must consist of 1 to 6 lower case letters, although a minimum of 3 letters is suggested. The type code portion of an NMDC id must match the regular expression [a-z]{1,6}.

  3. <shoulder>: A code that indicates what organization minted the identifier. Shoulder values must be zero to six lower case letters, flanked by one digit on either side. Answers the question \"what organization minted this id\"? The central identifier endpoint, hosted at LBL, uses the shoulder 00. Should organizations like JGI or EMSL need to mint identifiers in bulk, they would be assigned other shoulders, so that id values aren't reused. The shoulder portion of an NMDC id must match the regular expression [0-9][a-z]{0,6}[0-9].

  4. <blade>: The fully unique part of the identifier under a given type code and shoulder namespace. The shoulder and blade together make up the key of the identifier. The blade is an alphanumeric string of open-ended length with at least one character, following the regular expression: [A-Za-z0-9]+.

  5. <.version>: Differentiates multiple iterations of a workflow. The delimiter used to separate the version from the blade and everything before it is a dot (.). The version is a potentially repeating alphanumeric pattern with a minimum length of 1 character. The version portion of an NMDC id must match the regular expression (\\.[A-Za-z0-9]+)*.

  6. <_locus>: Indicates the contig on which a genomic feature is found, along with its start and end coordinates. Delimited from the rest of the id by an underscore (_). The locus part, if present, must have at least one character from the set off uppercase letters, lower case letters, digits, underscores (_), dots (.) and hyphens (-). The regular expression that the locus will follow is: _[A-Za-z0-9_\\.-]+.

The per-part regular expression described above can be composed into one complete regular expression. Named capture groups have been used to tie in the part names.

^(?<prefix>nmdc):(?<typecode>[a-z]{1,6})-(?<shoulder>[0-9][a-z]{0,6}[0-9])-(?<blade>[A-Za-z0-9]+)(?<version>(\\.[A-Za-z0-9]+)*)(?<locus>_[A-Za-z0-9_\\.-]+)?$\n
"},{"location":"identifiers/#annotation-identifiers","title":"Annotation identifiers","text":"

Both metaG and metaT analyses produce GFF3 files. See issue 184 for more on how the GFF is modeled.

The main entity we care about in these is the [gene product] https://microbiomedata.github.io/nmdc-metadata/docs/GeneProduct) ID (usually a protein), this is what functional annotation hangs off.

This is typically a protein encoded by a CDS, e.g.

Ga0185794_41    GeneMark.hmm-2 v1.05    CDS     48      1037    56.13   +       0       ID=Ga0185794_41_48_1037;translation_table=11;start_type=ATG;product=5-methylthioadenosine/S-adenosylhomocysteine deaminase;product_source=KO:K12960;cath_funfam=3.20.20.140;cog=COG0402;ko=KO:K12960;ec_number=EC:3.5.4.28,EC:3.5.4.31;pfam=PF01979;superfamily=51338,51556\n

When converting col9 we ensure that each ID is correctly prefixed. So for example, we use KEGG.OTHOLOGY:K12960 not KO:K12960 as the former is the official prefix according to KEGG and identifiers.org

We will also later need a policy for IDs for the sequences in col1 (ie genome or transcript), please return later for more details...

"},{"location":"identifiers/#reuse-vs-minting-new-ids","title":"Reuse vs minting new IDs","text":"

In 2023 NMDC transitioned from reusing identifiers from other organizations to using NMDC minted identifiers as the primary identifier. In April 2024 NMDC will update legacy records to use NMDC minted identifers as the primary identifier. The table below provides information is how legacy identifiers can be found in updated records.

"},{"location":"identifiers/#identifier-mapping","title":"Identifier mapping","text":"Identifier Example NMDC Schema Class NMDC Schema Slot gold:Gs* gold:Gs0114675 Study gold_study_identifiers gold:Gb* gold:Gb0110739 Biosample gold_biosample_identifiers emsl:* emsl:63ca2f94-6647-11eb-ae93-0242ac130002 Biosample emsl_biosample_identifiers igsn:* igsn:IEWFS001H Biosample igsn_biosample_identifiers gold:Gp* gold:Gp0452734 OmicsProcessing gold_sequencing_project_identifiers emsl:* emsl:598506 OmicsProcessing alternative_identifiers

Some legacy data object identifiers were based on file md5sums, either with or without a prefix (nmdc, jgi, emsl). In some cases the legacy value can be found by removing the prefix and searching DataObject records on slot md5_checksum. If you are having trouble finding information based on legacy identifiers please contact support@microbiomedata.org.

"},{"location":"identifiers/#additional-details-on-legacy-identifiers","title":"Additional details on legacy identifiers","text":"

Legacy metagenomics omics objects look like this:

      id: \"gold:Gp0108335\"\n      name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n      has_input:\n        - \"gold:Gb0108335\"\n      part_of:\n        - \"gold:Gs0112340\"\n      has_output:\n        - \"jgi:551a20d30d878525404e90d5\"\n      omics_type: Metagenome\n      type: \"nmdc:OmicsProcessing\"\n      add_date: \"30-OCT-14 12.00.00.000000000 AM\"\n      mod_date: \"22-MAY-20 06.13.12.927000000 PM\"\n      ncbi_project_name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n      processing_institution: \"Joint Genome Institute\"\n      principal_investigator_name: \"Virginia Rich\"\n

the linked data object uses a jgi prefix and an md5 hash

      id: \"jgi:551a20d30d878525404e90d5\"\n      name: \"8871.1.114459.GCCAAT.fastq.gz\"\n      description: \"Raw sequencer read data\"\n      file_size_bytes: 17586370657\n      type: \"nmdc:DataObject\"\n

Legacy metaproteomics omics objects look like this:

      id: \"emsl:404590\"\n      name: \"FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n      description: \"High res MS with low res CID MSn\"\n      part_of:\n        - \"gold:Gs0110132\"\n      has_output:\n        - \"emsl:output_404590\"\n      omics_type: Proteomics\n      type: \"nmdc:OmicsProcessing\"\n      instrument_name: \"VOrbiETD03\"\n      processing_institution: \"Environmental Molecular Sciences Lab\"\n

the output data objects are formed from these:

      id: \"emsl:output_404590\"\n      name: \"output: FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n      description: \"High res MS with low res CID MSn\"\n      file_size_bytes: 503296678\n      type: \"nmdc:DataObject\"\n

the data objects use hashes (md5) prefixed with nmdc:

      name: \"404590_resultant.tsv\"\n      description: \"Aggregation of analysis tools{MSGFplus, MASIC} results\"\n      file_size_bytes: 10948480\n      type: \"nmdc:DataObject\"\n      id: \"nmdc:e0c70280a7a23c7c5cc1e589f72e896e\"\n
"},{"location":"identifiers/#mixs-term-identifiers","title":"MIxS term identifiers","text":"

We are working with the GSC to provide permanent IDs for MIxS terms. Note these terms are schema-level rather than data-level.

Please check this section later

For now we place these in the nmdc namespaces, e.g

nmdc:alt

"},{"location":"identifiers/#identifiers-and-semantic-web-uris","title":"Identifiers and semantic web URIs","text":"

We produce a JSON-LD context with the schema:

When this is combined with schema-conformant JSON, RDF can be automatically created using the intended URIs

"},{"location":"igsn_biosample_identifiers/","title":"Slot: IGSN Biosample Identifiers (igsn_biosample_identifiers)","text":"

A list of identifiers for the biosample from the IGSN database.

URI: nmdc:igsn_biosample_identifiers

"},{"location":"igsn_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"igsn_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"igsn_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"igsn_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"igsn_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"igsn_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: igsn_biosample_identifiers\ndescription: A list of identifiers for the biosample from the IGSN database.\ntitle: IGSN Biosample Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- igsn_identifiers\nalias: igsn_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"igsn_identifiers/","title":"Slot: igsn_identifiers","text":"

URI: nmdc:igsn_identifiers

"},{"location":"igsn_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database None Biosample"},{"location":"igsn_identifiers/#properties","title":"Properties","text":""},{"location":"igsn_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"igsn_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"igsn_identifiers/#linkml-source","title":"LinkML Source","text":"
name: igsn_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: igsn_identifiers\nrange: string\n\n
"},{"location":"img_identifiers/","title":"Slot: IMG Identifiers (img_identifiers)","text":"

A list of identifiers that relate the biosample to records in the IMG database.

URI: nmdc:img_identifiers

"},{"location":"img_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"img_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes Biosample Biological source material which can be characterized by an experiment no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes MetatranscriptomeAnnotation yes"},{"location":"img_identifiers/#properties","title":"Properties","text":""},{"location":"img_identifiers/#todos","title":"TODOs","text":""},{"location":"img_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"img_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"img_identifiers/#linkml-source","title":"LinkML Source","text":"
name: img_identifiers\ndescription: A list of identifiers that relate the biosample to records in the IMG\n  database.\ntitle: IMG Identifiers\ntodos:\n- add is_a or mixin modeling, like other external_database_identifiers\n- what class would IMG records belong to?! Are they Studies, Biosamples, or something\n  else?\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nalias: img_identifiers\ndomain_of:\n- MetagenomeAnnotation\n- Biosample\n- MetatranscriptomeAnnotation\n- MetatranscriptomeExpressionAnalysis\n- MagsAnalysis\nrange: external_identifier\nmultivalued: true\npattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n\n
"},{"location":"in_manifest/","title":"Slot: in_manifest","text":"

URI: nmdc:in_manifest

"},{"location":"in_manifest/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"in_manifest/#properties","title":"Properties","text":""},{"location":"in_manifest/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"in_manifest/#schema-source","title":"Schema Source","text":""},{"location":"in_manifest/#linkml-source","title":"LinkML Source","text":"
name: in_manifest\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: in_manifest\ndomain_of:\n- DataObject\nrange: Manifest\nmultivalued: true\n\n
"},{"location":"inchi/","title":"Slot: inchi","text":"

URI: nmdc:inchi

"},{"location":"inchi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"inchi/#properties","title":"Properties","text":""},{"location":"inchi/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"inchi/#schema-source","title":"Schema Source","text":""},{"location":"inchi/#linkml-source","title":"LinkML Source","text":"
name: inchi\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi\ndomain_of:\n- ChemicalEntity\nrange: string\n\n
"},{"location":"inchi_key/","title":"Slot: inchi_key","text":"

URI: nmdc:inchi_key

"},{"location":"inchi_key/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"inchi_key/#properties","title":"Properties","text":""},{"location":"inchi_key/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"inchi_key/#schema-source","title":"Schema Source","text":""},{"location":"inchi_key/#linkml-source","title":"LinkML Source","text":"
name: inchi_key\nnotes:\n- 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n  K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n  testing. J Cheminform. 4:12'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi_key\ndomain_of:\n- ChemicalEntity\nrange: string\n\n
"},{"location":"indoor_space/","title":"Slot: indoor space (indoor_space)","text":"

A distinguishable space within a structure, the purpose for which discrete areas of a building is used

URI: MIXS:0000763

"},{"location":"indoor_space/#inheritance","title":"Inheritance","text":""},{"location":"indoor_space/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"indoor_space/#properties","title":"Properties","text":""},{"location":"indoor_space/#aliases","title":"Aliases","text":""},{"location":"indoor_space/#examples","title":"Examples","text":"Value foyer"},{"location":"indoor_space/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"indoor_space/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"indoor_space/#schema-source","title":"Schema Source","text":""},{"location":"indoor_space/#linkml-source","title":"LinkML Source","text":"
name: indoor_space\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A distinguishable space within a structure, the purpose for which discrete\n  areas of a building is used\ntitle: indoor space\nexamples:\n- value: foyer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor space\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000763\nalias: indoor_space\ndomain_of:\n- Biosample\nrange: indoor_space_enum\nmultivalued: false\n\n
"},{"location":"indoor_surf/","title":"Slot: indoor surface (indoor_surf)","text":"

Type of indoor surface

URI: MIXS:0000764

"},{"location":"indoor_surf/#inheritance","title":"Inheritance","text":""},{"location":"indoor_surf/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"indoor_surf/#properties","title":"Properties","text":""},{"location":"indoor_surf/#aliases","title":"Aliases","text":""},{"location":"indoor_surf/#examples","title":"Examples","text":"Value wall"},{"location":"indoor_surf/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"indoor_surf/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"indoor_surf/#schema-source","title":"Schema Source","text":""},{"location":"indoor_surf/#linkml-source","title":"LinkML Source","text":"
name: indoor_surf\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Type of indoor surface\ntitle: indoor surface\nexamples:\n- value: wall\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor surface\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000764\nalias: indoor_surf\ndomain_of:\n- Biosample\nrange: indoor_surf_enum\nmultivalued: false\n\n
"},{"location":"indust_eff_percent/","title":"Slot: industrial effluent percent (indust_eff_percent)","text":"

Percentage of industrial effluents received by wastewater treatment plant

URI: MIXS:0000662

"},{"location":"indust_eff_percent/#inheritance","title":"Inheritance","text":""},{"location":"indust_eff_percent/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"indust_eff_percent/#properties","title":"Properties","text":""},{"location":"indust_eff_percent/#aliases","title":"Aliases","text":""},{"location":"indust_eff_percent/#examples","title":"Examples","text":"Value"},{"location":"indust_eff_percent/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"indust_eff_percent/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"indust_eff_percent/#schema-source","title":"Schema Source","text":""},{"location":"indust_eff_percent/#linkml-source","title":"LinkML Source","text":"
name: indust_eff_percent\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Percentage of industrial effluents received by wastewater treatment plant\ntitle: industrial effluent percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- industrial effluent percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000662\nalias: indust_eff_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"infiltrations/","title":"Slot: infiltrations","text":"

The amount of time it takes to complete each infiltration activity

URI: nmdc:infiltrations

"},{"location":"infiltrations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"infiltrations/#properties","title":"Properties","text":""},{"location":"infiltrations/#aliases","title":"Aliases","text":""},{"location":"infiltrations/#examples","title":"Examples","text":"Value ['00:01:32', '00:00:53']"},{"location":"infiltrations/#see-also","title":"See Also","text":""},{"location":"infiltrations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"infiltrations/#schema-source","title":"Schema Source","text":""},{"location":"infiltrations/#linkml-source","title":"LinkML Source","text":"
name: infiltrations\ndescription: The amount of time it takes to complete each infiltration activity\nexamples:\n- value: '[''00:01:32'', ''00:00:53'']'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1\naliases:\n- infiltration_1\n- infiltration_2\nrank: 1000\nlist_elements_ordered: true\nalias: infiltrations\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\npattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$\n\n
"},{"location":"inorg_particles/","title":"Slot: inorganic particles (inorg_particles)","text":"

Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles

URI: MIXS:0000664

"},{"location":"inorg_particles/#inheritance","title":"Inheritance","text":""},{"location":"inorg_particles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"inorg_particles/#properties","title":"Properties","text":""},{"location":"inorg_particles/#aliases","title":"Aliases","text":""},{"location":"inorg_particles/#examples","title":"Examples","text":"Value"},{"location":"inorg_particles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"inorg_particles/#annotations","title":"Annotations","text":"property value expected_value inorganic particle name;measurement value"},{"location":"inorg_particles/#schema-source","title":"Schema Source","text":""},{"location":"inorg_particles/#linkml-source","title":"LinkML Source","text":"
name: inorg_particles\nannotations:\n  expected_value:\n    tag: expected_value\n    value: inorganic particle name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of particles such as sand, grit, metal particles, ceramics,\n  etc.; can include multiple particles\ntitle: inorganic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inorganic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000664\nalias: inorg_particles\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"input_base_count/","title":"Slot: input_base_count","text":"

The nucleotide base count number of input reads for QC analysis.

URI: nmdc:input_base_count

"},{"location":"input_base_count/#inheritance","title":"Inheritance","text":""},{"location":"input_base_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_base_count/#properties","title":"Properties","text":""},{"location":"input_base_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_base_count/#schema-source","title":"Schema Source","text":""},{"location":"input_base_count/#linkml-source","title":"LinkML Source","text":"
name: input_base_count\ndescription: The nucleotide base count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_base_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"input_contig_num/","title":"Slot: input_contig_num","text":"

URI: nmdc:input_contig_num

"},{"location":"input_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"input_contig_num/#properties","title":"Properties","text":""},{"location":"input_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"input_contig_num/#linkml-source","title":"LinkML Source","text":"
name: input_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"input_mass/","title":"Slot: sample mass used (input_mass)","text":"

Total mass of sample used in activity.

URI: nmdc:input_mass

"},{"location":"input_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"input_mass/#properties","title":"Properties","text":""},{"location":"input_mass/#aliases","title":"Aliases","text":""},{"location":"input_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_mass/#schema-source","title":"Schema Source","text":""},{"location":"input_mass/#linkml-source","title":"LinkML Source","text":"
name: input_mass\ndescription: Total mass of sample used in activity.\ntitle: sample mass used\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample mass\n- sample weight\nexact_mappings:\n- MS:1000004\nnarrow_mappings:\n- MIXS:0000111\nrank: 1000\nalias: input_mass\ndomain_of:\n- Extraction\nrange: QuantityValue\n\n
"},{"location":"input_read_bases/","title":"Slot: input_read_bases","text":"

_TODO _

URI: nmdc:input_read_bases

"},{"location":"input_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_read_bases/#properties","title":"Properties","text":""},{"location":"input_read_bases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_read_bases/#schema-source","title":"Schema Source","text":""},{"location":"input_read_bases/#linkml-source","title":"LinkML Source","text":"
name: input_read_bases\ndescription: 'TODO      '\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_read_bases\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"input_read_count/","title":"Slot: input_read_count","text":"

The sequence count number of input reads for QC analysis.

URI: nmdc:input_read_count

"},{"location":"input_read_count/#inheritance","title":"Inheritance","text":""},{"location":"input_read_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_read_count/#properties","title":"Properties","text":""},{"location":"input_read_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_read_count/#schema-source","title":"Schema Source","text":""},{"location":"input_read_count/#linkml-source","title":"LinkML Source","text":"
name: input_read_count\ndescription: The sequence count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_read_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"input_volume/","title":"Slot: input_volume","text":"

The volume of the input sample.

URI: nmdc:input_volume

"},{"location":"input_volume/#properties","title":"Properties","text":""},{"location":"input_volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_volume/#schema-source","title":"Schema Source","text":""},{"location":"input_volume/#linkml-source","title":"LinkML Source","text":"
name: input_volume\ndescription: The volume of the input sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_volume\nrange: QuantityValue\n\n
"},{"location":"insdc_analysis_identifiers/","title":"Slot: insdc_analysis_identifiers","text":"

URI: nmdc:insdc_analysis_identifiers

"},{"location":"insdc_analysis_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_analysis_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_analysis_identifiers/#examples","title":"Examples","text":"Value https://www.ebi.ac.uk/metagenomics/runs/DRR218479 https://www.ebi.ac.uk/ena/browser/view/ERR436051"},{"location":"insdc_analysis_identifiers/#comments","title":"Comments","text":""},{"location":"insdc_analysis_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_analysis_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_analysis_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_analysis_identifiers\ncomments:\n- in INSDC this is a run but it corresponds to a GOLD analysis\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/runs/DRR218479\n  description: Illumina MiSeq paired end sequencing of SAMD00212331\n- value: https://www.ebi.ac.uk/ena/browser/view/ERR436051\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$\n\n
"},{"location":"insdc_assembly_identifiers/","title":"Slot: insdc_assembly_identifiers","text":"

URI: nmdc:insdc_assembly_identifiers

"},{"location":"insdc_assembly_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_assembly_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"insdc_assembly_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_assembly_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_assembly_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_assembly_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: assembly_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_assembly_identifiers\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: string\npattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n\n
"},{"location":"insdc_bioproject_identifiers/","title":"Slot: insdc_bioproject_identifiers","text":"

identifiers for corresponding project in INSDC Bioproject

URI: nmdc:insdc_bioproject_identifiers

"},{"location":"insdc_bioproject_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_bioproject_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"insdc_bioproject_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_bioproject_identifiers/#aliases","title":"Aliases","text":""},{"location":"insdc_bioproject_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/bioproject:PRJNA366857"},{"location":"insdc_bioproject_identifiers/#comments","title":"Comments","text":""},{"location":"insdc_bioproject_identifiers/#see-also","title":"See Also","text":""},{"location":"insdc_bioproject_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_bioproject_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_bioproject_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_bioproject_identifiers\ndescription: identifiers for corresponding project in INSDC Bioproject\ncomments:\n- these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n  one to one\nexamples:\n- value: https://bioregistry.io/bioproject:PRJNA366857\n  description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ncbi.nlm.nih.gov/bioproject/\n- https://www.ddbj.nig.ac.jp/bioproject/index-e.html\naliases:\n- NCBI bioproject identifiers\n- DDBJ bioproject identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_bioproject_identifiers\ndomain_of:\n- NucleotideSequencing\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n\n
"},{"location":"insdc_biosample_identifiers/","title":"Slot: insdc_biosample_identifiers","text":"

identifiers for corresponding sample in INSDC

URI: nmdc:insdc_biosample_identifiers

"},{"location":"insdc_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"insdc_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_biosample_identifiers/#aliases","title":"Aliases","text":""},{"location":"insdc_biosample_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/biosample:SAMEA5989477 https://bioregistry.io/biosample:SAMD00212331"},{"location":"insdc_biosample_identifiers/#see-also","title":"See Also","text":""},{"location":"insdc_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_biosample_identifiers\ndescription: identifiers for corresponding sample in INSDC\nexamples:\n- value: https://bioregistry.io/biosample:SAMEA5989477\n- value: https://bioregistry.io/biosample:SAMD00212331\n  description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/108\n- https://www.ebi.ac.uk/biosamples/\n- https://www.ncbi.nlm.nih.gov/biosample\n- https://www.ddbj.nig.ac.jp/biosample/index-e.html\naliases:\n- EBI biosample identifiers\n- NCBI biosample identifiers\n- DDBJ biosample identifiers\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n\n
"},{"location":"insdc_experiment_identifiers/","title":"Slot: insdc_experiment_identifiers","text":"

URI: nmdc:insdc_experiment_identifiers

"},{"location":"insdc_experiment_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_experiment_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no DataObject An object that primarily consists of symbols that represent information no"},{"location":"insdc_experiment_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_experiment_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_experiment_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_experiment_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_experiment_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_experiment_identifiers\ndomain_of:\n- NucleotideSequencing\n- DataObject\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n\n
"},{"location":"insdc_identifiers/","title":"Slot: insdc_identifiers","text":"

Any identifier covered by the International Nucleotide Sequence Database Collaboration

URI: nmdc:insdc_identifiers

"},{"location":"insdc_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA None insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject None Study, NucleotideSequencing insdc_biosample_identifiers identifiers for corresponding sample in INSDC None Biosample insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC None insdc_experiment_identifiers None NucleotideSequencing, DataObject insdc_analysis_identifiers None insdc_assembly_identifiers None MetagenomeAssembly, MetatranscriptomeAssembly"},{"location":"insdc_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_identifiers/#aliases","title":"Aliases","text":""},{"location":"insdc_identifiers/#comments","title":"Comments","text":""},{"location":"insdc_identifiers/#see-also","title":"See Also","text":""},{"location":"insdc_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_identifiers\ndescription: Any identifier covered by the International Nucleotide Sequence Database\n  Collaboration\ncomments:\n- note that we deliberately abstract over which of the partner databases accepted\n  the initial submission\n- 'the first letter of the accession indicates which partner accepted the initial\n  submission: E for ENA, D for DDBJ, or S or N for NCBI.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.insdc.org/\n- https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html\naliases:\n- EBI identifiers\n- NCBI identifiers\n- DDBJ identifiers\nrank: 1000\nmixin: true\nalias: insdc_identifiers\nrange: string\n\n
"},{"location":"insdc_secondary_sample_identifiers/","title":"Slot: insdc_secondary_sample_identifiers","text":"

secondary identifiers for corresponding sample in INSDC

URI: nmdc:insdc_secondary_sample_identifiers

"},{"location":"insdc_secondary_sample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_secondary_sample_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_secondary_sample_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/insdc.sra:DRS166340"},{"location":"insdc_secondary_sample_identifiers/#comments","title":"Comments","text":""},{"location":"insdc_secondary_sample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_secondary_sample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_secondary_sample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_secondary_sample_identifiers\ndescription: secondary identifiers for corresponding sample in INSDC\ncomments:\n- ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340\n  -> SAMD00212331\n- MGnify uses these as their primary sample IDs\nexamples:\n- value: https://bioregistry.io/insdc.sra:DRS166340\n  description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_secondary_sample_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^biosample:(E|D|S)RS[0-9]{6,}$\n\n
"},{"location":"insdc_sra_ena_study_identifiers/","title":"Slot: insdc_sra_ena_study_identifiers","text":"

identifiers for corresponding project in INSDC SRA / ENA

URI: nmdc:insdc_sra_ena_study_identifiers

"},{"location":"insdc_sra_ena_study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_sra_ena_study_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_sra_ena_study_identifiers/#aliases","title":"Aliases","text":""},{"location":"insdc_sra_ena_study_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/insdc.sra:SRP121659"},{"location":"insdc_sra_ena_study_identifiers/#see-also","title":"See Also","text":""},{"location":"insdc_sra_ena_study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_sra_ena_study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_sra_ena_study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_sra_ena_study_identifiers\ndescription: identifiers for corresponding project in INSDC SRA / ENA\nexamples:\n- value: https://bioregistry.io/insdc.sra:SRP121659\n  description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/109\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\naliases:\n- EBI ENA study identifiers\n- NCBI SRA identifiers\n- DDBJ SRA identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_sra_ena_study_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$\n\n
"},{"location":"inside_lux/","title":"Slot: inside lux light (inside_lux)","text":"

The recorded value at sampling time (power density)

URI: MIXS:0000168

"},{"location":"inside_lux/#inheritance","title":"Inheritance","text":""},{"location":"inside_lux/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"inside_lux/#properties","title":"Properties","text":""},{"location":"inside_lux/#aliases","title":"Aliases","text":""},{"location":"inside_lux/#examples","title":"Examples","text":"Value"},{"location":"inside_lux/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"inside_lux/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"inside_lux/#schema-source","title":"Schema Source","text":""},{"location":"inside_lux/#linkml-source","title":"LinkML Source","text":"
name: inside_lux\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilowatt per square metre\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The recorded value at sampling time (power density)\ntitle: inside lux light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inside lux light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000168\nalias: inside_lux\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"instrument_set/","title":"Slot: instrument_set","text":"

This property links a database object to the set of instruments within it.

URI: nmdc:instrument_set

"},{"location":"instrument_set/#inheritance","title":"Inheritance","text":""},{"location":"instrument_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"instrument_set/#properties","title":"Properties","text":""},{"location":"instrument_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"instrument_set/#schema-source","title":"Schema Source","text":""},{"location":"instrument_set/#linkml-source","title":"LinkML Source","text":"
name: instrument_set\ndescription: This property links a database object to the set of instruments within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: instrument_set\ndomain_of:\n- Database\nrange: Instrument\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"instrument_used/","title":"Slot: instrument_used","text":"

What instrument was used during DataGeneration or MaterialProcessing.

URI: nmdc:instrument_used

"},{"location":"instrument_used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no Pooling physical combination of several instances of like material no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"instrument_used/#properties","title":"Properties","text":""},{"location":"instrument_used/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"instrument_used/#schema-source","title":"Schema Source","text":""},{"location":"instrument_used/#linkml-source","title":"LinkML Source","text":"
name: instrument_used\ndescription: What instrument was used during DataGeneration or MaterialProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: instrument_used\ndomain_of:\n- MaterialProcessing\n- DataGeneration\nrange: Instrument\nmultivalued: true\n\n
"},{"location":"int_wall_cond/","title":"Slot: interior wall condition (int_wall_cond)","text":"

The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas

URI: MIXS:0000813

"},{"location":"int_wall_cond/#inheritance","title":"Inheritance","text":""},{"location":"int_wall_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"int_wall_cond/#properties","title":"Properties","text":""},{"location":"int_wall_cond/#aliases","title":"Aliases","text":""},{"location":"int_wall_cond/#examples","title":"Examples","text":"Value damaged"},{"location":"int_wall_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"int_wall_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"int_wall_cond/#schema-source","title":"Schema Source","text":""},{"location":"int_wall_cond/#linkml-source","title":"LinkML Source","text":"
name: int_wall_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the wall at the time of sampling; photos or\n  video preferred; use drawings to indicate location of damaged areas\ntitle: interior wall condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- interior wall condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000813\nalias: int_wall_cond\ndomain_of:\n- Biosample\nrange: int_wall_cond_enum\nmultivalued: false\n\n
"},{"location":"internal_calibration/","title":"Slot: internal_calibration","text":"

whether internal calibration was used, if false, external calibration was used

URI: nmdc:internal_calibration

"},{"location":"internal_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process yes"},{"location":"internal_calibration/#properties","title":"Properties","text":""},{"location":"internal_calibration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"internal_calibration/#schema-source","title":"Schema Source","text":""},{"location":"internal_calibration/#linkml-source","title":"LinkML Source","text":"
name: internal_calibration\ndescription: whether internal calibration was used, if false, external calibration\n  was used\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: internal_calibration\ndomain_of:\n- CalibrationInformation\nrange: boolean\n\n
"},{"location":"investigation_field/","title":"Slot: investigation_field","text":"

field describing aspect of the investigation/study to which the sample belongs

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:investigation_field

"},{"location":"investigation_field/#inheritance","title":"Inheritance","text":""},{"location":"investigation_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"investigation_field/#properties","title":"Properties","text":""},{"location":"investigation_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"investigation_field/#schema-source","title":"Schema Source","text":""},{"location":"investigation_field/#linkml-source","title":"LinkML Source","text":"
name: investigation field\ndescription: field describing aspect of the investigation/study to which the sample\n  belongs\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: investigation_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"ionization_source/","title":"Slot: ionization_source","text":"

The ionization source used to introduce processed samples into a mass spectrometer

URI: nmdc:ionization_source

"},{"location":"ionization_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"ionization_source/#properties","title":"Properties","text":""},{"location":"ionization_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ionization_source/#schema-source","title":"Schema Source","text":""},{"location":"ionization_source/#linkml-source","title":"LinkML Source","text":"
name: ionization_source\ndescription: The ionization source used to introduce processed samples into a mass\n  spectrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1000008\nrank: 1000\nalias: ionization_source\ndomain_of:\n- MassSpectrometryConfiguration\nrange: IonizationSourceEnum\n\n
"},{"location":"is_pressurized/","title":"Slot: is_pressurized","text":"

Whether or not pressure was applied to a thing or process.

URI: nmdc:is_pressurized

"},{"location":"is_pressurized/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"is_pressurized/#properties","title":"Properties","text":""},{"location":"is_pressurized/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"is_pressurized/#schema-source","title":"Schema Source","text":""},{"location":"is_pressurized/#linkml-source","title":"LinkML Source","text":"
name: is_pressurized\ndescription: Whether or not pressure was applied to a thing or process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_pressurized\ndomain_of:\n- FiltrationProcess\nrange: boolean\n\n
"},{"location":"is_stranded/","title":"Slot: is_stranded","text":"

Is the (RNA) library stranded or non-stranded (unstranded).

URI: nmdc:is_stranded

"},{"location":"is_stranded/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"is_stranded/#properties","title":"Properties","text":""},{"location":"is_stranded/#comments","title":"Comments","text":""},{"location":"is_stranded/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"is_stranded/#schema-source","title":"Schema Source","text":""},{"location":"is_stranded/#linkml-source","title":"LinkML Source","text":"
name: is_stranded\ndescription: Is the (RNA) library stranded or non-stranded (unstranded).\ncomments:\n- A value of true means the library is stranded, flase means non-stranded.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_stranded\ndomain_of:\n- LibraryPreparation\nrange: boolean\n\n
"},{"location":"isotope_exposure/","title":"Slot: isotope exposure/addition (isotope_exposure)","text":"

List isotope exposure or addition applied to your sample.

URI: nmdc:isotope_exposure

"},{"location":"isotope_exposure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"isotope_exposure/#properties","title":"Properties","text":""},{"location":"isotope_exposure/#examples","title":"Examples","text":"Value 13C glucose H218O"},{"location":"isotope_exposure/#comments","title":"Comments","text":""},{"location":"isotope_exposure/#todos","title":"TODOs","text":""},{"location":"isotope_exposure/#see-also","title":"See Also","text":""},{"location":"isotope_exposure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"isotope_exposure/#schema-source","title":"Schema Source","text":""},{"location":"isotope_exposure/#linkml-source","title":"LinkML Source","text":"
name: isotope_exposure\ndescription: List isotope exposure or addition applied to your sample.\ntitle: isotope exposure/addition\ntodos:\n- Can we make the H218O correctly super and subscripted?\ncomments:\n- This is required when your experimental design includes the use of isotopically\n  labeled compounds\nexamples:\n- value: 13C glucose\n- value: H218O\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000751\nrank: 16\nstring_serialization: '{termLabel} {[termID]}; {timestamp}'\nalias: isotope_exposure\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"iw_bt_date_well/","title":"Slot: injection water breakthrough date of specific well (iw_bt_date_well)","text":"

Injection water breakthrough date per well following a secondary and/or tertiary recovery

URI: MIXS:0001010

"},{"location":"iw_bt_date_well/#inheritance","title":"Inheritance","text":""},{"location":"iw_bt_date_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"iw_bt_date_well/#properties","title":"Properties","text":""},{"location":"iw_bt_date_well/#aliases","title":"Aliases","text":""},{"location":"iw_bt_date_well/#examples","title":"Examples","text":"Value 2018-05-11"},{"location":"iw_bt_date_well/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"iw_bt_date_well/#annotations","title":"Annotations","text":"property value expected_value timestamp"},{"location":"iw_bt_date_well/#schema-source","title":"Schema Source","text":""},{"location":"iw_bt_date_well/#linkml-source","title":"LinkML Source","text":"
name: iw_bt_date_well\nannotations:\n  expected_value:\n    tag: expected_value\n    value: timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Injection water breakthrough date per well following a secondary and/or\n  tertiary recovery\ntitle: injection water breakthrough date of specific well\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water breakthrough date of specific well\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001010\nalias: iw_bt_date_well\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"iwf/","title":"Slot: injection water fraction (iwf)","text":"

Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)

URI: MIXS:0000455

"},{"location":"iwf/#inheritance","title":"Inheritance","text":""},{"location":"iwf/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"iwf/#properties","title":"Properties","text":""},{"location":"iwf/#aliases","title":"Aliases","text":""},{"location":"iwf/#examples","title":"Examples","text":"Value"},{"location":"iwf/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"iwf/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"iwf/#schema-source","title":"Schema Source","text":""},{"location":"iwf/#linkml-source","title":"LinkML Source","text":"
name: iwf\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Proportion of the produced fluids derived from injected water at the\n  time of sampling. (e.g. 87%)\ntitle: injection water fraction\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water fraction\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000455\nalias: iwf\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"jgi_portal_analysis_project_identifiers/","title":"Slot: jgi_portal_analysis_project_identifiers","text":"

identifiers for corresponding analysis projects in JGI Portal

URI: nmdc:jgi_portal_analysis_project_identifiers

"},{"location":"jgi_portal_analysis_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"jgi_portal_analysis_project_identifiers/#properties","title":"Properties","text":""},{"location":"jgi_portal_analysis_project_identifiers/#examples","title":"Examples","text":"Value https://data.jgi.doe.gov/search?q=1414320"},{"location":"jgi_portal_analysis_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"jgi_portal_analysis_project_identifiers/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"jgi_portal_analysis_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"jgi_portal_analysis_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: jgi_portal_analysis_project_identifiers\nid_prefixes:\n- jgi.analysis\ndescription: identifiers for corresponding analysis projects in JGI Portal\nexamples:\n- value: https://data.jgi.doe.gov/search?q=1414320\n  description: Metagenome - Draft Assembly YELL_051-M-20210705-comp-DNA1\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- jgi_portal_identifiers\nalias: jgi_portal_analysis_project_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^jgi.analysis:[0-9]+$\n\n
"},{"location":"jgi_portal_identifiers/","title":"Slot: jgi_portal_identifiers","text":"

identifiers for entities according to JGI Portal

URI: nmdc:jgi_portal_identifiers

"},{"location":"jgi_portal_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... None Study jgi_portal_analysis_project_identifiers identifiers for corresponding analysis projects in JGI Portal None"},{"location":"jgi_portal_identifiers/#properties","title":"Properties","text":""},{"location":"jgi_portal_identifiers/#see-also","title":"See Also","text":""},{"location":"jgi_portal_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"jgi_portal_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"jgi_portal_identifiers/#linkml-source","title":"LinkML Source","text":"
name: jgi_portal_identifiers\ndescription: identifiers for entities according to JGI Portal\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://data.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: jgi_portal_identifiers\nrange: string\n\n
"},{"location":"jgi_portal_study_identifiers/","title":"Slot: JGI Portal Study identifiers (jgi_portal_study_identifiers)","text":"

Identifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier.

URI: nmdc:jgi_portal_study_identifiers

"},{"location":"jgi_portal_study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"jgi_portal_study_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"jgi_portal_study_identifiers/#properties","title":"Properties","text":""},{"location":"jgi_portal_study_identifiers/#examples","title":"Examples","text":"Value jgi.proposal:507130"},{"location":"jgi_portal_study_identifiers/#comments","title":"Comments","text":""},{"location":"jgi_portal_study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"jgi_portal_study_identifiers/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"jgi_portal_study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"jgi_portal_study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: jgi_portal_study_identifiers\nid_prefixes:\n- jgi.proposal\ndescription: Identifiers that link a NMDC study to a website hosting raw and analyzed\n  data for a JGI proposal.  The suffix of the curie can used to query the GOLD API\n  and is interoperable with an award DOI from OSTI and a GOLD study identifier.\ntitle: JGI Portal Study identifiers\ncomments:\n- Could this could be considered a related identifier?\n- Curie suffix is the Site Award Number from an OSTI award page\n- Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD study\n  identifier gold:Gs0154044\n- bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\nexamples:\n- value: jgi.proposal:507130\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- jgi_portal_identifiers\nalias: jgi_portal_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^jgi.proposal:\\d+$\n\n
"},{"location":"known_as/","title":"Slot: known_as","text":"

URI: nmdc:known_as

"},{"location":"known_as/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"known_as/#properties","title":"Properties","text":""},{"location":"known_as/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"known_as/#schema-source","title":"Schema Source","text":""},{"location":"known_as/#linkml-source","title":"LinkML Source","text":"
name: known_as\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: known_as\ndomain_of:\n- PortionOfSubstance\nrange: ChemicalEntity\n\n
"},{"location":"language/","title":"Slot: language","text":"

Should use ISO 639-1 code e.g. \"en\", \"fr\"

URI: nmdc:language

"},{"location":"language/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextValue A basic string value no"},{"location":"language/#properties","title":"Properties","text":""},{"location":"language/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"language/#schema-source","title":"Schema Source","text":""},{"location":"language/#linkml-source","title":"LinkML Source","text":"
name: language\ndescription: Should use ISO 639-1 code e.g. \"en\", \"fr\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: language\ndomain_of:\n- TextValue\nrange: language code\n\n
"},{"location":"last_clean/","title":"Slot: last time swept/mopped/vacuumed (last_clean)","text":"

The last time the floor was cleaned (swept, mopped, vacuumed)

URI: MIXS:0000814

"},{"location":"last_clean/#inheritance","title":"Inheritance","text":""},{"location":"last_clean/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"last_clean/#properties","title":"Properties","text":""},{"location":"last_clean/#aliases","title":"Aliases","text":""},{"location":"last_clean/#examples","title":"Examples","text":"Value 2018-05-11:T14:30Z"},{"location":"last_clean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"last_clean/#annotations","title":"Annotations","text":"property value expected_value timestamp"},{"location":"last_clean/#schema-source","title":"Schema Source","text":""},{"location":"last_clean/#linkml-source","title":"LinkML Source","text":"
name: last_clean\nannotations:\n  expected_value:\n    tag: expected_value\n    value: timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The last time the floor was cleaned (swept, mopped, vacuumed)\ntitle: last time swept/mopped/vacuumed\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- last time swept/mopped/vacuumed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000814\nalias: last_clean\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"lat_lon/","title":"Slot: geographic location (latitude and longitude) (lat_lon)","text":"

The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system

URI: MIXS:0000009

"},{"location":"lat_lon/#inheritance","title":"Inheritance","text":""},{"location":"lat_lon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment yes"},{"location":"lat_lon/#properties","title":"Properties","text":""},{"location":"lat_lon/#aliases","title":"Aliases","text":""},{"location":"lat_lon/#examples","title":"Examples","text":"Value 50.586825 6.408977"},{"location":"lat_lon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"lat_lon/#annotations","title":"Annotations","text":"property value expected_value decimal degrees, limit to 8 decimal points"},{"location":"lat_lon/#schema-source","title":"Schema Source","text":""},{"location":"lat_lon/#linkml-source","title":"LinkML Source","text":"
name: lat_lon\nannotations:\n  expected_value:\n    tag: expected_value\n    value: decimal degrees,  limit to 8 decimal points\ndescription: The geographical origin of the sample as defined by latitude and longitude.\n  The values should be reported in decimal degrees and in WGS84 system\ntitle: geographic location (latitude and longitude)\nexamples:\n- value: 50.586825 6.408977\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (latitude and longitude)\nrank: 1000\nis_a: environment field\nstring_serialization: '{float} {float}'\nslot_uri: MIXS:0000009\nalias: lat_lon\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: GeolocationValue\nmultivalued: false\n\n
"},{"location":"latitude/","title":"Slot: latitude","text":"

latitude

URI: wgs84:lat

"},{"location":"latitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"latitude/#properties","title":"Properties","text":""},{"location":"latitude/#examples","title":"Examples","text":"Value -33.460524"},{"location":"latitude/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"latitude/#schema-source","title":"Schema Source","text":""},{"location":"latitude/#linkml-source","title":"LinkML Source","text":"
name: latitude\ndescription: latitude\nexamples:\n- value: '-33.460524'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:latitude\nrank: 1000\nslot_uri: wgs84:lat\nalias: latitude\ndomain_of:\n- GeolocationValue\nrange: decimal degree\n\n
"},{"location":"lbc_thirty/","title":"Slot: lime buffer capacity (at 30 minutes) (lbc_thirty)","text":"

lime buffer capacity, determined after 30 minute incubation

URI: nmdc:lbc_thirty

"},{"location":"lbc_thirty/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lbc_thirty/#properties","title":"Properties","text":""},{"location":"lbc_thirty/#aliases","title":"Aliases","text":""},{"location":"lbc_thirty/#examples","title":"Examples","text":"Value 543 mg/kg"},{"location":"lbc_thirty/#comments","title":"Comments","text":""},{"location":"lbc_thirty/#see-also","title":"See Also","text":""},{"location":"lbc_thirty/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"lbc_thirty/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"lbc_thirty/#schema-source","title":"Schema Source","text":""},{"location":"lbc_thirty/#linkml-source","title":"LinkML Source","text":"
name: lbc_thirty\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: ppm CaCO3/pH\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: lime buffer capacity, determined after 30 minute incubation\ntitle: lime buffer capacity (at 30 minutes)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n  pH unit\nexamples:\n- value: 543 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\n- https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\naliases:\n- lbc_thirty\n- lbc30\n- lime buffer capacity (at 30 minutes)\nrank: 1000\nalias: lbc_thirty\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"lbceq/","title":"Slot: lime buffer capacity (after 5 day incubation) (lbceq)","text":"

lime buffer capacity, determined at equilibrium after 5 day incubation

URI: nmdc:lbceq

"},{"location":"lbceq/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lbceq/#properties","title":"Properties","text":""},{"location":"lbceq/#aliases","title":"Aliases","text":""},{"location":"lbceq/#examples","title":"Examples","text":"Value 1575 mg/kg"},{"location":"lbceq/#comments","title":"Comments","text":""},{"location":"lbceq/#see-also","title":"See Also","text":""},{"location":"lbceq/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"lbceq/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"lbceq/#schema-source","title":"Schema Source","text":""},{"location":"lbceq/#linkml-source","title":"LinkML Source","text":"
name: lbceq\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: ppm CaCO3/pH\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: lime buffer capacity, determined at equilibrium after 5 day incubation\ntitle: lime buffer capacity (after 5 day incubation)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n  pH unit\nexamples:\n- value: 1575 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- lbceq\n- lime buffer capacity (at 5-day equilibrium)\nrank: 1000\nalias: lbceq\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"library_preparation_kit/","title":"Slot: library_preparation_kit","text":"

URI: nmdc:library_preparation_kit

"},{"location":"library_preparation_kit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_preparation_kit/#properties","title":"Properties","text":""},{"location":"library_preparation_kit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"library_preparation_kit/#schema-source","title":"Schema Source","text":""},{"location":"library_preparation_kit/#linkml-source","title":"LinkML Source","text":"
name: library_preparation_kit\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_preparation_kit\ndomain_of:\n- LibraryPreparation\nrange: string\n\n
"},{"location":"library_type/","title":"Slot: library type (library_type)","text":"

URI: nmdc:library_type

"},{"location":"library_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_type/#properties","title":"Properties","text":""},{"location":"library_type/#examples","title":"Examples","text":"Value DNA"},{"location":"library_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"library_type/#schema-source","title":"Schema Source","text":""},{"location":"library_type/#linkml-source","title":"LinkML Source","text":"
name: library_type\ntitle: library type\nexamples:\n- value: DNA\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_type\ndomain_of:\n- LibraryPreparation\nrange: LibraryTypeEnum\n\n
"},{"location":"light_intensity/","title":"Slot: light intensity (light_intensity)","text":"

Measurement of light intensity

URI: MIXS:0000706

"},{"location":"light_intensity/#inheritance","title":"Inheritance","text":""},{"location":"light_intensity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"light_intensity/#properties","title":"Properties","text":""},{"location":"light_intensity/#aliases","title":"Aliases","text":""},{"location":"light_intensity/#examples","title":"Examples","text":"Value 0.3 lux"},{"location":"light_intensity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"light_intensity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"light_intensity/#schema-source","title":"Schema Source","text":""},{"location":"light_intensity/#linkml-source","title":"LinkML Source","text":"
name: light_intensity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: lux\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of light intensity\ntitle: light intensity\nexamples:\n- value: 0.3 lux\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light intensity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000706\nalias: light_intensity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"light_regm/","title":"Slot: light regimen (light_regm)","text":"

Information about treatment(s) involving exposure to light, including both light intensity and quality.

URI: MIXS:0000569

"},{"location":"light_regm/#inheritance","title":"Inheritance","text":""},{"location":"light_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"light_regm/#properties","title":"Properties","text":""},{"location":"light_regm/#aliases","title":"Aliases","text":""},{"location":"light_regm/#examples","title":"Examples","text":"Value incandescant light;10 lux;450 nanometer"},{"location":"light_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"light_regm/#annotations","title":"Annotations","text":"property value expected_value exposure type;light intensity;light quality"},{"location":"light_regm/#schema-source","title":"Schema Source","text":""},{"location":"light_regm/#linkml-source","title":"LinkML Source","text":"
name: light_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: exposure type;light intensity;light quality\n  preferred_unit:\n    tag: preferred_unit\n    value: lux; micrometer, nanometer, angstrom\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information about treatment(s) involving exposure to light, including\n  both light intensity and quality.\ntitle: light regimen\nexamples:\n- value: incandescant light;10 lux;450 nanometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000569\nalias: light_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"light_type/","title":"Slot: light type (light_type)","text":"

Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light

URI: MIXS:0000769

"},{"location":"light_type/#inheritance","title":"Inheritance","text":""},{"location":"light_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"light_type/#properties","title":"Properties","text":""},{"location":"light_type/#aliases","title":"Aliases","text":""},{"location":"light_type/#examples","title":"Examples","text":"Value desk lamp"},{"location":"light_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"light_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"light_type/#schema-source","title":"Schema Source","text":""},{"location":"light_type/#linkml-source","title":"LinkML Source","text":"
name: light_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Application of light to achieve some practical or aesthetic effect. Lighting\n  includes the use of both artificial light sources such as lamps and light fixtures,\n  as well as natural illumination by capturing daylight. Can also include absence\n  of light\ntitle: light type\nexamples:\n- value: desk lamp\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000769\nalias: light_type\ndomain_of:\n- Biosample\nrange: light_type_enum\nmultivalued: true\n\n
"},{"location":"link_addit_analys/","title":"Slot: links to additional analysis (link_addit_analys)","text":"

Link to additional analysis results performed on the sample

URI: MIXS:0000340

"},{"location":"link_addit_analys/#inheritance","title":"Inheritance","text":""},{"location":"link_addit_analys/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"link_addit_analys/#properties","title":"Properties","text":""},{"location":"link_addit_analys/#aliases","title":"Aliases","text":""},{"location":"link_addit_analys/#examples","title":"Examples","text":"Value"},{"location":"link_addit_analys/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"link_addit_analys/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"link_addit_analys/#schema-source","title":"Schema Source","text":""},{"location":"link_addit_analys/#linkml-source","title":"LinkML Source","text":"
name: link_addit_analys\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Link to additional analysis results performed on the sample\ntitle: links to additional analysis\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- links to additional analysis\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000340\nalias: link_addit_analys\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"link_class_info/","title":"Slot: link to classification information (link_class_info)","text":"

Link to digitized soil maps or other soil classification information

URI: MIXS:0000329

"},{"location":"link_class_info/#inheritance","title":"Inheritance","text":""},{"location":"link_class_info/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"link_class_info/#properties","title":"Properties","text":""},{"location":"link_class_info/#aliases","title":"Aliases","text":""},{"location":"link_class_info/#examples","title":"Examples","text":"Value"},{"location":"link_class_info/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"link_class_info/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"link_class_info/#schema-source","title":"Schema Source","text":""},{"location":"link_class_info/#linkml-source","title":"LinkML Source","text":"
name: link_class_info\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Link to digitized soil maps or other soil classification information\ntitle: link to classification information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to classification information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000329\nalias: link_class_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"link_climate_info/","title":"Slot: link to climate information (link_climate_info)","text":"

Link to climate resource

URI: MIXS:0000328

"},{"location":"link_climate_info/#inheritance","title":"Inheritance","text":""},{"location":"link_climate_info/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"link_climate_info/#properties","title":"Properties","text":""},{"location":"link_climate_info/#aliases","title":"Aliases","text":""},{"location":"link_climate_info/#examples","title":"Examples","text":"Value"},{"location":"link_climate_info/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"link_climate_info/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"link_climate_info/#schema-source","title":"Schema Source","text":""},{"location":"link_climate_info/#linkml-source","title":"LinkML Source","text":"
name: link_climate_info\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Link to climate resource\ntitle: link to climate information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to climate information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000328\nalias: link_climate_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"lithology/","title":"Slot: lithology (lithology)","text":"

Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000990

"},{"location":"lithology/#inheritance","title":"Inheritance","text":""},{"location":"lithology/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lithology/#properties","title":"Properties","text":""},{"location":"lithology/#aliases","title":"Aliases","text":""},{"location":"lithology/#examples","title":"Examples","text":"Value Volcanic"},{"location":"lithology/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"lithology/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"lithology/#schema-source","title":"Schema Source","text":""},{"location":"lithology/#linkml-source","title":"LinkML Source","text":"
name: lithology\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n  If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: lithology\nexamples:\n- value: Volcanic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000990\nalias: lithology\ndomain_of:\n- Biosample\nrange: lithology_enum\nmultivalued: false\n\n
"},{"location":"local_class/","title":"Slot: soil_taxonomic/local classification (local_class)","text":"

Soil classification based on local soil classification system

URI: MIXS:0000330

"},{"location":"local_class/#inheritance","title":"Inheritance","text":""},{"location":"local_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment no"},{"location":"local_class/#properties","title":"Properties","text":""},{"location":"local_class/#aliases","title":"Aliases","text":""},{"location":"local_class/#examples","title":"Examples","text":"Value"},{"location":"local_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"local_class/#annotations","title":"Annotations","text":"property value expected_value local classification name"},{"location":"local_class/#schema-source","title":"Schema Source","text":""},{"location":"local_class/#linkml-source","title":"LinkML Source","text":"
name: local_class\nannotations:\n  expected_value:\n    tag: expected_value\n    value: local classification name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Soil classification based on local soil classification system\ntitle: soil_taxonomic/local classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000330\nalias: local_class\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"local_class_meth/","title":"Slot: soil_taxonomic/local classification method (local_class_meth)","text":"

Reference or method used in determining the local soil classification

URI: MIXS:0000331

"},{"location":"local_class_meth/#inheritance","title":"Inheritance","text":""},{"location":"local_class_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"local_class_meth/#properties","title":"Properties","text":""},{"location":"local_class_meth/#aliases","title":"Aliases","text":""},{"location":"local_class_meth/#examples","title":"Examples","text":"Value"},{"location":"local_class_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"local_class_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"local_class_meth/#schema-source","title":"Schema Source","text":""},{"location":"local_class_meth/#linkml-source","title":"LinkML Source","text":"
name: local_class_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining the local soil classification\ntitle: soil_taxonomic/local classification method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000331\nalias: local_class_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"location/","title":"Slot: location","text":"

URI: nmdc:location

"},{"location":"location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"location/#properties","title":"Properties","text":""},{"location":"location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"location/#schema-source","title":"Schema Source","text":""},{"location":"location/#linkml-source","title":"LinkML Source","text":"
name: location\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: location\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"longitude/","title":"Slot: longitude","text":"

longitude

URI: wgs84:long

"},{"location":"longitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"longitude/#properties","title":"Properties","text":""},{"location":"longitude/#examples","title":"Examples","text":"Value 150.168149"},{"location":"longitude/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"longitude/#schema-source","title":"Schema Source","text":""},{"location":"longitude/#linkml-source","title":"LinkML Source","text":"
name: longitude\ndescription: longitude\nexamples:\n- value: '150.168149'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:longitude\nrank: 1000\nslot_uri: wgs84:long\nalias: longitude\ndomain_of:\n- GeolocationValue\nrange: decimal degree\n\n
"},{"location":"low_depth_contig_num/","title":"Slot: low_depth_contig_num","text":"

URI: nmdc:low_depth_contig_num

"},{"location":"low_depth_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"low_depth_contig_num/#properties","title":"Properties","text":""},{"location":"low_depth_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"low_depth_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"low_depth_contig_num/#linkml-source","title":"LinkML Source","text":"
name: low_depth_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: low_depth_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"magnesium/","title":"Slot: magnesium (magnesium)","text":"

Concentration of magnesium in the sample

URI: MIXS:0000431

"},{"location":"magnesium/#inheritance","title":"Inheritance","text":""},{"location":"magnesium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"magnesium/#properties","title":"Properties","text":""},{"location":"magnesium/#aliases","title":"Aliases","text":""},{"location":"magnesium/#examples","title":"Examples","text":"Value 52.8 micromole per kilogram"},{"location":"magnesium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"magnesium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"magnesium/#schema-source","title":"Schema Source","text":""},{"location":"magnesium/#linkml-source","title":"LinkML Source","text":"
name: magnesium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per liter, milligram per liter, parts per million, micromole per kilogram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of magnesium in the sample\ntitle: magnesium\nexamples:\n- value: 52.8 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- magnesium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000431\nalias: magnesium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"mags_list/","title":"Slot: mags_list","text":"

URI: nmdc:mags_list

"},{"location":"mags_list/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"mags_list/#properties","title":"Properties","text":""},{"location":"mags_list/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mags_list/#schema-source","title":"Schema Source","text":""},{"location":"mags_list/#linkml-source","title":"LinkML Source","text":"
name: mags_list\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mags_list\ndomain_of:\n- MagsAnalysis\nrange: MagBin\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"manganese/","title":"Slot: manganese (manganese)","text":"

Concentration of manganese in the sample

URI: nmdc:manganese

"},{"location":"manganese/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"manganese/#properties","title":"Properties","text":""},{"location":"manganese/#aliases","title":"Aliases","text":""},{"location":"manganese/#examples","title":"Examples","text":"Value 24.7 mg/kg"},{"location":"manganese/#see-also","title":"See Also","text":""},{"location":"manganese/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"manganese/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"manganese/#schema-source","title":"Schema Source","text":""},{"location":"manganese/#linkml-source","title":"LinkML Source","text":"
name: manganese\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg (ppm)\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of manganese in the sample\ntitle: manganese\nexamples:\n- value: 24.7 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- manganese\nrank: 1000\nalias: manganese\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"manifest_category/","title":"Slot: manifest_category","text":"

The type of collection that describes the data in the collection.

URI: nmdc:manifest_category

"},{"location":"manifest_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Manifest no"},{"location":"manifest_category/#properties","title":"Properties","text":""},{"location":"manifest_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"manifest_category/#schema-source","title":"Schema Source","text":""},{"location":"manifest_category/#linkml-source","title":"LinkML Source","text":"
name: manifest_category\ndescription: The type of collection that describes the data in the collection.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: manifest_category\ndomain_of:\n- Manifest\nrange: ManifestCategoryEnum\nrequired: true\n\n
"},{"location":"manifest_set/","title":"Slot: manifest_set","text":"

This property links a database object to the set of manifests within it.

URI: nmdc:manifest_set

"},{"location":"manifest_set/#inheritance","title":"Inheritance","text":""},{"location":"manifest_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"manifest_set/#properties","title":"Properties","text":""},{"location":"manifest_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"manifest_set/#schema-source","title":"Schema Source","text":""},{"location":"manifest_set/#linkml-source","title":"LinkML Source","text":"
name: manifest_set\ndescription: This property links a database object to the set of manifests within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: manifest_set\ndomain_of:\n- Database\nrange: Manifest\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mass/","title":"Slot: mass (mass)","text":"

A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.

URI: nmdc:mass

"},{"location":"mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes"},{"location":"mass/#properties","title":"Properties","text":""},{"location":"mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mass/#schema-source","title":"Schema Source","text":""},{"location":"mass/#linkml-source","title":"LinkML Source","text":"
name: mass\ndescription: A physical quality that inheres in a bearer by virtue of the proportion\n  of the bearer's amount of matter.\ntitle: mass\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- PATO:0000125\nrank: 1000\nalias: mass\ndomain_of:\n- SubSamplingProcess\n- PortionOfSubstance\nrange: QuantityValue\n\n
"},{"location":"mass_analyzers/","title":"Slot: mass_analyzers","text":"

The kind of mass analyzer(s) used during the spectra collection.

URI: nmdc:mass_analyzers

"},{"location":"mass_analyzers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_analyzers/#properties","title":"Properties","text":""},{"location":"mass_analyzers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mass_analyzers/#schema-source","title":"Schema Source","text":""},{"location":"mass_analyzers/#linkml-source","title":"LinkML Source","text":"
name: mass_analyzers\ndescription: The kind of mass analyzer(s) used during the spectra collection.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1000443\nrank: 1000\nalias: mass_analyzers\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassAnalyzerEnum\nmultivalued: true\n\n
"},{"location":"mass_spectrometry_acquisition_strategy/","title":"Slot: mass_spectrometry_acquisition_strategy","text":"

Mode of running a mass spectrometer method by which m/z ranges are selected and ions possibly fragment.

URI: nmdc:mass_spectrometry_acquisition_strategy

"},{"location":"mass_spectrometry_acquisition_strategy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_spectrometry_acquisition_strategy/#properties","title":"Properties","text":""},{"location":"mass_spectrometry_acquisition_strategy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mass_spectrometry_acquisition_strategy/#schema-source","title":"Schema Source","text":""},{"location":"mass_spectrometry_acquisition_strategy/#linkml-source","title":"LinkML Source","text":"
name: mass_spectrometry_acquisition_strategy\ndescription: Mode of running a mass spectrometer method by which m/z ranges are selected\n  and ions possibly fragment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1003213\nrank: 1000\nalias: mass_spectrometry_acquisition_strategy\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassSpectrometryAcquisitionStrategyEnum\n\n
"},{"location":"mass_spectrum_collection_modes/","title":"Slot: mass_spectrum_collection_modes","text":"

Indicates whether mass spectra were collected in full profile, reduced profile, or centroid mode during acquisition.

URI: nmdc:mass_spectrum_collection_modes

"},{"location":"mass_spectrum_collection_modes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_spectrum_collection_modes/#properties","title":"Properties","text":""},{"location":"mass_spectrum_collection_modes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mass_spectrum_collection_modes/#schema-source","title":"Schema Source","text":""},{"location":"mass_spectrum_collection_modes/#linkml-source","title":"LinkML Source","text":"
name: mass_spectrum_collection_modes\ndescription: Indicates whether mass spectra were collected in full profile, reduced\n  profile, or centroid mode during acquisition.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mass_spectrum_collection_modes\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassSpectrumCollectionModeEnum\nmultivalued: true\n\n
"},{"location":"material_component_separation/","title":"Slot: material_component_separation","text":"

A material processing in which components of an input material become segregated in space

URI: nmdc:material_component_separation

"},{"location":"material_component_separation/#properties","title":"Properties","text":""},{"location":"material_component_separation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"material_component_separation/#schema-source","title":"Schema Source","text":""},{"location":"material_component_separation/#linkml-source","title":"LinkML Source","text":"
name: material_component_separation\ndescription: A material processing in which components of an input material become\n  segregated in space\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: material_component_separation\nrange: string\n\n
"},{"location":"material_processing_set/","title":"Slot: material_processing_set","text":"

This property links a database object to the set of material processing within it.

URI: nmdc:material_processing_set

"},{"location":"material_processing_set/#inheritance","title":"Inheritance","text":""},{"location":"material_processing_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"material_processing_set/#properties","title":"Properties","text":""},{"location":"material_processing_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"material_processing_set/#schema-source","title":"Schema Source","text":""},{"location":"material_processing_set/#linkml-source","title":"LinkML Source","text":"
name: material_processing_set\ndescription: This property links a database object to the set of material processing\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: material_processing_set\ndomain_of:\n- Database\nrange: MaterialProcessing\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"max_occup/","title":"Slot: maximum occupancy (max_occup)","text":"

The maximum amount of people allowed in the indoor environment

URI: MIXS:0000229

"},{"location":"max_occup/#inheritance","title":"Inheritance","text":""},{"location":"max_occup/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"max_occup/#properties","title":"Properties","text":""},{"location":"max_occup/#aliases","title":"Aliases","text":""},{"location":"max_occup/#examples","title":"Examples","text":"Value"},{"location":"max_occup/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"max_occup/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"max_occup/#schema-source","title":"Schema Source","text":""},{"location":"max_occup/#linkml-source","title":"LinkML Source","text":"
name: max_occup\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The maximum amount of people allowed in the indoor environment\ntitle: maximum occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- maximum occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000229\nalias: max_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"md5_checksum/","title":"Slot: md5_checksum","text":"

MD5 checksum of file (pre-compressed)

URI: nmdc:md5_checksum

"},{"location":"md5_checksum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"md5_checksum/#properties","title":"Properties","text":""},{"location":"md5_checksum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"md5_checksum/#schema-source","title":"Schema Source","text":""},{"location":"md5_checksum/#linkml-source","title":"LinkML Source","text":"
name: md5_checksum\ndescription: MD5 checksum of file (pre-compressed)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: md5_checksum\ndomain_of:\n- DataObject\nrange: string\n\n
"},{"location":"mean_frict_vel/","title":"Slot: mean friction velocity (mean_frict_vel)","text":"

Measurement of mean friction velocity

URI: MIXS:0000498

"},{"location":"mean_frict_vel/#inheritance","title":"Inheritance","text":""},{"location":"mean_frict_vel/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mean_frict_vel/#properties","title":"Properties","text":""},{"location":"mean_frict_vel/#aliases","title":"Aliases","text":""},{"location":"mean_frict_vel/#examples","title":"Examples","text":"Value 0.5 meter per second"},{"location":"mean_frict_vel/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mean_frict_vel/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"mean_frict_vel/#schema-source","title":"Schema Source","text":""},{"location":"mean_frict_vel/#linkml-source","title":"LinkML Source","text":"
name: mean_frict_vel\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of mean friction velocity\ntitle: mean friction velocity\nexamples:\n- value: 0.5 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000498\nalias: mean_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"mean_peak_frict_vel/","title":"Slot: mean peak friction velocity (mean_peak_frict_vel)","text":"

Measurement of mean peak friction velocity

URI: MIXS:0000502

"},{"location":"mean_peak_frict_vel/#inheritance","title":"Inheritance","text":""},{"location":"mean_peak_frict_vel/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mean_peak_frict_vel/#properties","title":"Properties","text":""},{"location":"mean_peak_frict_vel/#aliases","title":"Aliases","text":""},{"location":"mean_peak_frict_vel/#examples","title":"Examples","text":"Value 1 meter per second"},{"location":"mean_peak_frict_vel/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mean_peak_frict_vel/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"mean_peak_frict_vel/#schema-source","title":"Schema Source","text":""},{"location":"mean_peak_frict_vel/#linkml-source","title":"LinkML Source","text":"
name: mean_peak_frict_vel\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of mean peak friction velocity\ntitle: mean peak friction velocity\nexamples:\n- value: 1 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean peak friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000502\nalias: mean_peak_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"mech_struc/","title":"Slot: mechanical structure (mech_struc)","text":"

mechanical structure: a moving structure

URI: MIXS:0000815

"},{"location":"mech_struc/#inheritance","title":"Inheritance","text":""},{"location":"mech_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mech_struc/#properties","title":"Properties","text":""},{"location":"mech_struc/#aliases","title":"Aliases","text":""},{"location":"mech_struc/#examples","title":"Examples","text":"Value elevator"},{"location":"mech_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mech_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"mech_struc/#schema-source","title":"Schema Source","text":""},{"location":"mech_struc/#linkml-source","title":"LinkML Source","text":"
name: mech_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'mechanical structure: a moving structure'\ntitle: mechanical structure\nexamples:\n- value: elevator\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000815\nalias: mech_struc\ndomain_of:\n- Biosample\nrange: mech_struc_enum\nmultivalued: false\n\n
"},{"location":"mechanical_damage/","title":"Slot: mechanical damage (mechanical_damage)","text":"

Information about any mechanical damage exerted on the plant; can include multiple damages and sites

URI: MIXS:0001052

"},{"location":"mechanical_damage/#inheritance","title":"Inheritance","text":""},{"location":"mechanical_damage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mechanical_damage/#properties","title":"Properties","text":""},{"location":"mechanical_damage/#aliases","title":"Aliases","text":""},{"location":"mechanical_damage/#examples","title":"Examples","text":"Value pruning;bark"},{"location":"mechanical_damage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mechanical_damage/#annotations","title":"Annotations","text":"property value expected_value damage type;body site"},{"location":"mechanical_damage/#schema-source","title":"Schema Source","text":""},{"location":"mechanical_damage/#linkml-source","title":"LinkML Source","text":"
name: mechanical_damage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: damage type;body site\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about any mechanical damage exerted on the plant; can include\n  multiple damages and sites\ntitle: mechanical damage\nexamples:\n- value: pruning;bark\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical damage\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0001052\nalias: mechanical_damage\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"members_id/","title":"Slot: members_id","text":"

URI: nmdc:members_id

"},{"location":"members_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"members_id/#properties","title":"Properties","text":""},{"location":"members_id/#todos","title":"TODOs","text":""},{"location":"members_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"members_id/#schema-source","title":"Schema Source","text":""},{"location":"members_id/#linkml-source","title":"LinkML Source","text":"
name: members_id\ntodos:\n- this slot needs some basic textual annotations and constraints\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: members_id\ndomain_of:\n- MagBin\nrange: string\nmultivalued: true\n\n
"},{"location":"metabolite_identified/","title":"Slot: metabolite_identified","text":"

the specific metabolite identifier

URI: nmdc:metabolite_identified

"},{"location":"metabolite_identified/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"metabolite_identified/#properties","title":"Properties","text":""},{"location":"metabolite_identified/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolite_identified/#schema-source","title":"Schema Source","text":""},{"location":"metabolite_identified/#linkml-source","title":"LinkML Source","text":"
name: metabolite_identified\ndescription: the specific metabolite identifier\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metabolite_identified\ndomain_of:\n- MetaboliteIdentification\nrange: ChemicalEntity\n\n
"},{"location":"metagenome_annotation_id/","title":"Slot: metagenome_annotation_id","text":"

The identifier for the analysis activity that generated the functional annotation results, where the analysis activity is an instance of the/an appropriate subclass of WorkflowExecution

URI: nmdc:metagenome_annotation_id

"},{"location":"metagenome_annotation_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember yes"},{"location":"metagenome_annotation_id/#properties","title":"Properties","text":""},{"location":"metagenome_annotation_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_annotation_id/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_annotation_id/#linkml-source","title":"LinkML Source","text":"
name: metagenome_annotation_id\ndescription: The identifier for the analysis activity that generated the functional\n  annotation results, where the analysis activity is an instance of the/an appropriate\n  subclass of WorkflowExecution\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metagenome_annotation_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: WorkflowExecution\nrequired: true\nany_of:\n- range: MetagenomeAnnotation\n- range: MetatranscriptomeAnnotation\n\n
"},{"location":"metagenome_assembly_parameter/","title":"Slot: metagenome_assembly_parameter","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:metagenome_assembly_parameter

"},{"location":"metagenome_assembly_parameter/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_assembly_parameter/#properties","title":"Properties","text":""},{"location":"metagenome_assembly_parameter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_assembly_parameter/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_assembly_parameter/#linkml-source","title":"LinkML Source","text":"
name: metagenome_assembly_parameter\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: metagenome_assembly_parameter\nrange: string\n\n
"},{"location":"methane/","title":"Slot: methane (methane)","text":"

Methane (gas) amount or concentration at the time of sampling

URI: MIXS:0000101

"},{"location":"methane/#inheritance","title":"Inheritance","text":""},{"location":"methane/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"methane/#properties","title":"Properties","text":""},{"location":"methane/#aliases","title":"Aliases","text":""},{"location":"methane/#examples","title":"Examples","text":"Value 1800 parts per billion"},{"location":"methane/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"methane/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"methane/#schema-source","title":"Schema Source","text":""},{"location":"methane/#linkml-source","title":"LinkML Source","text":"
name: methane\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, parts per billion, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Methane (gas) amount or concentration at the time of sampling\ntitle: methane\nexamples:\n- value: 1800 parts per billion\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- methane\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000101\nalias: methane\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"mgnify_analysis_identifiers/","title":"Slot: mgnify_analysis_identifiers","text":"

URI: nmdc:mgnify_analysis_identifiers

"},{"location":"mgnify_analysis_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"mgnify_analysis_identifiers/#properties","title":"Properties","text":""},{"location":"mgnify_analysis_identifiers/#examples","title":"Examples","text":"Value https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270"},{"location":"mgnify_analysis_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mgnify_analysis_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"mgnify_analysis_identifiers/#linkml-source","title":"LinkML Source","text":"
name: mgnify_analysis_identifiers\nnotes:\n- 'removed pattern: \"^mgnify:MGYA[0-9]+$\" ## TODO https://github.com/bioregistry/bioregistry/issues/109'\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270\n  description: combined analyses (taxonomic, functional) of sample ERS438107\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- mgnify_identifiers\nalias: mgnify_analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"mgnify_identifiers/","title":"Slot: mgnify_identifiers","text":"

URI: nmdc:mgnify_identifiers

"},{"location":"mgnify_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain mgnify_project_identifiers identifiers for corresponding project in MGnify None Study mgnify_analysis_identifiers None"},{"location":"mgnify_identifiers/#properties","title":"Properties","text":""},{"location":"mgnify_identifiers/#see-also","title":"See Also","text":""},{"location":"mgnify_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mgnify_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"mgnify_identifiers/#linkml-source","title":"LinkML Source","text":"
name: mgnify_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ebi.ac.uk/metagenomics/\nrank: 1000\nmixin: true\nalias: mgnify_identifiers\nrange: string\n\n
"},{"location":"mgnify_project_identifiers/","title":"Slot: mgnify_project_identifiers","text":"

identifiers for corresponding project in MGnify

URI: nmdc:mgnify_project_identifiers

"},{"location":"mgnify_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"mgnify_project_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"mgnify_project_identifiers/#properties","title":"Properties","text":""},{"location":"mgnify_project_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/mgnify.proj:MGYS00005757"},{"location":"mgnify_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mgnify_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"mgnify_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: mgnify_project_identifiers\ndescription: identifiers for corresponding project in MGnify\nexamples:\n- value: https://bioregistry.io/mgnify.proj:MGYS00005757\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- mgnify_identifiers\nalias: mgnify_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^mgnify.proj:[A-Z]+[0-9]+$\n\n
"},{"location":"micro_biomass_c_meth/","title":"Slot: microbial biomass carbon method (micro_biomass_c_meth)","text":"

Reference or method used in determining microbial biomass carbon

URI: nmdc:micro_biomass_c_meth

"},{"location":"micro_biomass_c_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_c_meth/#properties","title":"Properties","text":""},{"location":"micro_biomass_c_meth/#examples","title":"Examples","text":"Value https://doi.org/10.1016/0038-0717(87)90052-6 https://doi.org/10.1016/0038-0717(87)90052-6"},{"location":"micro_biomass_c_meth/#comments","title":"Comments","text":""},{"location":"micro_biomass_c_meth/#todos","title":"TODOs","text":""},{"location":"micro_biomass_c_meth/#see-also","title":"See Also","text":""},{"location":"micro_biomass_c_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"micro_biomass_c_meth/#schema-source","title":"Schema Source","text":""},{"location":"micro_biomass_c_meth/#linkml-source","title":"LinkML Source","text":"
name: micro_biomass_c_meth\ndescription: Reference or method used in determining microbial biomass carbon\ntitle: microbial biomass carbon method\ntodos:\n- How should we separate values? | or ;? lets be consistent\ncomments:\n- required if \"microbial_biomass_c\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000339\nrank: 11\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_c_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"micro_biomass_meth/","title":"Slot: microbial biomass method (micro_biomass_meth)","text":"

Reference or method used in determining microbial biomass

URI: MIXS:0000339

"},{"location":"micro_biomass_meth/#inheritance","title":"Inheritance","text":""},{"location":"micro_biomass_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_meth/#properties","title":"Properties","text":""},{"location":"micro_biomass_meth/#aliases","title":"Aliases","text":""},{"location":"micro_biomass_meth/#examples","title":"Examples","text":"Value"},{"location":"micro_biomass_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"micro_biomass_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"micro_biomass_meth/#schema-source","title":"Schema Source","text":""},{"location":"micro_biomass_meth/#linkml-source","title":"LinkML Source","text":"
name: micro_biomass_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining microbial biomass\ntitle: microbial biomass method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000339\nalias: micro_biomass_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"micro_biomass_n_meth/","title":"Slot: microbial biomass nitrogen method (micro_biomass_n_meth)","text":"

Reference or method used in determining microbial biomass nitrogen

URI: nmdc:micro_biomass_n_meth

"},{"location":"micro_biomass_n_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_n_meth/#properties","title":"Properties","text":""},{"location":"micro_biomass_n_meth/#examples","title":"Examples","text":"Value https://doi.org/10.1016/0038-0717(87)90052-6 https://doi.org/10.1016/0038-0717(87)90052-6"},{"location":"micro_biomass_n_meth/#comments","title":"Comments","text":""},{"location":"micro_biomass_n_meth/#see-also","title":"See Also","text":""},{"location":"micro_biomass_n_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"micro_biomass_n_meth/#schema-source","title":"Schema Source","text":""},{"location":"micro_biomass_n_meth/#linkml-source","title":"LinkML Source","text":"
name: micro_biomass_n_meth\ndescription: Reference or method used in determining microbial biomass nitrogen\ntitle: microbial biomass nitrogen method\ncomments:\n- required if \"microbial_biomass_n\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000339\nrank: 13\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_n_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"microbial_biomass/","title":"Slot: microbial biomass (microbial_biomass)","text":"

The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units

URI: MIXS:0000650

"},{"location":"microbial_biomass/#inheritance","title":"Inheritance","text":""},{"location":"microbial_biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass/#properties","title":"Properties","text":""},{"location":"microbial_biomass/#aliases","title":"Aliases","text":""},{"location":"microbial_biomass/#examples","title":"Examples","text":"Value"},{"location":"microbial_biomass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"microbial_biomass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"microbial_biomass/#schema-source","title":"Schema Source","text":""},{"location":"microbial_biomass/#linkml-source","title":"LinkML Source","text":"
name: microbial_biomass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: ton, kilogram, gram per kilogram soil\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n  smaller than 5-10 micrometer. If you keep this, you would need to have correction\n  factors used for conversion to the final units\ntitle: microbial biomass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000650\nalias: microbial_biomass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"microbial_biomass_c/","title":"Slot: microbial biomass carbon (microbial_biomass_c)","text":"

The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.

URI: nmdc:microbial_biomass_c

"},{"location":"microbial_biomass_c/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_c/#properties","title":"Properties","text":""},{"location":"microbial_biomass_c/#examples","title":"Examples","text":"Value 0.05 ug C/g dry soil"},{"location":"microbial_biomass_c/#comments","title":"Comments","text":""},{"location":"microbial_biomass_c/#see-also","title":"See Also","text":""},{"location":"microbial_biomass_c/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"microbial_biomass_c/#schema-source","title":"Schema Source","text":""},{"location":"microbial_biomass_c/#linkml-source","title":"LinkML Source","text":"
name: microbial_biomass_c\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n  smaller than 5-10 micrometer.\ntitle: microbial biomass carbon\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n  method are required\nexamples:\n- value: 0.05 ug C/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 10\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_c\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"microbial_biomass_n/","title":"Slot: microbial biomass nitrogen (microbial_biomass_n)","text":"

The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.

URI: nmdc:microbial_biomass_n

"},{"location":"microbial_biomass_n/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_n/#properties","title":"Properties","text":""},{"location":"microbial_biomass_n/#examples","title":"Examples","text":"Value 0.05 ug N/g dry soil"},{"location":"microbial_biomass_n/#comments","title":"Comments","text":""},{"location":"microbial_biomass_n/#see-also","title":"See Also","text":""},{"location":"microbial_biomass_n/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"microbial_biomass_n/#schema-source","title":"Schema Source","text":""},{"location":"microbial_biomass_n/#linkml-source","title":"LinkML Source","text":"
name: microbial_biomass_n\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n  smaller than 5-10 micrometer.\ntitle: microbial biomass nitrogen\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n  method are required\nexamples:\n- value: 0.05 ug N/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 12\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_n\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"min_q_value/","title":"Slot: min_q_value","text":"

smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool

URI: nmdc:min_q_value

"},{"location":"min_q_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"min_q_value/#properties","title":"Properties","text":""},{"location":"min_q_value/#see-also","title":"See Also","text":""},{"location":"min_q_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"min_q_value/#schema-source","title":"Schema Source","text":""},{"location":"min_q_value/#linkml-source","title":"LinkML Source","text":"
name: min_q_value\ndescription: smallest Q-Value associated with the peptide sequence as provided by\n  MSGFPlus tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- OBI:0001442\nrank: 1000\nalias: min_q_value\ndomain_of:\n- PeptideQuantification\nrange: float\n\n
"},{"location":"mineral_nutr_regm/","title":"Slot: mineral nutrient regimen (mineral_nutr_regm)","text":"

Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens

URI: MIXS:0000570

"},{"location":"mineral_nutr_regm/#inheritance","title":"Inheritance","text":""},{"location":"mineral_nutr_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mineral_nutr_regm/#properties","title":"Properties","text":""},{"location":"mineral_nutr_regm/#aliases","title":"Aliases","text":""},{"location":"mineral_nutr_regm/#examples","title":"Examples","text":"Value potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"mineral_nutr_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mineral_nutr_regm/#annotations","title":"Annotations","text":"property value expected_value mineral nutrient name;mineral nutrient amount;treatment interval and duration"},{"location":"mineral_nutr_regm/#schema-source","title":"Schema Source","text":""},{"location":"mineral_nutr_regm/#linkml-source","title":"LinkML Source","text":"
name: mineral_nutr_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: mineral nutrient name;mineral nutrient amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving the use of mineral supplements;\n  should include the name of mineral nutrient, amount administered, treatment regimen\n  including how many times the treatment was repeated, how long each treatment lasted,\n  and the start and end time of the entire treatment; can include multiple mineral\n  nutrient regimens\ntitle: mineral nutrient regimen\nexamples:\n- value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000570\nalias: mineral_nutr_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"misc_param/","title":"Slot: miscellaneous parameter (misc_param)","text":"

Any other measurement performed or parameter collected, that is not listed here

URI: MIXS:0000752

"},{"location":"misc_param/#inheritance","title":"Inheritance","text":""},{"location":"misc_param/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"misc_param/#properties","title":"Properties","text":""},{"location":"misc_param/#aliases","title":"Aliases","text":""},{"location":"misc_param/#examples","title":"Examples","text":"Value Bicarbonate ion concentration;2075 micromole per kilogram"},{"location":"misc_param/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"misc_param/#annotations","title":"Annotations","text":"property value expected_value parameter name;measurement value"},{"location":"misc_param/#schema-source","title":"Schema Source","text":""},{"location":"misc_param/#linkml-source","title":"LinkML Source","text":"
name: misc_param\nannotations:\n  expected_value:\n    tag: expected_value\n    value: parameter name;measurement value\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Any other measurement performed or parameter collected, that is not listed\n  here\ntitle: miscellaneous parameter\nexamples:\n- value: Bicarbonate ion concentration;2075 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- miscellaneous parameter\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000752\nalias: misc_param\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mod_date/","title":"Slot: mod_date","text":"

The last date on which the database information was modified.

URI: nmdc:mod_date

"},{"location":"mod_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no Biosample Biological source material which can be characterized by an experiment no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"mod_date/#properties","title":"Properties","text":""},{"location":"mod_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mod_date/#schema-source","title":"Schema Source","text":""},{"location":"mod_date/#linkml-source","title":"LinkML Source","text":"
name: mod_date\ndescription: The last date on which the database information was modified.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mod_date\ndomain_of:\n- Biosample\n- DataGeneration\nrange: string\n\n
"},{"location":"model/","title":"Slot: model","text":"

URI: nmdc:model

"},{"location":"model/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Instrument A material entity that is designed to perform a function in a scientific inve... no"},{"location":"model/#properties","title":"Properties","text":""},{"location":"model/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"model/#schema-source","title":"Schema Source","text":""},{"location":"model/#linkml-source","title":"LinkML Source","text":"
name: model\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: model\ndomain_of:\n- Instrument\nrange: InstrumentModelEnum\n\n
"},{"location":"modifier_substance/","title":"Slot: modifier_substance","text":"

The type of modification being done

URI: nmdc:modifier_substance

"},{"location":"modifier_substance/#properties","title":"Properties","text":""},{"location":"modifier_substance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"modifier_substance/#schema-source","title":"Schema Source","text":""},{"location":"modifier_substance/#linkml-source","title":"LinkML Source","text":"
name: modifier_substance\ndescription: The type of modification being done\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: modifier_substance\nrange: string\n\n
"},{"location":"n_alkanes/","title":"Slot: n-alkanes (n_alkanes)","text":"

Concentration of n-alkanes; can include multiple n-alkanes

URI: MIXS:0000503

"},{"location":"n_alkanes/#inheritance","title":"Inheritance","text":""},{"location":"n_alkanes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"n_alkanes/#properties","title":"Properties","text":""},{"location":"n_alkanes/#aliases","title":"Aliases","text":""},{"location":"n_alkanes/#examples","title":"Examples","text":"Value n-hexadecane;100 milligram per liter"},{"location":"n_alkanes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"n_alkanes/#annotations","title":"Annotations","text":"property value expected_value n-alkane name;measurement value"},{"location":"n_alkanes/#schema-source","title":"Schema Source","text":""},{"location":"n_alkanes/#linkml-source","title":"LinkML Source","text":"
name: n_alkanes\nannotations:\n  expected_value:\n    tag: expected_value\n    value: n-alkane name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of n-alkanes; can include multiple n-alkanes\ntitle: n-alkanes\nexamples:\n- value: n-hexadecane;100 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- n-alkanes\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000503\nalias: n_alkanes\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"name/","title":"Slot: name","text":"

A human readable label for an entity

URI: nmdc:name

"},{"location":"name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... no NamedThing a databased entity or concept/class no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no WorkflowExecution Represents an instance of an execution of a particular workflow no Biosample Biological source material which can be characterized by an experiment no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no Configuration A set of parameters that define the actions of a process and is shared among ... no PersonValue An attribute value representing a person yes MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no Site no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes MetabolomicsAnalysis no ProcessedSample no OntologyClass no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DataObject An object that primarily consists of symbols that represent information yes GeneProduct A molecule encoded by a gene that has an evolved function no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no Instrument A material entity that is designed to perform a function in a scientific inve... no MetatranscriptomeAssembly no ChemicalEntity An atom or molecule that can be represented with a chemical formula no FiltrationProcess The process of segregation of phases; e no MetagenomeSequencing Initial sequencing activity that precedes any analysis no EnvironmentalMaterialTerm no LibraryPreparation no Pooling physical combination of several instances of like material no MaterialEntity no CalibrationInformation A calibration object that is associated with a process no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no DataGeneration The methods and processes used to generate omics data from a biosample or org... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no OrthologyGroup A set of genes or gene products in which all members are orthologous no PlannedProcess no Protocol no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no Study A study summarizes the overall goal of a research initiative and outlines the... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no Manifest no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"name/#properties","title":"Properties","text":""},{"location":"name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"name/#schema-source","title":"Schema Source","text":""},{"location":"name/#linkml-source","title":"LinkML Source","text":"
name: name\ndescription: A human readable label for an entity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: name\ndomain_of:\n- PersonValue\n- NamedThing\n- Protocol\nrange: string\n\n
"},{"location":"ncbi_lineage/","title":"Slot: ncbi_lineage","text":"

Comma delimited ordered list of NCBI taxonomy names.

URI: nmdc:ncbi_lineage

"},{"location":"ncbi_lineage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"ncbi_lineage/#properties","title":"Properties","text":""},{"location":"ncbi_lineage/#comments","title":"Comments","text":""},{"location":"ncbi_lineage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ncbi_lineage/#schema-source","title":"Schema Source","text":""},{"location":"ncbi_lineage/#linkml-source","title":"LinkML Source","text":"
name: ncbi_lineage\ndescription: Comma delimited ordered list of NCBI taxonomy names.\ncomments:\n- Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_lineage\ndomain_of:\n- EukEval\nrange: string\n\n
"},{"location":"ncbi_lineage_tax_ids/","title":"Slot: ncbi_lineage_tax_ids","text":"

Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)

URI: nmdc:ncbi_lineage_tax_ids

"},{"location":"ncbi_lineage_tax_ids/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"ncbi_lineage_tax_ids/#properties","title":"Properties","text":""},{"location":"ncbi_lineage_tax_ids/#comments","title":"Comments","text":""},{"location":"ncbi_lineage_tax_ids/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ncbi_lineage_tax_ids/#schema-source","title":"Schema Source","text":""},{"location":"ncbi_lineage_tax_ids/#linkml-source","title":"LinkML Source","text":"
name: ncbi_lineage_tax_ids\ndescription: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)\ncomments:\n- Example 1-131567-2759-2611352-33682-191814-2603949\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_lineage_tax_ids\ndomain_of:\n- EukEval\nrange: string\npattern: ^\\d+(-\\d+)*$\n\n
"},{"location":"ncbi_project_name/","title":"Slot: ncbi_project_name","text":"

URI: nmdc:ncbi_project_name

"},{"location":"ncbi_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"ncbi_project_name/#properties","title":"Properties","text":""},{"location":"ncbi_project_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ncbi_project_name/#schema-source","title":"Schema Source","text":""},{"location":"ncbi_project_name/#linkml-source","title":"LinkML Source","text":"
name: ncbi_project_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_project_name\ndomain_of:\n- NucleotideSequencing\nrange: string\n\n
"},{"location":"ncbi_taxonomy_name/","title":"Slot: ncbi_taxonomy_name","text":"

URI: nmdc:ncbi_taxonomy_name

"},{"location":"ncbi_taxonomy_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ncbi_taxonomy_name/#properties","title":"Properties","text":""},{"location":"ncbi_taxonomy_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ncbi_taxonomy_name/#schema-source","title":"Schema Source","text":""},{"location":"ncbi_taxonomy_name/#linkml-source","title":"LinkML Source","text":"
name: ncbi_taxonomy_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_taxonomy_name\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"neon_biosample_identifiers/","title":"Slot: neon_biosample_identifiers","text":"

URI: nmdc:neon_biosample_identifiers

"},{"location":"neon_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"neon_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"neon_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"neon_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"neon_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"neon_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: neon_biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- neon_identifiers\nalias: neon_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"neon_identifiers/","title":"Slot: neon_identifiers","text":"

identifiers for entities according to NEON

URI: nmdc:neon_identifiers

"},{"location":"neon_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain neon_study_identifiers None Study neon_biosample_identifiers None Biosample"},{"location":"neon_identifiers/#properties","title":"Properties","text":""},{"location":"neon_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"neon_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"neon_identifiers/#linkml-source","title":"LinkML Source","text":"
name: neon_identifiers\ndescription: identifiers for entities according to NEON\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: neon_identifiers\nrange: string\n\n
"},{"location":"neon_study_identifiers/","title":"Slot: neon_study_identifiers","text":"

URI: nmdc:neon_study_identifiers

"},{"location":"neon_study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"neon_study_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"neon_study_identifiers/#properties","title":"Properties","text":""},{"location":"neon_study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"neon_study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"neon_study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: neon_study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- neon_identifiers\nalias: neon_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"nitrate/","title":"Slot: nitrate (nitrate)","text":"

Concentration of nitrate in the sample

URI: MIXS:0000425

"},{"location":"nitrate/#inheritance","title":"Inheritance","text":""},{"location":"nitrate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrate/#properties","title":"Properties","text":""},{"location":"nitrate/#aliases","title":"Aliases","text":""},{"location":"nitrate/#examples","title":"Examples","text":"Value 65 micromole per liter"},{"location":"nitrate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitrate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitrate/#schema-source","title":"Schema Source","text":""},{"location":"nitrate/#linkml-source","title":"LinkML Source","text":"
name: nitrate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrate in the sample\ntitle: nitrate\nexamples:\n- value: 65 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000425\nalias: nitrate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"nitrate_nitrogen/","title":"Slot: nitrate_nitrogen (nitrate_nitrogen)","text":"

Concentration of nitrate nitrogen in the sample

URI: nmdc:nitrate_nitrogen

"},{"location":"nitrate_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrate_nitrogen/#properties","title":"Properties","text":""},{"location":"nitrate_nitrogen/#aliases","title":"Aliases","text":""},{"location":"nitrate_nitrogen/#examples","title":"Examples","text":"Value 0.29 mg/kg"},{"location":"nitrate_nitrogen/#comments","title":"Comments","text":""},{"location":"nitrate_nitrogen/#see-also","title":"See Also","text":""},{"location":"nitrate_nitrogen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitrate_nitrogen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitrate_nitrogen/#schema-source","title":"Schema Source","text":""},{"location":"nitrate_nitrogen/#linkml-source","title":"LinkML Source","text":"
name: nitrate_nitrogen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrate nitrogen in the sample\ntitle: nitrate_nitrogen\ncomments:\n- often below some specified limit of detection\nexamples:\n- value: 0.29 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrate_nitrogen\n- NO3-N\nrank: 1000\nalias: nitrate_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"nitrite/","title":"Slot: nitrite (nitrite)","text":"

Concentration of nitrite in the sample

URI: MIXS:0000426

"},{"location":"nitrite/#inheritance","title":"Inheritance","text":""},{"location":"nitrite/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrite/#properties","title":"Properties","text":""},{"location":"nitrite/#aliases","title":"Aliases","text":""},{"location":"nitrite/#examples","title":"Examples","text":"Value 0.5 micromole per liter"},{"location":"nitrite/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitrite/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitrite/#schema-source","title":"Schema Source","text":""},{"location":"nitrite/#linkml-source","title":"LinkML Source","text":"
name: nitrite\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrite in the sample\ntitle: nitrite\nexamples:\n- value: 0.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000426\nalias: nitrite\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"nitrite_nitrogen/","title":"Slot: nitrite_nitrogen (nitrite_nitrogen)","text":"

Concentration of nitrite nitrogen in the sample

URI: nmdc:nitrite_nitrogen

"},{"location":"nitrite_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrite_nitrogen/#properties","title":"Properties","text":""},{"location":"nitrite_nitrogen/#aliases","title":"Aliases","text":""},{"location":"nitrite_nitrogen/#examples","title":"Examples","text":"Value 1.2 mg/kg"},{"location":"nitrite_nitrogen/#see-also","title":"See Also","text":""},{"location":"nitrite_nitrogen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitrite_nitrogen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitrite_nitrogen/#schema-source","title":"Schema Source","text":""},{"location":"nitrite_nitrogen/#linkml-source","title":"LinkML Source","text":"
name: nitrite_nitrogen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrite nitrogen in the sample\ntitle: nitrite_nitrogen\nexamples:\n- value: 1.2 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrite_nitrogen\n- NO2-N\nrank: 1000\nalias: nitrite_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"nitro/","title":"Slot: nitrogen (nitro)","text":"

Concentration of nitrogen (total)

URI: MIXS:0000504

"},{"location":"nitro/#inheritance","title":"Inheritance","text":""},{"location":"nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitro/#properties","title":"Properties","text":""},{"location":"nitro/#aliases","title":"Aliases","text":""},{"location":"nitro/#examples","title":"Examples","text":"Value 4.2 micromole per liter"},{"location":"nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitro/#schema-source","title":"Schema Source","text":""},{"location":"nitro/#linkml-source","title":"LinkML Source","text":"
name: nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrogen (total)\ntitle: nitrogen\nexamples:\n- value: 4.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000504\nalias: nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"non_microb_biomass/","title":"Slot: non-microbial biomass (non_microb_biomass)","text":"

Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;

URI: nmdc:non_microb_biomass

"},{"location":"non_microb_biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass/#properties","title":"Properties","text":""},{"location":"non_microb_biomass/#examples","title":"Examples","text":"Value insect 0.23 ug; plant 1g"},{"location":"non_microb_biomass/#see-also","title":"See Also","text":""},{"location":"non_microb_biomass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"non_microb_biomass/#schema-source","title":"Schema Source","text":""},{"location":"non_microb_biomass/#linkml-source","title":"LinkML Source","text":"
name: non_microb_biomass\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n  e.g.insect, plant, total. Can include multiple measurements separated by ;\ntitle: non-microbial biomass\nexamples:\n- value: insect 0.23 ug; plant 1g\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000174\n- MIXS:0000650\nrank: 8\nstring_serialization: '{text};{float} {unit}'\nalias: non_microb_biomass\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"non_microb_biomass_method/","title":"Slot: non-microbial biomass method (non_microb_biomass_method)","text":"

Reference or method used in determining biomass

URI: nmdc:non_microb_biomass_method

"},{"location":"non_microb_biomass_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass_method/#properties","title":"Properties","text":""},{"location":"non_microb_biomass_method/#examples","title":"Examples","text":"Value https://doi.org/10.1038/s41467-021-26181-3"},{"location":"non_microb_biomass_method/#comments","title":"Comments","text":""},{"location":"non_microb_biomass_method/#see-also","title":"See Also","text":""},{"location":"non_microb_biomass_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"non_microb_biomass_method/#schema-source","title":"Schema Source","text":""},{"location":"non_microb_biomass_method/#linkml-source","title":"LinkML Source","text":"
name: non_microb_biomass_method\ndescription: Reference or method used in determining biomass\ntitle: non-microbial biomass method\ncomments:\n- required if \"non-microbial biomass\" is provided\nexamples:\n- value: https://doi.org/10.1038/s41467-021-26181-3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 9\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: non_microb_biomass_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"non_min_nutr_regm/","title":"Slot: non-mineral nutrient regimen (non_min_nutr_regm)","text":"

Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens

URI: MIXS:0000571

"},{"location":"non_min_nutr_regm/#inheritance","title":"Inheritance","text":""},{"location":"non_min_nutr_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_min_nutr_regm/#properties","title":"Properties","text":""},{"location":"non_min_nutr_regm/#aliases","title":"Aliases","text":""},{"location":"non_min_nutr_regm/#examples","title":"Examples","text":"Value carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"non_min_nutr_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"non_min_nutr_regm/#annotations","title":"Annotations","text":"property value expected_value non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration"},{"location":"non_min_nutr_regm/#schema-source","title":"Schema Source","text":""},{"location":"non_min_nutr_regm/#linkml-source","title":"LinkML Source","text":"
name: non_min_nutr_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n      and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving the exposure of plant to non-mineral\n  nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n  nutrient, amount administered, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include multiple non-mineral nutrient regimens\ntitle: non-mineral nutrient regimen\nexamples:\n- value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- non-mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000571\nalias: non_min_nutr_regm\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\n
"},{"location":"notes/","title":"Slot: notes","text":"

URI: nmdc:notes

"},{"location":"notes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"notes/#properties","title":"Properties","text":""},{"location":"notes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"notes/#schema-source","title":"Schema Source","text":""},{"location":"notes/#linkml-source","title":"LinkML Source","text":"
name: notes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: notes\ndomain_of:\n- Study\nrange: string\n\n
"},{"location":"nucl_acid_amp/","title":"Slot: nucleic acid amplification (nucl_acid_amp)","text":"

A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids

URI: MIXS:0000038

"},{"location":"nucl_acid_amp/#inheritance","title":"Inheritance","text":""},{"location":"nucl_acid_amp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"nucl_acid_amp/#properties","title":"Properties","text":""},{"location":"nucl_acid_amp/#aliases","title":"Aliases","text":""},{"location":"nucl_acid_amp/#examples","title":"Examples","text":"Value https://phylogenomics.me/protocols/16s-pcr-protocol/"},{"location":"nucl_acid_amp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nucl_acid_amp/#annotations","title":"Annotations","text":"property value expected_value PMID, DOI or URL"},{"location":"nucl_acid_amp/#schema-source","title":"Schema Source","text":""},{"location":"nucl_acid_amp/#linkml-source","title":"LinkML Source","text":"
name: nucl_acid_amp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n  procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of\n  specific nucleic acids\ntitle: nucleic acid amplification\nexamples:\n- value: https://phylogenomics.me/protocols/16s-pcr-protocol/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid amplification\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000038\nalias: nucl_acid_amp\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"nucl_acid_ext/","title":"Slot: nucleic acid extraction (nucl_acid_ext)","text":"

A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample

URI: MIXS:0000037

"},{"location":"nucl_acid_ext/#inheritance","title":"Inheritance","text":""},{"location":"nucl_acid_ext/#properties","title":"Properties","text":""},{"location":"nucl_acid_ext/#aliases","title":"Aliases","text":""},{"location":"nucl_acid_ext/#examples","title":"Examples","text":"Value https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf"},{"location":"nucl_acid_ext/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nucl_acid_ext/#annotations","title":"Annotations","text":"property value expected_value PMID, DOI or URL"},{"location":"nucl_acid_ext/#schema-source","title":"Schema Source","text":""},{"location":"nucl_acid_ext/#linkml-source","title":"LinkML Source","text":"
name: nucl_acid_ext\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n  procedure (SOP), that describes the material separation to recover the nucleic acid\n  fraction from a sample\ntitle: nucleic acid extraction\nexamples:\n- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid extraction\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000037\nalias: nucl_acid_ext\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"nucleic_acid_sequence_source_field/","title":"Slot: nucleic_acid_sequence_source_field","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:nucleic_acid_sequence_source_field

"},{"location":"nucleic_acid_sequence_source_field/#inheritance","title":"Inheritance","text":""},{"location":"nucleic_acid_sequence_source_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nucleic_acid_sequence_source_field/#properties","title":"Properties","text":""},{"location":"nucleic_acid_sequence_source_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nucleic_acid_sequence_source_field/#schema-source","title":"Schema Source","text":""},{"location":"nucleic_acid_sequence_source_field/#linkml-source","title":"LinkML Source","text":"
name: nucleic acid sequence source field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: nucleic_acid_sequence_source_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"num_16s/","title":"Slot: num_16s","text":"

URI: nmdc:num_16s

"},{"location":"num_16s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_16s/#properties","title":"Properties","text":""},{"location":"num_16s/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_16s/#schema-source","title":"Schema Source","text":""},{"location":"num_16s/#linkml-source","title":"LinkML Source","text":"
name: num_16s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_16s\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"num_23s/","title":"Slot: num_23s","text":"

URI: nmdc:num_23s

"},{"location":"num_23s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_23s/#properties","title":"Properties","text":""},{"location":"num_23s/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_23s/#schema-source","title":"Schema Source","text":""},{"location":"num_23s/#linkml-source","title":"LinkML Source","text":"
name: num_23s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_23s\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"num_5s/","title":"Slot: num_5s","text":"

URI: nmdc:num_5s

"},{"location":"num_5s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_5s/#properties","title":"Properties","text":""},{"location":"num_5s/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_5s/#schema-source","title":"Schema Source","text":""},{"location":"num_5s/#linkml-source","title":"LinkML Source","text":"
name: num_5s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_5s\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"num_aligned_reads/","title":"Slot: num_aligned_reads","text":"

The sequence count number of input reads aligned to assembled contigs.

URI: nmdc:num_aligned_reads

"},{"location":"num_aligned_reads/#inheritance","title":"Inheritance","text":""},{"location":"num_aligned_reads/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"num_aligned_reads/#properties","title":"Properties","text":""},{"location":"num_aligned_reads/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_aligned_reads/#schema-source","title":"Schema Source","text":""},{"location":"num_aligned_reads/#linkml-source","title":"LinkML Source","text":"
name: num_aligned_reads\ndescription: The sequence count number of input reads aligned to assembled contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_aligned_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"num_input_reads/","title":"Slot: num_input_reads","text":"

The sequence count number of input reads for assembly.

URI: nmdc:num_input_reads

"},{"location":"num_input_reads/#inheritance","title":"Inheritance","text":""},{"location":"num_input_reads/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"num_input_reads/#properties","title":"Properties","text":""},{"location":"num_input_reads/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_input_reads/#schema-source","title":"Schema Source","text":""},{"location":"num_input_reads/#linkml-source","title":"LinkML Source","text":"
name: num_input_reads\ndescription: The sequence count number of input reads for assembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_input_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"num_t_rna/","title":"Slot: num_t_rna","text":"

URI: nmdc:num_t_rna

"},{"location":"num_t_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_t_rna/#properties","title":"Properties","text":""},{"location":"num_t_rna/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_t_rna/#schema-source","title":"Schema Source","text":""},{"location":"num_t_rna/#linkml-source","title":"LinkML Source","text":"
name: num_t_rna\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_t_rna\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"number_of_contig/","title":"Slot: number_of_contig","text":"

URI: nmdc:number_of_contig

"},{"location":"number_of_contig/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"number_of_contig/#properties","title":"Properties","text":""},{"location":"number_of_contig/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"number_of_contig/#schema-source","title":"Schema Source","text":""},{"location":"number_of_contig/#linkml-source","title":"LinkML Source","text":"
name: number_of_contig\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: number_of_contig\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"number_pets/","title":"Slot: number of pets (number_pets)","text":"

The number of pets residing in the sampled space

URI: MIXS:0000231

"},{"location":"number_pets/#inheritance","title":"Inheritance","text":""},{"location":"number_pets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"number_pets/#properties","title":"Properties","text":""},{"location":"number_pets/#aliases","title":"Aliases","text":""},{"location":"number_pets/#examples","title":"Examples","text":"Value"},{"location":"number_pets/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"number_pets/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"number_pets/#schema-source","title":"Schema Source","text":""},{"location":"number_pets/#linkml-source","title":"LinkML Source","text":"
name: number_pets\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of pets residing in the sampled space\ntitle: number of pets\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of pets\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000231\nalias: number_pets\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"number_plants/","title":"Slot: number of houseplants (number_plants)","text":"

The number of plant(s) in the sampling space

URI: MIXS:0000230

"},{"location":"number_plants/#inheritance","title":"Inheritance","text":""},{"location":"number_plants/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"number_plants/#properties","title":"Properties","text":""},{"location":"number_plants/#aliases","title":"Aliases","text":""},{"location":"number_plants/#examples","title":"Examples","text":"Value"},{"location":"number_plants/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"number_plants/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"number_plants/#schema-source","title":"Schema Source","text":""},{"location":"number_plants/#linkml-source","title":"LinkML Source","text":"
name: number_plants\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of plant(s) in the sampling space\ntitle: number of houseplants\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of houseplants\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000230\nalias: number_plants\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"number_resident/","title":"Slot: number of residents (number_resident)","text":"

The number of individuals currently occupying in the sampling location

URI: MIXS:0000232

"},{"location":"number_resident/#inheritance","title":"Inheritance","text":""},{"location":"number_resident/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"number_resident/#properties","title":"Properties","text":""},{"location":"number_resident/#aliases","title":"Aliases","text":""},{"location":"number_resident/#examples","title":"Examples","text":"Value"},{"location":"number_resident/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"number_resident/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"number_resident/#schema-source","title":"Schema Source","text":""},{"location":"number_resident/#linkml-source","title":"LinkML Source","text":"
name: number_resident\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of individuals currently occupying in the sampling location\ntitle: number of residents\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of residents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000232\nalias: number_resident\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"object_set/","title":"Slot: object_set","text":"

Applies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types

URI: nmdc:object_set

"},{"location":"object_set/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain chemical_entity_set This property links a database object to the set of chemical entities within ... ChemicalEntity Database biosample_set This property links a database object to the set of samples within it Biosample Database study_set This property links a database object to the set of studies within it Study Database field_research_site_set FieldResearchSite Database collecting_biosamples_from_site_set CollectingBiosamplesFromSite Database data_object_set This property links a database object to the set of data objects within it DataObject Database genome_feature_set This property links a database object to the set of all features GenomeFeature Database functional_annotation_set This property links a database object to the set of all functional annotation... FunctionalAnnotation Database workflow_execution_set This property links a database object to the set of workflow executions WorkflowExecution Database data_generation_set This property links a database object to the set of data generations within i... DataGeneration Database processed_sample_set This property links a database object to the set of processed samples within ... ProcessedSample Database instrument_set This property links a database object to the set of instruments within it Instrument Database calibration_set This property links a database object to the set of calibrations within it CalibrationInformation Database configuration_set This property links a database object to the set of configurations within it Configuration Database manifest_set This property links a database object to the set of manifests within it Manifest Database protocol_execution_set This property links a database object to the set of protocol executions withi... ProtocolExecution Database storage_process_set This property links a database object to the set of storage processes within ... StorageProcess Database material_processing_set This property links a database object to the set of material processing withi... MaterialProcessing Database"},{"location":"object_set/#properties","title":"Properties","text":""},{"location":"object_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"object_set/#schema-source","title":"Schema Source","text":""},{"location":"object_set/#linkml-source","title":"LinkML Source","text":"
name: object_set\ndescription: Applies to a property that links a database object to a set of objects.\n  This is necessary in a json document to provide context for a list, and to allow\n  for a single json object that combines multiple object types\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: object_set\nrange: string\nmultivalued: true\ninlined_as_list: true\n\n
"},{"location":"objective/","title":"Slot: objective","text":"

The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.

URI: nmdc:objective

"},{"location":"objective/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"objective/#properties","title":"Properties","text":""},{"location":"objective/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"objective/#schema-source","title":"Schema Source","text":""},{"location":"objective/#linkml-source","title":"LinkML Source","text":"
name: objective\ndescription: The scientific objectives associated with the entity. It SHOULD correspond\n  to scientific norms for objectives field in a structured abstract.\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- SIO:000337\nrank: 1000\nalias: objective\ndomain_of:\n- Study\nrange: string\n\n
"},{"location":"occup_density_samp/","title":"Slot: occupant density at sampling (occup_density_samp)","text":"

Average number of occupants at time of sampling per square footage

URI: MIXS:0000217

"},{"location":"occup_density_samp/#inheritance","title":"Inheritance","text":""},{"location":"occup_density_samp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"occup_density_samp/#properties","title":"Properties","text":""},{"location":"occup_density_samp/#aliases","title":"Aliases","text":""},{"location":"occup_density_samp/#examples","title":"Examples","text":"Value"},{"location":"occup_density_samp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"occup_density_samp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"occup_density_samp/#schema-source","title":"Schema Source","text":""},{"location":"occup_density_samp/#linkml-source","title":"LinkML Source","text":"
name: occup_density_samp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Average number of occupants at time of sampling per square footage\ntitle: occupant density at sampling\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupant density at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000217\nalias: occup_density_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"occup_document/","title":"Slot: occupancy documentation (occup_document)","text":"

The type of documentation of occupancy

URI: MIXS:0000816

"},{"location":"occup_document/#inheritance","title":"Inheritance","text":""},{"location":"occup_document/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"occup_document/#properties","title":"Properties","text":""},{"location":"occup_document/#aliases","title":"Aliases","text":""},{"location":"occup_document/#examples","title":"Examples","text":"Value estimate"},{"location":"occup_document/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"occup_document/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"occup_document/#schema-source","title":"Schema Source","text":""},{"location":"occup_document/#linkml-source","title":"LinkML Source","text":"
name: occup_document\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of documentation of occupancy\ntitle: occupancy documentation\nexamples:\n- value: estimate\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy documentation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000816\nalias: occup_document\ndomain_of:\n- Biosample\nrange: occup_document_enum\nmultivalued: false\n\n
"},{"location":"occup_samp/","title":"Slot: occupancy at sampling (occup_samp)","text":"

Number of occupants present at time of sample within the given space

URI: MIXS:0000772

"},{"location":"occup_samp/#inheritance","title":"Inheritance","text":""},{"location":"occup_samp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"occup_samp/#properties","title":"Properties","text":""},{"location":"occup_samp/#aliases","title":"Aliases","text":""},{"location":"occup_samp/#examples","title":"Examples","text":"Value 10"},{"location":"occup_samp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"occup_samp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"occup_samp/#schema-source","title":"Schema Source","text":""},{"location":"occup_samp/#linkml-source","title":"LinkML Source","text":"
name: occup_samp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Number of occupants present at time of sample within the given space\ntitle: occupancy at sampling\nexamples:\n- value: '10'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000772\nalias: occup_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"omics_processing_identifiers/","title":"Slot: omics_processing_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:omics_processing_identifiers

"},{"location":"omics_processing_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"omics_processing_identifiers/#properties","title":"Properties","text":""},{"location":"omics_processing_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"omics_processing_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"omics_processing_identifiers/#linkml-source","title":"LinkML Source","text":"
name: omics_processing_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: omics_processing_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"omics_type/","title":"Slot: omics_type (DEPRECATED)

The type of omics data

URI: nmdc:omics_type

","text":""},{"location":"omics_type/#properties","title":"Properties","text":""},{"location":"omics_type/#examples","title":"Examples","text":"Value metatranscriptome metagenome"},{"location":"omics_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"omics_type/#schema-source","title":"Schema Source","text":""},{"location":"omics_type/#linkml-source","title":"LinkML Source","text":"
name: omics_type\ndescription: The type of omics data\ndeprecated: 'True'\nexamples:\n- value: metatranscriptome\n- value: metagenome\nfrom_schema: https://w3id.org/nmdc/nmdc\ndeprecated_element_has_exact_replacement: analyte_category\nrank: 1000\nalias: omics_type\nrange: string\n\n
"},{"location":"orcid/","title":"Slot: orcid","text":"

The ORCID of a person.

URI: nmdc:orcid

"},{"location":"orcid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"orcid/#properties","title":"Properties","text":""},{"location":"orcid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"orcid/#schema-source","title":"Schema Source","text":""},{"location":"orcid/#linkml-source","title":"LinkML Source","text":"
name: orcid\ndescription: The ORCID of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: orcid\ndomain_of:\n- PersonValue\nrange: string\n\n
"},{"location":"ordered_mobile_phases/","title":"Slot: ordered_mobile_phases","text":"

The solution(s) that moves through a chromatography column.

URI: nmdc:ordered_mobile_phases

"},{"location":"ordered_mobile_phases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no"},{"location":"ordered_mobile_phases/#properties","title":"Properties","text":""},{"location":"ordered_mobile_phases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ordered_mobile_phases/#schema-source","title":"Schema Source","text":""},{"location":"ordered_mobile_phases/#linkml-source","title":"LinkML Source","text":"
name: ordered_mobile_phases\ndescription: The solution(s) that moves through a chromatography column.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: ordered_mobile_phases\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: MobilePhaseSegment\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"org_carb/","title":"Slot: organic carbon (org_carb)","text":"

Concentration of organic carbon

URI: MIXS:0000508

"},{"location":"org_carb/#inheritance","title":"Inheritance","text":""},{"location":"org_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_carb/#properties","title":"Properties","text":""},{"location":"org_carb/#aliases","title":"Aliases","text":""},{"location":"org_carb/#examples","title":"Examples","text":"Value 1.5 microgram per liter"},{"location":"org_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"org_carb/#schema-source","title":"Schema Source","text":""},{"location":"org_carb/#linkml-source","title":"LinkML Source","text":"
name: org_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of organic carbon\ntitle: organic carbon\nexamples:\n- value: 1.5 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000508\nalias: org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"org_count_qpcr_info/","title":"Slot: organism count qPCR information (org_count_qpcr_info)","text":"

If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)

URI: MIXS:0000099

"},{"location":"org_count_qpcr_info/#inheritance","title":"Inheritance","text":""},{"location":"org_count_qpcr_info/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_count_qpcr_info/#properties","title":"Properties","text":""},{"location":"org_count_qpcr_info/#aliases","title":"Aliases","text":""},{"location":"org_count_qpcr_info/#examples","title":"Examples","text":"Value"},{"location":"org_count_qpcr_info/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_count_qpcr_info/#annotations","title":"Annotations","text":"property value expected_value gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles"},{"location":"org_count_qpcr_info/#schema-source","title":"Schema Source","text":""},{"location":"org_count_qpcr_info/#linkml-source","title":"LinkML Source","text":"
name: org_count_qpcr_info\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n      denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n      elongation:degrees_minutes; total cycles\n  preferred_unit:\n    tag: preferred_unit\n    value: number of cells per gram (or ml or cm^2)\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'If qpcr was used for the cell count, the target gene name, the primer\n  sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n  FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n  annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n  30 cycles)'\ntitle: organism count qPCR information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count qPCR information\nrank: 1000\nis_a: core field\nstring_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n  elongation:degrees_minutes; total cycles'\nslot_uri: MIXS:0000099\nalias: org_count_qpcr_info\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"org_matter/","title":"Slot: organic matter (org_matter)","text":"

Concentration of organic matter

URI: MIXS:0000204

"},{"location":"org_matter/#inheritance","title":"Inheritance","text":""},{"location":"org_matter/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_matter/#properties","title":"Properties","text":""},{"location":"org_matter/#aliases","title":"Aliases","text":""},{"location":"org_matter/#examples","title":"Examples","text":"Value 1.75 milligram per cubic meter"},{"location":"org_matter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_matter/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"org_matter/#schema-source","title":"Schema Source","text":""},{"location":"org_matter/#linkml-source","title":"LinkML Source","text":"
name: org_matter\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of organic matter\ntitle: organic matter\nexamples:\n- value: 1.75 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000204\nalias: org_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"org_nitro/","title":"Slot: organic nitrogen (org_nitro)","text":"

Concentration of organic nitrogen

URI: MIXS:0000205

"},{"location":"org_nitro/#inheritance","title":"Inheritance","text":""},{"location":"org_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_nitro/#properties","title":"Properties","text":""},{"location":"org_nitro/#aliases","title":"Aliases","text":""},{"location":"org_nitro/#examples","title":"Examples","text":"Value 4 micromole per liter"},{"location":"org_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"org_nitro/#schema-source","title":"Schema Source","text":""},{"location":"org_nitro/#linkml-source","title":"LinkML Source","text":"
name: org_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of organic nitrogen\ntitle: organic nitrogen\nexamples:\n- value: 4 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000205\nalias: org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"org_nitro_method/","title":"Slot: organic nitrogen method (org_nitro_method)","text":"

Method used for obtaining organic nitrogen

URI: nmdc:org_nitro_method

"},{"location":"org_nitro_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_nitro_method/#properties","title":"Properties","text":""},{"location":"org_nitro_method/#examples","title":"Examples","text":"Value https://doi.org/10.1016/0038-0717(85)90144-0"},{"location":"org_nitro_method/#comments","title":"Comments","text":""},{"location":"org_nitro_method/#see-also","title":"See Also","text":""},{"location":"org_nitro_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_nitro_method/#schema-source","title":"Schema Source","text":""},{"location":"org_nitro_method/#linkml-source","title":"LinkML Source","text":"
name: org_nitro_method\ndescription: Method used for obtaining organic nitrogen\ntitle: organic nitrogen method\ncomments:\n- required if \"org_nitro\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(85)90144-0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000338\n- MIXS:0000205\nrank: 14\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: org_nitro_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"org_particles/","title":"Slot: organic particles (org_particles)","text":"

Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.

URI: MIXS:0000665

"},{"location":"org_particles/#inheritance","title":"Inheritance","text":""},{"location":"org_particles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_particles/#properties","title":"Properties","text":""},{"location":"org_particles/#aliases","title":"Aliases","text":""},{"location":"org_particles/#examples","title":"Examples","text":"Value"},{"location":"org_particles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_particles/#annotations","title":"Annotations","text":"property value expected_value particle name;measurement value"},{"location":"org_particles/#schema-source","title":"Schema Source","text":""},{"location":"org_particles/#linkml-source","title":"LinkML Source","text":"
name: org_particles\nannotations:\n  expected_value:\n    tag: expected_value\n    value: particle name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of particles such as faeces, hairs, food, vomit, paper\n  fibers, plant material, humus, etc.\ntitle: organic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000665\nalias: org_particles\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"organism_count/","title":"Slot: organism count (organism_count)","text":"

Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)

URI: MIXS:0000103

"},{"location":"organism_count/#inheritance","title":"Inheritance","text":""},{"location":"organism_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"organism_count/#properties","title":"Properties","text":""},{"location":"organism_count/#aliases","title":"Aliases","text":""},{"location":"organism_count/#examples","title":"Examples","text":"Value total prokaryotes;3.5e7 cells per milliliter;qPCR"},{"location":"organism_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"organism_count/#annotations","title":"Annotations","text":"property value expected_value organism name;measurement value;enumeration"},{"location":"organism_count/#schema-source","title":"Schema Source","text":""},{"location":"organism_count/#linkml-source","title":"LinkML Source","text":"
name: organism_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: organism name;measurement value;enumeration\n  preferred_unit:\n    tag: preferred_unit\n    value: number of cells per cubic meter, number of cells per milliliter, number\n      of cells per cubic centimeter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: 'Total cell count of any organism (or group of organisms) per gram, volume\n  or area of sample, should include name of organism followed by count. The method\n  that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided.\n  (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\ntitle: organism count\nexamples:\n- value: total prokaryotes;3.5e7 cells per milliliter;qPCR\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000103\nalias: organism_count\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"other_treatment/","title":"Slot: other treatments (other_treatment)","text":"

Other treatments applied to your samples that are not applicable to the provided fields

URI: nmdc:other_treatment

"},{"location":"other_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"other_treatment/#properties","title":"Properties","text":""},{"location":"other_treatment/#comments","title":"Comments","text":""},{"location":"other_treatment/#see-also","title":"See Also","text":""},{"location":"other_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"other_treatment/#schema-source","title":"Schema Source","text":""},{"location":"other_treatment/#linkml-source","title":"LinkML Source","text":"
name: other_treatment\ndescription: Other treatments applied to your samples that are not applicable to the\n  provided fields\ntitle: other treatments\nnotes:\n- Values entered here will be used to determine potential new slots.\ncomments:\n- This is an open text field to provide any treatments that cannot be captured in\n  the provided slots.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000300\nrank: 15\nstring_serialization: '{text}'\nalias: other_treatment\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"output_base_count/","title":"Slot: output_base_count","text":"

After QC analysis nucleotide base count number.

URI: nmdc:output_base_count

"},{"location":"output_base_count/#inheritance","title":"Inheritance","text":""},{"location":"output_base_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_base_count/#properties","title":"Properties","text":""},{"location":"output_base_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"output_base_count/#schema-source","title":"Schema Source","text":""},{"location":"output_base_count/#linkml-source","title":"LinkML Source","text":"
name: output_base_count\ndescription: After QC analysis nucleotide base count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_base_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"output_read_bases/","title":"Slot: output_read_bases","text":"

TODO

URI: nmdc:output_read_bases

"},{"location":"output_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_read_bases/#properties","title":"Properties","text":""},{"location":"output_read_bases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"output_read_bases/#schema-source","title":"Schema Source","text":""},{"location":"output_read_bases/#linkml-source","title":"LinkML Source","text":"
name: output_read_bases\ndescription: TODO\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: output_read_bases\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"output_read_count/","title":"Slot: output_read_count","text":"

After QC analysis sequence count number.

URI: nmdc:output_read_count

"},{"location":"output_read_count/#inheritance","title":"Inheritance","text":""},{"location":"output_read_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_read_count/#properties","title":"Properties","text":""},{"location":"output_read_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"output_read_count/#schema-source","title":"Schema Source","text":""},{"location":"output_read_count/#linkml-source","title":"LinkML Source","text":"
name: output_read_count\ndescription: After QC analysis sequence count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_read_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"owc_tvdss/","title":"Slot: oil water contact depth (owc_tvdss)","text":"

Depth of the original oil water contact (OWC) zone (average) (m TVDSS)

URI: MIXS:0000405

"},{"location":"owc_tvdss/#inheritance","title":"Inheritance","text":""},{"location":"owc_tvdss/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"owc_tvdss/#properties","title":"Properties","text":""},{"location":"owc_tvdss/#aliases","title":"Aliases","text":""},{"location":"owc_tvdss/#examples","title":"Examples","text":"Value"},{"location":"owc_tvdss/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"owc_tvdss/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"owc_tvdss/#schema-source","title":"Schema Source","text":""},{"location":"owc_tvdss/#linkml-source","title":"LinkML Source","text":"
name: owc_tvdss\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\ntitle: oil water contact depth\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oil water contact depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000405\nalias: owc_tvdss\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"oxy_stat_samp/","title":"Slot: oxygenation status of sample (oxy_stat_samp)","text":"

Oxygenation status of sample

URI: MIXS:0000753

"},{"location":"oxy_stat_samp/#inheritance","title":"Inheritance","text":""},{"location":"oxy_stat_samp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"oxy_stat_samp/#properties","title":"Properties","text":""},{"location":"oxy_stat_samp/#aliases","title":"Aliases","text":""},{"location":"oxy_stat_samp/#examples","title":"Examples","text":"Value aerobic"},{"location":"oxy_stat_samp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"oxy_stat_samp/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"oxy_stat_samp/#schema-source","title":"Schema Source","text":""},{"location":"oxy_stat_samp/#linkml-source","title":"LinkML Source","text":"
name: oxy_stat_samp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Oxygenation status of sample\ntitle: oxygenation status of sample\nexamples:\n- value: aerobic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygenation status of sample\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000753\nalias: oxy_stat_samp\ndomain_of:\n- Biosample\nrange: oxy_stat_samp_enum\nmultivalued: false\n\n
"},{"location":"oxygen/","title":"Slot: oxygen (oxygen)","text":"

Oxygen (gas) amount or concentration at the time of sampling

URI: MIXS:0000104

"},{"location":"oxygen/#inheritance","title":"Inheritance","text":""},{"location":"oxygen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"oxygen/#properties","title":"Properties","text":""},{"location":"oxygen/#aliases","title":"Aliases","text":""},{"location":"oxygen/#examples","title":"Examples","text":"Value 600 parts per million"},{"location":"oxygen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"oxygen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"oxygen/#schema-source","title":"Schema Source","text":""},{"location":"oxygen/#linkml-source","title":"LinkML Source","text":"
name: oxygen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Oxygen (gas) amount or concentration at the time of sampling\ntitle: oxygen\nexamples:\n- value: 600 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000104\nalias: oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"part_of/","title":"Slot: part_of","text":"

Links a resource to another resource that either logically or physically includes it.

URI: dcterms:isPartOf

"},{"location":"part_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"part_of/#properties","title":"Properties","text":""},{"location":"part_of/#aliases","title":"Aliases","text":""},{"location":"part_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"part_of/#schema-source","title":"Schema Source","text":""},{"location":"part_of/#linkml-source","title":"LinkML Source","text":"
name: part_of\ndescription: Links a resource to another resource that either logically or physically\n  includes it.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- is part of\nrank: 1000\nslot_uri: dcterms:isPartOf\nalias: part_of\ndomain_of:\n- FieldResearchSite\n- Study\nrange: NamedThing\nmultivalued: true\n\n
"},{"location":"part_org_carb/","title":"Slot: particulate organic carbon (part_org_carb)","text":"

Concentration of particulate organic carbon

URI: MIXS:0000515

"},{"location":"part_org_carb/#inheritance","title":"Inheritance","text":""},{"location":"part_org_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"part_org_carb/#properties","title":"Properties","text":""},{"location":"part_org_carb/#aliases","title":"Aliases","text":""},{"location":"part_org_carb/#examples","title":"Examples","text":"Value 1.92 micromole per liter"},{"location":"part_org_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"part_org_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"part_org_carb/#schema-source","title":"Schema Source","text":""},{"location":"part_org_carb/#linkml-source","title":"LinkML Source","text":"
name: part_org_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of particulate organic carbon\ntitle: particulate organic carbon\nexamples:\n- value: 1.92 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000515\nalias: part_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"part_org_nitro/","title":"Slot: particulate organic nitrogen (part_org_nitro)","text":"

Concentration of particulate organic nitrogen

URI: MIXS:0000719

"},{"location":"part_org_nitro/#inheritance","title":"Inheritance","text":""},{"location":"part_org_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"part_org_nitro/#properties","title":"Properties","text":""},{"location":"part_org_nitro/#aliases","title":"Aliases","text":""},{"location":"part_org_nitro/#examples","title":"Examples","text":"Value 0.3 micromole per liter"},{"location":"part_org_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"part_org_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"part_org_nitro/#schema-source","title":"Schema Source","text":""},{"location":"part_org_nitro/#linkml-source","title":"LinkML Source","text":"
name: part_org_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of particulate organic nitrogen\ntitle: particulate organic nitrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000719\nalias: part_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"particle_class/","title":"Slot: particle classification (particle_class)","text":"

Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values

URI: MIXS:0000206

"},{"location":"particle_class/#inheritance","title":"Inheritance","text":""},{"location":"particle_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"particle_class/#properties","title":"Properties","text":""},{"location":"particle_class/#aliases","title":"Aliases","text":""},{"location":"particle_class/#examples","title":"Examples","text":"Value"},{"location":"particle_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"particle_class/#annotations","title":"Annotations","text":"property value expected_value particle name;measurement value"},{"location":"particle_class/#schema-source","title":"Schema Source","text":""},{"location":"particle_class/#linkml-source","title":"LinkML Source","text":"
name: particle_class\nannotations:\n  expected_value:\n    tag: expected_value\n    value: particle name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micrometer\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Particles are classified, based on their size, into six general categories:clay,\n  silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded\n  by the name of the particle type; can include multiple values\ntitle: particle classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particle classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000206\nalias: particle_class\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"pcr_cond/","title":"Slot: pcr conditions (pcr_cond)","text":"

Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'

URI: MIXS:0000049

"},{"location":"pcr_cond/#inheritance","title":"Inheritance","text":""},{"location":"pcr_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation yes"},{"location":"pcr_cond/#properties","title":"Properties","text":""},{"location":"pcr_cond/#aliases","title":"Aliases","text":""},{"location":"pcr_cond/#examples","title":"Examples","text":"Value initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35"},{"location":"pcr_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pcr_cond/#annotations","title":"Annotations","text":"property value expected_value initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles"},{"location":"pcr_cond/#schema-source","title":"Schema Source","text":""},{"location":"pcr_cond/#linkml-source","title":"LinkML Source","text":"
name: pcr_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n      elongation:degrees_minutes;total cycles\ndescription: Description of reaction conditions and components of PCR in the form\n  of 'initial denaturation:94degC_1.5min; annealing=...'\ntitle: pcr conditions\nexamples:\n- value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr conditions\nrank: 1000\nis_a: sequencing field\nstring_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n  elongation:degrees_minutes;total cycles\nslot_uri: MIXS:0000049\nalias: pcr_cond\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"pcr_cycles/","title":"Slot: pcr_cycles","text":"

URI: nmdc:pcr_cycles

"},{"location":"pcr_cycles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"pcr_cycles/#properties","title":"Properties","text":""},{"location":"pcr_cycles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pcr_cycles/#schema-source","title":"Schema Source","text":""},{"location":"pcr_cycles/#linkml-source","title":"LinkML Source","text":"
name: pcr_cycles\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0002475\nrank: 1000\nalias: pcr_cycles\ndomain_of:\n- LibraryPreparation\nrange: integer\n\n
"},{"location":"pcr_primers/","title":"Slot: pcr primers (pcr_primers)","text":"

PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters

URI: MIXS:0000046

"},{"location":"pcr_primers/#inheritance","title":"Inheritance","text":""},{"location":"pcr_primers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"pcr_primers/#properties","title":"Properties","text":""},{"location":"pcr_primers/#aliases","title":"Aliases","text":""},{"location":"pcr_primers/#examples","title":"Examples","text":"Value FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT"},{"location":"pcr_primers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pcr_primers/#annotations","title":"Annotations","text":"property value expected_value FWD: forward primer sequence;REV:reverse primer sequence"},{"location":"pcr_primers/#schema-source","title":"Schema Source","text":""},{"location":"pcr_primers/#linkml-source","title":"LinkML Source","text":"
name: pcr_primers\nannotations:\n  expected_value:\n    tag: expected_value\n    value: 'FWD: forward primer sequence;REV:reverse primer sequence'\ndescription: PCR primers that were used to amplify the sequence of the targeted gene,\n  locus or subfragment. This field should contain all the primers used for a single\n  PCR reaction if multiple forward or reverse primers are present in a single PCR\n  reaction. The primer sequence should be reported in uppercase letters\ntitle: pcr primers\nexamples:\n- value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr primers\nrank: 1000\nis_a: sequencing field\nstring_serialization: FWD:{dna};REV:{dna}\nslot_uri: MIXS:0000046\nalias: pcr_primers\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"peptide_sequence/","title":"Slot: peptide_sequence","text":"

URI: nmdc:peptide_sequence

"},{"location":"peptide_sequence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sequence/#properties","title":"Properties","text":""},{"location":"peptide_sequence/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"peptide_sequence/#schema-source","title":"Schema Source","text":""},{"location":"peptide_sequence/#linkml-source","title":"LinkML Source","text":"
name: peptide_sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence\ndomain_of:\n- PeptideQuantification\nrange: string\n\n
"},{"location":"peptide_sequence_count/","title":"Slot: peptide_sequence_count","text":"

count of peptide sequences grouped to the best_protein

URI: nmdc:peptide_sequence_count

"},{"location":"peptide_sequence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"peptide_sequence_count/#properties","title":"Properties","text":""},{"location":"peptide_sequence_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"peptide_sequence_count/#schema-source","title":"Schema Source","text":""},{"location":"peptide_sequence_count/#linkml-source","title":"LinkML Source","text":"
name: peptide_sequence_count\ndescription: count of peptide sequences grouped to the best_protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\n
"},{"location":"peptide_spectral_count/","title":"Slot: peptide_spectral_count","text":"

sum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file

URI: nmdc:peptide_spectral_count

"},{"location":"peptide_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_spectral_count/#properties","title":"Properties","text":""},{"location":"peptide_spectral_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"peptide_spectral_count/#schema-source","title":"Schema Source","text":""},{"location":"peptide_spectral_count/#linkml-source","title":"LinkML Source","text":"
name: peptide_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the peptide sequence\n  within a given LC-MS/MS data file\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_spectral_count\ndomain_of:\n- PeptideQuantification\nrange: integer\n\n
"},{"location":"peptide_sum_masic_abundance/","title":"Slot: peptide_sum_masic_abundance","text":"

combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool

URI: nmdc:peptide_sum_masic_abundance

"},{"location":"peptide_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sum_masic_abundance/#properties","title":"Properties","text":""},{"location":"peptide_sum_masic_abundance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"peptide_sum_masic_abundance/#schema-source","title":"Schema Source","text":""},{"location":"peptide_sum_masic_abundance/#linkml-source","title":"LinkML Source","text":"
name: peptide_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n  with the peptide sequence from a given LC-MS/MS data file using the MASIC tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sum_masic_abundance\ndomain_of:\n- PeptideQuantification\nrange: integer\n\n
"},{"location":"permeability/","title":"Slot: permeability (permeability)","text":"

Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))

URI: MIXS:0000404

"},{"location":"permeability/#inheritance","title":"Inheritance","text":""},{"location":"permeability/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"permeability/#properties","title":"Properties","text":""},{"location":"permeability/#aliases","title":"Aliases","text":""},{"location":"permeability/#examples","title":"Examples","text":"Value"},{"location":"permeability/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"permeability/#annotations","title":"Annotations","text":"property value expected_value measurement value range"},{"location":"permeability/#schema-source","title":"Schema Source","text":""},{"location":"permeability/#linkml-source","title":"LinkML Source","text":"
name: permeability\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: mD\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Measure of the ability of a hydrocarbon resource to allow fluids to\n  pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\ntitle: permeability\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- permeability\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} - {integer} {unit}'\nslot_uri: MIXS:0000404\nalias: permeability\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"perturbation/","title":"Slot: perturbation (perturbation)","text":"

Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types

URI: MIXS:0000754

"},{"location":"perturbation/#inheritance","title":"Inheritance","text":""},{"location":"perturbation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"perturbation/#properties","title":"Properties","text":""},{"location":"perturbation/#aliases","title":"Aliases","text":""},{"location":"perturbation/#examples","title":"Examples","text":"Value antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M"},{"location":"perturbation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"perturbation/#annotations","title":"Annotations","text":"property value expected_value perturbation type name;perturbation interval and duration"},{"location":"perturbation/#schema-source","title":"Schema Source","text":""},{"location":"perturbation/#linkml-source","title":"LinkML Source","text":"
name: perturbation\nannotations:\n  expected_value:\n    tag: expected_value\n    value: perturbation type name;perturbation interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Type of perturbation, e.g. chemical administration, physical disturbance,\n  etc., coupled with perturbation regimen including how many times the perturbation\n  was repeated, how long each perturbation lasted, and the start and end time of the\n  entire perturbation period; can include multiple perturbation types\ntitle: perturbation\nexamples:\n- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- perturbation\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000754\nalias: perturbation\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"pesticide_regm/","title":"Slot: pesticide regimen (pesticide_regm)","text":"

Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens

URI: MIXS:0000573

"},{"location":"pesticide_regm/#inheritance","title":"Inheritance","text":""},{"location":"pesticide_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pesticide_regm/#properties","title":"Properties","text":""},{"location":"pesticide_regm/#aliases","title":"Aliases","text":""},{"location":"pesticide_regm/#examples","title":"Examples","text":"Value pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"pesticide_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pesticide_regm/#annotations","title":"Annotations","text":"property value expected_value pesticide name;pesticide amount;treatment interval and duration"},{"location":"pesticide_regm/#schema-source","title":"Schema Source","text":""},{"location":"pesticide_regm/#linkml-source","title":"LinkML Source","text":"
name: pesticide_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: pesticide name;pesticide amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of insecticides; should include\n  the name of pesticide, amount administered, treatment regimen including how many\n  times the treatment was repeated, how long each treatment lasted, and the start\n  and end time of the entire treatment; can include multiple pesticide regimens\ntitle: pesticide regimen\nexamples:\n- value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pesticide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000573\nalias: pesticide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"petroleum_hydrocarb/","title":"Slot: petroleum hydrocarbon (petroleum_hydrocarb)","text":"

Concentration of petroleum hydrocarbon

URI: MIXS:0000516

"},{"location":"petroleum_hydrocarb/#inheritance","title":"Inheritance","text":""},{"location":"petroleum_hydrocarb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"petroleum_hydrocarb/#properties","title":"Properties","text":""},{"location":"petroleum_hydrocarb/#aliases","title":"Aliases","text":""},{"location":"petroleum_hydrocarb/#examples","title":"Examples","text":"Value 0.05 micromole per liter"},{"location":"petroleum_hydrocarb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"petroleum_hydrocarb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"petroleum_hydrocarb/#schema-source","title":"Schema Source","text":""},{"location":"petroleum_hydrocarb/#linkml-source","title":"LinkML Source","text":"
name: petroleum_hydrocarb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of petroleum hydrocarbon\ntitle: petroleum hydrocarbon\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- petroleum hydrocarbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000516\nalias: petroleum_hydrocarb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ph/","title":"Slot: pH (ph)","text":"

Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid

URI: MIXS:0001001

"},{"location":"ph/#inheritance","title":"Inheritance","text":""},{"location":"ph/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ph/#properties","title":"Properties","text":""},{"location":"ph/#aliases","title":"Aliases","text":""},{"location":"ph/#examples","title":"Examples","text":"Value 7.2"},{"location":"ph/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ph/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ph/#schema-source","title":"Schema Source","text":""},{"location":"ph/#linkml-source","title":"LinkML Source","text":"
name: ph\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Ph measurement of the sample, or liquid portion of sample, or aqueous\n  phase of the fluid\ntitle: pH\nexamples:\n- value: '7.2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001001\nalias: ph\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\n
"},{"location":"ph_meth/","title":"Slot: pH method (ph_meth)","text":"

Reference or method used in determining ph

URI: MIXS:0001106

"},{"location":"ph_meth/#inheritance","title":"Inheritance","text":""},{"location":"ph_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"ph_meth/#properties","title":"Properties","text":""},{"location":"ph_meth/#aliases","title":"Aliases","text":""},{"location":"ph_meth/#examples","title":"Examples","text":"Value"},{"location":"ph_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ph_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"ph_meth/#schema-source","title":"Schema Source","text":""},{"location":"ph_meth/#linkml-source","title":"LinkML Source","text":"
name: ph_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining ph\ntitle: pH method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001106\nalias: ph_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ph_regm/","title":"Slot: pH regimen (ph_regm)","text":"

Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen

URI: MIXS:0001056

"},{"location":"ph_regm/#inheritance","title":"Inheritance","text":""},{"location":"ph_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ph_regm/#properties","title":"Properties","text":""},{"location":"ph_regm/#aliases","title":"Aliases","text":""},{"location":"ph_regm/#examples","title":"Examples","text":"Value 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M"},{"location":"ph_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ph_regm/#annotations","title":"Annotations","text":"property value expected_value measurement value;treatment interval and duration"},{"location":"ph_regm/#schema-source","title":"Schema Source","text":""},{"location":"ph_regm/#linkml-source","title":"LinkML Source","text":"
name: ph_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;treatment interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving exposure of plants to varying levels\n  of ph of the growth media, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include multiple regimen\ntitle: pH regimen\nexamples:\n- value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001056\nalias: ph_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"phaeopigments/","title":"Slot: phaeopigments (phaeopigments)","text":"

Concentration of phaeopigments; can include multiple phaeopigments

URI: MIXS:0000180

"},{"location":"phaeopigments/#inheritance","title":"Inheritance","text":""},{"location":"phaeopigments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"phaeopigments/#properties","title":"Properties","text":""},{"location":"phaeopigments/#aliases","title":"Aliases","text":""},{"location":"phaeopigments/#examples","title":"Examples","text":"Value 2.5 milligram per cubic meter"},{"location":"phaeopigments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phaeopigments/#annotations","title":"Annotations","text":"property value expected_value phaeopigment name;measurement value"},{"location":"phaeopigments/#schema-source","title":"Schema Source","text":""},{"location":"phaeopigments/#linkml-source","title":"LinkML Source","text":"
name: phaeopigments\nannotations:\n  expected_value:\n    tag: expected_value\n    value: phaeopigment name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of phaeopigments; can include multiple phaeopigments\ntitle: phaeopigments\nexamples:\n- value: 2.5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phaeopigments\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000180\nalias: phaeopigments\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"phase/","title":"Slot: phase","text":"

The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.

URI: nmdc:phase

"},{"location":"phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"phase/#properties","title":"Properties","text":""},{"location":"phase/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phase/#schema-source","title":"Schema Source","text":""},{"location":"phase/#linkml-source","title":"LinkML Source","text":"
name: phase\ndescription: The phase for a coding sequence entity. For example, phase of a CDS as\n  represented in a GFF3 with a value of 0, 1 or 2.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:phase\nrank: 1000\nalias: phase\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 0\nmaximum_value: 2\n\n
"},{"location":"phosphate/","title":"Slot: phosphate (phosphate)","text":"

Concentration of phosphate

URI: MIXS:0000505

"},{"location":"phosphate/#inheritance","title":"Inheritance","text":""},{"location":"phosphate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"phosphate/#properties","title":"Properties","text":""},{"location":"phosphate/#aliases","title":"Aliases","text":""},{"location":"phosphate/#examples","title":"Examples","text":"Value 0.7 micromole per liter"},{"location":"phosphate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phosphate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"phosphate/#schema-source","title":"Schema Source","text":""},{"location":"phosphate/#linkml-source","title":"LinkML Source","text":"
name: phosphate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of phosphate\ntitle: phosphate\nexamples:\n- value: 0.7 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000505\nalias: phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"phosplipid_fatt_acid/","title":"Slot: phospholipid fatty acid (phosplipid_fatt_acid)","text":"

Concentration of phospholipid fatty acids; can include multiple values

URI: MIXS:0000181

"},{"location":"phosplipid_fatt_acid/#inheritance","title":"Inheritance","text":""},{"location":"phosplipid_fatt_acid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"phosplipid_fatt_acid/#properties","title":"Properties","text":""},{"location":"phosplipid_fatt_acid/#aliases","title":"Aliases","text":""},{"location":"phosplipid_fatt_acid/#examples","title":"Examples","text":"Value 2.98 milligram per liter"},{"location":"phosplipid_fatt_acid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phosplipid_fatt_acid/#annotations","title":"Annotations","text":"property value expected_value phospholipid fatty acid name;measurement value"},{"location":"phosplipid_fatt_acid/#schema-source","title":"Schema Source","text":""},{"location":"phosplipid_fatt_acid/#linkml-source","title":"LinkML Source","text":"
name: phosplipid_fatt_acid\nannotations:\n  expected_value:\n    tag: expected_value\n    value: phospholipid fatty acid name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per gram, mole per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of phospholipid fatty acids; can include multiple values\ntitle: phospholipid fatty acid\nexamples:\n- value: 2.98 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phospholipid fatty acid\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000181\nalias: phosplipid_fatt_acid\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"photon_flux/","title":"Slot: photon flux (photon_flux)","text":"

Measurement of photon flux

URI: MIXS:0000725

"},{"location":"photon_flux/#inheritance","title":"Inheritance","text":""},{"location":"photon_flux/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"photon_flux/#properties","title":"Properties","text":""},{"location":"photon_flux/#aliases","title":"Aliases","text":""},{"location":"photon_flux/#examples","title":"Examples","text":"Value 3.926 micromole photons per second per square meter"},{"location":"photon_flux/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"photon_flux/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"photon_flux/#schema-source","title":"Schema Source","text":""},{"location":"photon_flux/#linkml-source","title":"LinkML Source","text":"
name: photon_flux\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: number of photons per second per unit area\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of photon flux\ntitle: photon flux\nexamples:\n- value: 3.926 micromole photons per second per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- photon flux\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000725\nalias: photon_flux\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"plant_growth_med/","title":"Slot: plant growth medium (plant_growth_med)","text":"

Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary

URI: MIXS:0001057

"},{"location":"plant_growth_med/#inheritance","title":"Inheritance","text":""},{"location":"plant_growth_med/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"plant_growth_med/#properties","title":"Properties","text":""},{"location":"plant_growth_med/#aliases","title":"Aliases","text":""},{"location":"plant_growth_med/#examples","title":"Examples","text":"Value hydroponic plant culture media [EO:0007067]"},{"location":"plant_growth_med/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"plant_growth_med/#annotations","title":"Annotations","text":"property value expected_value EO or enumeration"},{"location":"plant_growth_med/#schema-source","title":"Schema Source","text":""},{"location":"plant_growth_med/#linkml-source","title":"LinkML Source","text":"
name: plant_growth_med\nannotations:\n  expected_value:\n    tag: expected_value\n    value: EO or enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Specification of the media for growing the plants or tissue cultured\n  samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro\n  liquid culture medium. Recommended value is a specific value from EO:plant growth\n  medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or\n  other controlled vocabulary\ntitle: plant growth medium\nexamples:\n- value: hydroponic plant culture media [EO:0007067]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant growth medium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001057\nalias: plant_growth_med\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"plant_product/","title":"Slot: plant product (plant_product)","text":"

Substance produced by the plant, where the sample was obtained from

URI: MIXS:0001058

"},{"location":"plant_product/#inheritance","title":"Inheritance","text":""},{"location":"plant_product/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"plant_product/#properties","title":"Properties","text":""},{"location":"plant_product/#aliases","title":"Aliases","text":""},{"location":"plant_product/#examples","title":"Examples","text":"Value xylem sap [PO:0025539]"},{"location":"plant_product/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"plant_product/#annotations","title":"Annotations","text":"property value expected_value product name"},{"location":"plant_product/#schema-source","title":"Schema Source","text":""},{"location":"plant_product/#linkml-source","title":"LinkML Source","text":"
name: plant_product\nannotations:\n  expected_value:\n    tag: expected_value\n    value: product name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Substance produced by the plant, where the sample was obtained from\ntitle: plant product\nexamples:\n- value: xylem sap [PO:0025539]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant product\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001058\nalias: plant_product\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"plant_sex/","title":"Slot: plant sex (plant_sex)","text":"

Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.

URI: MIXS:0001059

"},{"location":"plant_sex/#inheritance","title":"Inheritance","text":""},{"location":"plant_sex/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"plant_sex/#properties","title":"Properties","text":""},{"location":"plant_sex/#aliases","title":"Aliases","text":""},{"location":"plant_sex/#examples","title":"Examples","text":"Value Hermaphroditic"},{"location":"plant_sex/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"plant_sex/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"plant_sex/#schema-source","title":"Schema Source","text":""},{"location":"plant_sex/#linkml-source","title":"LinkML Source","text":"
name: plant_sex\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate,\n  monoecieous, hermaphrodite.\ntitle: plant sex\nexamples:\n- value: Hermaphroditic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001059\nalias: plant_sex\ndomain_of:\n- Biosample\nrange: plant_sex_enum\nmultivalued: false\n\n
"},{"location":"plant_struc/","title":"Slot: plant structure (plant_struc)","text":"

Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.

URI: MIXS:0001060

"},{"location":"plant_struc/#inheritance","title":"Inheritance","text":""},{"location":"plant_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"plant_struc/#properties","title":"Properties","text":""},{"location":"plant_struc/#aliases","title":"Aliases","text":""},{"location":"plant_struc/#examples","title":"Examples","text":"Value epidermis [PO:0005679]"},{"location":"plant_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"plant_struc/#annotations","title":"Annotations","text":"property value expected_value PO"},{"location":"plant_struc/#schema-source","title":"Schema Source","text":""},{"location":"plant_struc/#linkml-source","title":"LinkML Source","text":"
name: plant_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PO\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of plant structure the sample was obtained from; for Plant Ontology\n  (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n  e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex\n  of it can be recorded here.\ntitle: plant structure\nexamples:\n- value: epidermis [PO:0005679]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant structure\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0001060\nalias: plant_struc\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"polarity_mode/","title":"Slot: polarity_mode","text":"

the polarity of which ions are generated and detected

URI: nmdc:polarity_mode

"},{"location":"polarity_mode/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"polarity_mode/#properties","title":"Properties","text":""},{"location":"polarity_mode/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"polarity_mode/#schema-source","title":"Schema Source","text":""},{"location":"polarity_mode/#linkml-source","title":"LinkML Source","text":"
name: polarity_mode\ndescription: the polarity of which ions are generated and detected\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: polarity_mode\ndomain_of:\n- MassSpectrometryConfiguration\nrange: PolarityModeEnum\n\n
"},{"location":"pollutants/","title":"Slot: pollutants (pollutants)","text":"

Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant

URI: MIXS:0000107

"},{"location":"pollutants/#inheritance","title":"Inheritance","text":""},{"location":"pollutants/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pollutants/#properties","title":"Properties","text":""},{"location":"pollutants/#aliases","title":"Aliases","text":""},{"location":"pollutants/#examples","title":"Examples","text":"Value lead;0.15 microgram per cubic meter"},{"location":"pollutants/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pollutants/#annotations","title":"Annotations","text":"property value expected_value pollutant name;measurement value"},{"location":"pollutants/#schema-source","title":"Schema Source","text":""},{"location":"pollutants/#linkml-source","title":"LinkML Source","text":"
name: pollutants\nannotations:\n  expected_value:\n    tag: expected_value\n    value: pollutant name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter, microgram per cubic meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Pollutant types and, amount or concentrations measured at the time of\n  sampling; can report multiple pollutants by entering numeric values preceded by\n  name of pollutant\ntitle: pollutants\nexamples:\n- value: lead;0.15 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pollutants\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000107\nalias: pollutants\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"pool_dna_extracts/","title":"Slot: pooling of DNA extracts (if done) (pool_dna_extracts)","text":"

Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given

URI: MIXS:0000325

"},{"location":"pool_dna_extracts/#inheritance","title":"Inheritance","text":""},{"location":"pool_dna_extracts/#properties","title":"Properties","text":""},{"location":"pool_dna_extracts/#aliases","title":"Aliases","text":""},{"location":"pool_dna_extracts/#examples","title":"Examples","text":"Value yes;5"},{"location":"pool_dna_extracts/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pool_dna_extracts/#annotations","title":"Annotations","text":"property value expected_value pooling status;number of pooled extracts"},{"location":"pool_dna_extracts/#schema-source","title":"Schema Source","text":""},{"location":"pool_dna_extracts/#linkml-source","title":"LinkML Source","text":"
name: pool_dna_extracts\nannotations:\n  expected_value:\n    tag: expected_value\n    value: pooling status;number of pooled extracts\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Indicate whether multiple DNA extractions were mixed. If the answer yes,\n  the number of extracts that were pooled should be given\ntitle: pooling of DNA extracts (if done)\nexamples:\n- value: yes;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pooling of DNA extracts (if done)\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{integer}'\nslot_uri: MIXS:0000325\nalias: pool_dna_extracts\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"porosity/","title":"Slot: porosity (porosity)","text":"

Porosity of deposited sediment is volume of voids divided by the total volume of sample

URI: MIXS:0000211

"},{"location":"porosity/#inheritance","title":"Inheritance","text":""},{"location":"porosity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"porosity/#properties","title":"Properties","text":""},{"location":"porosity/#aliases","title":"Aliases","text":""},{"location":"porosity/#examples","title":"Examples","text":"Value"},{"location":"porosity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"porosity/#annotations","title":"Annotations","text":"property value expected_value measurement value or range"},{"location":"porosity/#schema-source","title":"Schema Source","text":""},{"location":"porosity/#linkml-source","title":"LinkML Source","text":"
name: porosity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value or range\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Porosity of deposited sediment is volume of voids divided by the total\n  volume of sample\ntitle: porosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- porosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000211\nalias: porosity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"potassium/","title":"Slot: potassium (potassium)","text":"

Concentration of potassium in the sample

URI: MIXS:0000430

"},{"location":"potassium/#inheritance","title":"Inheritance","text":""},{"location":"potassium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"potassium/#properties","title":"Properties","text":""},{"location":"potassium/#aliases","title":"Aliases","text":""},{"location":"potassium/#examples","title":"Examples","text":"Value 463 milligram per liter"},{"location":"potassium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"potassium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"potassium/#schema-source","title":"Schema Source","text":""},{"location":"potassium/#linkml-source","title":"LinkML Source","text":"
name: potassium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of potassium in the sample\ntitle: potassium\nexamples:\n- value: 463 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- potassium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000430\nalias: potassium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"pour_point/","title":"Slot: pour point (pour_point)","text":"

Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)

URI: MIXS:0000127

"},{"location":"pour_point/#inheritance","title":"Inheritance","text":""},{"location":"pour_point/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pour_point/#properties","title":"Properties","text":""},{"location":"pour_point/#aliases","title":"Aliases","text":""},{"location":"pour_point/#examples","title":"Examples","text":"Value"},{"location":"pour_point/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pour_point/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"pour_point/#schema-source","title":"Schema Source","text":""},{"location":"pour_point/#linkml-source","title":"LinkML Source","text":"
name: pour_point\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Temperature at which a liquid becomes semi solid and loses its flow\n  characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a\n  high paraffin content, typically found in crude deriving from a larger proportion\n  of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\ntitle: pour point\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pour point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000127\nalias: pour_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"pre_treatment/","title":"Slot: pre-treatment (pre_treatment)","text":"

The process of pre-treatment removes materials that can be easily collected from the raw wastewater

URI: MIXS:0000348

"},{"location":"pre_treatment/#inheritance","title":"Inheritance","text":""},{"location":"pre_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pre_treatment/#properties","title":"Properties","text":""},{"location":"pre_treatment/#aliases","title":"Aliases","text":""},{"location":"pre_treatment/#examples","title":"Examples","text":"Value"},{"location":"pre_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pre_treatment/#annotations","title":"Annotations","text":"property value expected_value pre-treatment type"},{"location":"pre_treatment/#schema-source","title":"Schema Source","text":""},{"location":"pre_treatment/#linkml-source","title":"LinkML Source","text":"
name: pre_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: pre-treatment type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The process of pre-treatment removes materials that can be easily collected\n  from the raw wastewater\ntitle: pre-treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pre-treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000348\nalias: pre_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"prefixes_curies_ids_mappings_etc/","title":"Notes about prefixes, CURIEs, identifiers and mappings:","text":""},{"location":"prefixes_curies_ids_mappings_etc/#an-nmdc-and-linkml-perspective","title":"An NMDC and LinkML perspective","text":""},{"location":"prefixes_curies_ids_mappings_etc/#first-draft-2023-09-18","title":"First Draft: 2023-09-18","text":""},{"location":"prefixes_curies_ids_mappings_etc/#the-nmdc-schema-is-a-framework-for-describing-multi-omics-microbiome-experiments","title":"The nmdc-schema is a framework for describing multi-omics microbiome experiments.","text":"

All metadata gathered and stored by the NMDC community must validate against the nmdc-schema.

"},{"location":"prefixes_curies_ids_mappings_etc/#the-nmdc-schema-is-expressed-in-the-linkml-schema-language","title":"The nmdc-schema is expressed in the LinkML schema language.","text":"

LinkML uses structures like classes, slots (for relationships and properties), types and enumerations. People with object-oriented programming experience might find this familiar.

"},{"location":"prefixes_curies_ids_mappings_etc/#the-name-linkml-indicates-that-its-a-modeling-language-for-linked-data","title":"The name \"LinkML\" indicates that it's a modeling language for linked data.","text":"

LinkML schemas generally make good use of terminology from external resources, especially ontologies, especially those from the OBO Foundry. In return, LinkML schema elements and the corresponding data should be interoperable with other ontologies and semantic databases.

"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-element-identifiers-in-the-schema-with-uris-and-curies","title":"Asserting element identifiers in the schema with URIs and CURIEs","text":"

One consequence of this semantic/linked data orientation is that all schema elements are identified by a URI, most often in the compact CURIe form: a prefix and a local identifier. Even if a class isn't decorated with a class_uri annotation, it will always have a key (in a JSON, YAML or Python Obj sense), which is sometimes reiterated as the name. In that case, the class' URI will be <prefix>:<key>. LinkML schemas should have default prefix assertions, but any element can use a different prefix, as long as an expansion is provided.

"},{"location":"prefixes_curies_ids_mappings_etc/#prefixes-in-linkml-schemas","title":"Prefixes in LinkML schemas","text":"

Prefixes used in a LinkML must be associated with an expansion in the schema (which may include imported modules). Ideally, the expanded URI should be web resolvable, but that is not required. The prefixes can be expanded to base URIs owned by a particular resource, or they can be expanded to base URIs owned by some resolving service, like the bioregistry.

"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-mappings-in-the-nmdc-schema","title":"Asserting mappings in the nmdc-schema","text":"

As mentioned above, URIs are assigned to most elements of a LinkML schema, either explicitly by the schema authors, or implicitly through the default prefix and the element's key. If an external prefix is used, that means the semantics of the element are identical to the external term, unless otherwise refined. Sometimes it is desirable to associate a LinkML schema element with a term from an external resource, without asserting that the semantics are identical. In this case, a variety of mapping terms can be used.

Adding mappings to a schema element is one of the best and most compact ways to clarify the meaning of that element.

Schema contributors are strongly encouraged to use mappings whose prefixes are already defined in the schema. Schema contributors are always responsible for having a holistic understanding of an external term to be mapped into the schema. This means gaining familiarity with the parent and child terms, as well as any other axioms applied to the term. The EBI Ontology Lookup Service is a good place to look for these details.

When it appears necessary to use a mapping whose prefix isn't already defined in the schema, the contributor is responsible for having a holistic understanding of the external namespace (not just the term to be mapped). There are several ways to start assessing an ontology that is being considered as a source of mappings. If the ontology is in the OBO Foundry, one can look at the OBO Foundry Dashboard.

"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-identifiers-in-linkml-data","title":"Asserting identifiers in LinkML data","text":"

Generally speaking, the smallest atom of LinkML data is an instance of one class. LinkML slots take values, but always in the context of some class (on the right hand side). LinkML data files are frequently collections of instances of one or more classes. The is no requirement that these classes provide a slot whose value uniquely identifies the instances, but LinkML provides a mechanism that is broadly followed: one slot available in each class is annotated with identifier: true. (Or at least, that's what it would look like in a YAML serialization.) That means that the slot is required in all instances of the class, and that any collection of instances from that class must have unique values in that slot. It is also typical to say that the range of the is type uriorcurie.

"},{"location":"prefixes_curies_ids_mappings_etc/#mentioning-identifiers-in-linkml-data","title":"Mentioning identifiers in LinkML data","text":"

A common pattern in the nmdc-schema is asserting that some identifiable process has inputs and outputs. 

pooling_set:\n  - id: pooling:1\n    inputs:\n      - biosample:1\n      - biosample:2\n      - biosample:3\n  - id: pooling:2\n    inputs:\n      - biosample:4\n      - biosample:5\n      - biosample:6\n

Here we have declared the existence of two pooling processes. A CURIe identifier is asserted for both of them, and three inputs are mentioned for each. The example CURIes above don't necessarily follow any nmdc-schema identifier pattern rules. If these were real CURIes, then the pooling and biosample prefixes would have to be defined in the schema files.

In this case, let's assume definitions for the biosample inputs should be defined elsewhere in an NMDC data set. Cases in which biosamples are mentioned without being defined would be considered violations of the referential integrity. The development of referential integrity validators for LinkML has begun in Autumn, 2023.

Another pattern is saying that something defined within a NMDC data set is equivalent to something defined elsewhere.

biosample_set:\n    - id: biosample:1\n      gold_biosample_identifiers:\n        - gold:1\n        - gold:2\n

In this case, the gold prefix must be defined in the schema. When expanded to URIs via the prefix definitions, these gold_biosample_identifiers would all be web-resolvable.

"},{"location":"prefixes_curies_ids_mappings_etc/#constraining-mentioned-identifiers","title":"Constraining mentioned identifiers","text":"

We can limit the values that go into any slot by using a pattern constraint. We can also use the id_prefixes constraint to limit the prefixes that are used in whatever slot has been declared to be the identifier of a class. (Attributes of a class are supposed to be cascaded to subclasses, via the is_a attribute. This may not always be the case though. In the nmdc-schema we have been using a belt-and-suspenders approach of re-declaring the uriorcurie range )

All prefixes used in the id_prefixes constraint must be defined in the schema. We should have a standing practice of reflecting on the declared id_prefixes, and removing prefixes that haven't been used yet and are not likely to eer be used.

Maintenance of the prefix portions of a pattern will generally require more manual checking. We shouldn't be constraining the values of slots to use a prefix that isn't declared, but no checks are automatically applied.

"},{"location":"prefixes_curies_ids_mappings_etc/#using-uris-supports-scoping-and-self-documentation","title":"Using URIs supports scoping and self-documentation","text":"

Any class could use any slot with any range to \"link to\" something external. A Person could have a place_of_birth slot, and that could take unconstrained string or enumerated values like \"Switzerland\". But that doesn't provide much support for people looking up more information about the place_of_birth. You could create wikidata_place_of_birth and dbpedia_place_of_birth slots and add annotations to the slot to aid in external lookups, but that isn't a good practice if supporting several external targets. A better practice is to have one place_of_birth slot, with the uriorcuire range. Then users can provide values like <http://www.wikidata.org/entity/Q39> or <http://dbpedia.org/resource/Switzerland>. Then there is no ambiguity about the target of the link.

"},{"location":"prefixes_curies_ids_mappings_etc/#using-curies-makes-things-more-compact-and-readable","title":"Using CURIes makes things more compact and readable","text":"

If the schema contains prefix definitions like wd: <http://www.wikidata.org/entity/> and dbpedia: <http://dbpedia.org/resource/>, then the values can be written as wd:Q39 and dbpedia:Switzerland. This is more compact and readable, but it requires that the prefixes be defined in the schema. Then, more constraint can be imposed with a pattern on the place_of_birth slot like '^(wd|dbpedia):.+$'

"},{"location":"prefixes_curies_ids_mappings_etc/#where-to-find-a-report-of-nmdc-prefixes","title":"Where to find a report of NMDC prefixes","text":""},{"location":"prefixes_curies_ids_mappings_etc/#prefix-id-and-curie-notes","title":"PREFIX, id and CURIe notes","text":""},{"location":"prefixes_curies_ids_mappings_etc/#see-locallintlog","title":"see local/lint.log","text":""},{"location":"prefixes_curies_ids_mappings_etc/#use-bioregistry-not-identifiersorg-but","title":"use bioregistry, not identifiers.org, BUT","text":"

warning Schema maps prefix 'CHEMBL.COMPOUND' to namespace 'https://bioregistry.io/chembl.compound:' instead of namespace 'http://identifiers.org/chembl.compound/' (canonical_prefixes)

warning Schema maps prefix 'rdf' to namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' instead of using prefix ' RDF' (canonical_prefixes) warning Schema maps prefix 'rdfs' to namespace 'http://www.w3.org/2000/01/rdf-schema#' instead of using prefix 'RDFS' ( canonical_prefixes)

"},{"location":"prefixes_curies_ids_mappings_etc/#typecodes","title":"Typecodes","text":"

Not only does NMDC require the use of the nmdc prefix in the primary identifier for data instances, but we also define a pattern that the local portion of the ids must follow. For example, an example id from the NamedThing class is 'nmdc:mgmag-00-x012.1_7_c1'. The text that comes immediately after the nmdc prefix and colon, and before the first hyphen is the typecode, mgmag in this case. Typecodes must correspond 1:1 to a class in the NMDC schema. The typecodes currently in use are available from the nmdc-runtime API: https://api.microbiomedata.org/nmdcschema/typecodes

The typecodes for each class are auto-discovered each time the nmdc-runtime API is restarted, and the API is restarted each time it is bound to a new version of the nmdc-schem.

We do not currently have any criteria for good typecodes, other than they are ideally between 3 and 6 characters in length.

"},{"location":"prefixes_curies_ids_mappings_etc/#unresolved","title":"unresolved","text":""},{"location":"pres_animal_insect/","title":"Slot: presence of pets, animals, or insects (pres_animal_insect)","text":"

The type and number of animals or insects present in the sampling space.

URI: MIXS:0000819

"},{"location":"pres_animal_insect/#inheritance","title":"Inheritance","text":""},{"location":"pres_animal_insect/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pres_animal_insect/#properties","title":"Properties","text":""},{"location":"pres_animal_insect/#aliases","title":"Aliases","text":""},{"location":"pres_animal_insect/#examples","title":"Examples","text":"Value cat;5"},{"location":"pres_animal_insect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pres_animal_insect/#annotations","title":"Annotations","text":"property value expected_value enumeration;count"},{"location":"pres_animal_insect/#schema-source","title":"Schema Source","text":""},{"location":"pres_animal_insect/#linkml-source","title":"LinkML Source","text":"
name: pres_animal_insect\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration;count\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type and number of animals or insects present in the sampling space.\ntitle: presence of pets, animals, or insects\nexamples:\n- value: cat;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- presence of pets, animals, or insects\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000819\nalias: pres_animal_insect\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\npattern: ^(cat|dog|rodent|snake|other);\\d+$\n\n
"},{"location":"pressure/","title":"Slot: pressure (pressure)","text":"

Pressure to which the sample is subject to, in atmospheres

URI: MIXS:0000412

"},{"location":"pressure/#inheritance","title":"Inheritance","text":""},{"location":"pressure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pressure/#properties","title":"Properties","text":""},{"location":"pressure/#aliases","title":"Aliases","text":""},{"location":"pressure/#examples","title":"Examples","text":"Value 50 atmosphere"},{"location":"pressure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pressure/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"pressure/#schema-source","title":"Schema Source","text":""},{"location":"pressure/#linkml-source","title":"LinkML Source","text":"
name: pressure\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: atmosphere\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Pressure to which the sample is subject to, in atmospheres\ntitle: pressure\nexamples:\n- value: 50 atmosphere\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000412\nalias: pressure\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"prev_land_use_meth/","title":"Slot: history/previous land use method (prev_land_use_meth)","text":"

Reference or method used in determining previous land use and dates

URI: MIXS:0000316

"},{"location":"prev_land_use_meth/#inheritance","title":"Inheritance","text":""},{"location":"prev_land_use_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"prev_land_use_meth/#properties","title":"Properties","text":""},{"location":"prev_land_use_meth/#aliases","title":"Aliases","text":""},{"location":"prev_land_use_meth/#examples","title":"Examples","text":"Value"},{"location":"prev_land_use_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"prev_land_use_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"prev_land_use_meth/#schema-source","title":"Schema Source","text":""},{"location":"prev_land_use_meth/#linkml-source","title":"LinkML Source","text":"
name: prev_land_use_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining previous land use and dates\ntitle: history/previous land use method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000316\nalias: prev_land_use_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"previous_land_use/","title":"Slot: history/previous land use (previous_land_use)","text":"

Previous land use and dates

URI: MIXS:0000315

"},{"location":"previous_land_use/#inheritance","title":"Inheritance","text":""},{"location":"previous_land_use/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"previous_land_use/#properties","title":"Properties","text":""},{"location":"previous_land_use/#aliases","title":"Aliases","text":""},{"location":"previous_land_use/#examples","title":"Examples","text":"Value"},{"location":"previous_land_use/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"previous_land_use/#annotations","title":"Annotations","text":"property value expected_value land use name;date"},{"location":"previous_land_use/#schema-source","title":"Schema Source","text":""},{"location":"previous_land_use/#linkml-source","title":"LinkML Source","text":"
name: previous_land_use\nannotations:\n  expected_value:\n    tag: expected_value\n    value: land use name;date\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Previous land use and dates\ntitle: history/previous land use\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{timestamp}'\nslot_uri: MIXS:0000315\nalias: previous_land_use\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"primary_prod/","title":"Slot: primary production (primary_prod)","text":"

Measurement of primary production, generally measured as isotope uptake

URI: MIXS:0000728

"},{"location":"primary_prod/#inheritance","title":"Inheritance","text":""},{"location":"primary_prod/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"primary_prod/#properties","title":"Properties","text":""},{"location":"primary_prod/#aliases","title":"Aliases","text":""},{"location":"primary_prod/#examples","title":"Examples","text":"Value 100 milligram per cubic meter per day"},{"location":"primary_prod/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"primary_prod/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"primary_prod/#schema-source","title":"Schema Source","text":""},{"location":"primary_prod/#linkml-source","title":"LinkML Source","text":"
name: primary_prod\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter per day, gram per square meter per day\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of primary production, generally measured as isotope uptake\ntitle: primary production\nexamples:\n- value: 100 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000728\nalias: primary_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"primary_treatment/","title":"Slot: primary treatment (primary_treatment)","text":"

The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed

URI: MIXS:0000349

"},{"location":"primary_treatment/#inheritance","title":"Inheritance","text":""},{"location":"primary_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"primary_treatment/#properties","title":"Properties","text":""},{"location":"primary_treatment/#aliases","title":"Aliases","text":""},{"location":"primary_treatment/#examples","title":"Examples","text":"Value"},{"location":"primary_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"primary_treatment/#annotations","title":"Annotations","text":"property value expected_value primary treatment type"},{"location":"primary_treatment/#schema-source","title":"Schema Source","text":""},{"location":"primary_treatment/#linkml-source","title":"LinkML Source","text":"
name: primary_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: primary treatment type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The process to produce both a generally homogeneous liquid capable of\n  being treated biologically and a sludge that can be separately treated or processed\ntitle: primary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000349\nalias: primary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"principal_investigator/","title":"Slot: principal_investigator","text":"

Principal Investigator who led the study and/or generated the dataset.

URI: nmdc:principal_investigator

"},{"location":"principal_investigator/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no Study A study summarizes the overall goal of a research initiative and outlines the... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"principal_investigator/#properties","title":"Properties","text":""},{"location":"principal_investigator/#aliases","title":"Aliases","text":""},{"location":"principal_investigator/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"principal_investigator/#schema-source","title":"Schema Source","text":""},{"location":"principal_investigator/#linkml-source","title":"LinkML Source","text":"
name: principal_investigator\ndescription: Principal Investigator who led the study and/or generated the dataset.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- PI\nrank: 1000\nalias: principal_investigator\ndomain_of:\n- Study\n- DataGeneration\nrange: PersonValue\n\n
"},{"location":"processed_sample_set/","title":"Slot: processed_sample_set","text":"

This property links a database object to the set of processed samples within it.

URI: nmdc:processed_sample_set

"},{"location":"processed_sample_set/#inheritance","title":"Inheritance","text":""},{"location":"processed_sample_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"processed_sample_set/#properties","title":"Properties","text":""},{"location":"processed_sample_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"processed_sample_set/#schema-source","title":"Schema Source","text":""},{"location":"processed_sample_set/#linkml-source","title":"LinkML Source","text":"
name: processed_sample_set\ndescription: This property links a database object to the set of processed samples\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: processed_sample_set\ndomain_of:\n- Database\nrange: ProcessedSample\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"processing_institution/","title":"Slot: processing_institution","text":"

The organization that processed the sample.

URI: nmdc:processing_institution

"},{"location":"processing_institution/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... no WorkflowExecution Represents an instance of an execution of a particular workflow no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetabolomicsAnalysis no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAssembly no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no LibraryPreparation no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"processing_institution/#properties","title":"Properties","text":""},{"location":"processing_institution/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"processing_institution/#schema-source","title":"Schema Source","text":""},{"location":"processing_institution/#linkml-source","title":"LinkML Source","text":"
name: processing_institution\ndescription: The organization that processed the sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: processing_institution\ndomain_of:\n- PlannedProcess\nrange: ProcessingInstitutionEnum\n\n
"},{"location":"prod_rate/","title":"Slot: production rate (prod_rate)","text":"

Oil and/or gas production rates per well (e.g. 524 m3 / day)

URI: MIXS:0000452

"},{"location":"prod_rate/#inheritance","title":"Inheritance","text":""},{"location":"prod_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"prod_rate/#properties","title":"Properties","text":""},{"location":"prod_rate/#aliases","title":"Aliases","text":""},{"location":"prod_rate/#examples","title":"Examples","text":"Value"},{"location":"prod_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"prod_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"prod_rate/#schema-source","title":"Schema Source","text":""},{"location":"prod_rate/#linkml-source","title":"LinkML Source","text":"
name: prod_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic meter per day\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Oil and/or gas production rates per well (e.g. 524 m3 / day)\ntitle: production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000452\nalias: prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"prod_start_date/","title":"Slot: production start date (prod_start_date)","text":"

Date of field's first production

URI: MIXS:0001008

"},{"location":"prod_start_date/#inheritance","title":"Inheritance","text":""},{"location":"prod_start_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"prod_start_date/#properties","title":"Properties","text":""},{"location":"prod_start_date/#aliases","title":"Aliases","text":""},{"location":"prod_start_date/#examples","title":"Examples","text":"Value 2018-05-11"},{"location":"prod_start_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"prod_start_date/#annotations","title":"Annotations","text":"property value expected_value timestamp"},{"location":"prod_start_date/#schema-source","title":"Schema Source","text":""},{"location":"prod_start_date/#linkml-source","title":"LinkML Source","text":"
name: prod_start_date\nannotations:\n  expected_value:\n    tag: expected_value\n    value: timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Date of field's first production\ntitle: production start date\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001008\nalias: prod_start_date\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"profile_image_url/","title":"Slot: profile_image_url","text":"

A url that points to an image of a person.

URI: nmdc:profile_image_url

"},{"location":"profile_image_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person no"},{"location":"profile_image_url/#properties","title":"Properties","text":""},{"location":"profile_image_url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"profile_image_url/#schema-source","title":"Schema Source","text":""},{"location":"profile_image_url/#linkml-source","title":"LinkML Source","text":"
name: profile_image_url\ndescription: A url that points to an image of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: profile_image_url\ndomain_of:\n- PersonValue\nrange: string\n\n
"},{"location":"profile_position/","title":"Slot: profile position (profile_position)","text":"

Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas

URI: MIXS:0001084

"},{"location":"profile_position/#inheritance","title":"Inheritance","text":""},{"location":"profile_position/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"profile_position/#properties","title":"Properties","text":""},{"location":"profile_position/#aliases","title":"Aliases","text":""},{"location":"profile_position/#examples","title":"Examples","text":"Value summit"},{"location":"profile_position/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"profile_position/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"profile_position/#schema-source","title":"Schema Source","text":""},{"location":"profile_position/#linkml-source","title":"LinkML Source","text":"
name: profile_position\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Cross-sectional position in the hillslope where sample was collected.sample\n  area position in relation to surrounding areas\ntitle: profile position\nexamples:\n- value: summit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- profile position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001084\nalias: profile_position\ndomain_of:\n- Biosample\nrange: profile_position_enum\nmultivalued: false\n\n
"},{"location":"project_id/","title":"Slot: project ID (project_id)","text":"

Proposal IDs or names associated with dataset

URI: nmdc:project_id

"},{"location":"project_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"project_id/#properties","title":"Properties","text":""},{"location":"project_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"project_id/#schema-source","title":"Schema Source","text":""},{"location":"project_id/#linkml-source","title":"LinkML Source","text":"
name: project_id\ndescription: Proposal IDs or names associated with dataset\ntitle: project ID\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: project_id\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"proport_woa_temperature/","title":"Slot: proport_woa_temperature","text":"

URI: nmdc:proport_woa_temperature

"},{"location":"proport_woa_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proport_woa_temperature/#properties","title":"Properties","text":""},{"location":"proport_woa_temperature/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"proport_woa_temperature/#schema-source","title":"Schema Source","text":""},{"location":"proport_woa_temperature/#linkml-source","title":"LinkML Source","text":"
name: proport_woa_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: proport_woa_temperature\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"proposal_dna/","title":"Slot: DNA proposal ID (proposal_dna)","text":"

URI: nmdc:proposal_dna

"},{"location":"proposal_dna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_dna/#properties","title":"Properties","text":""},{"location":"proposal_dna/#examples","title":"Examples","text":"Value 504000"},{"location":"proposal_dna/#comments","title":"Comments","text":""},{"location":"proposal_dna/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"proposal_dna/#schema-source","title":"Schema Source","text":""},{"location":"proposal_dna/#linkml-source","title":"LinkML Source","text":"
name: proposal_dna\ntitle: DNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_dna\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"proposal_rna/","title":"Slot: RNA proposal ID (proposal_rna)","text":"

URI: nmdc:proposal_rna

"},{"location":"proposal_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_rna/#properties","title":"Properties","text":""},{"location":"proposal_rna/#examples","title":"Examples","text":"Value 504000"},{"location":"proposal_rna/#comments","title":"Comments","text":""},{"location":"proposal_rna/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"proposal_rna/#schema-source","title":"Schema Source","text":""},{"location":"proposal_rna/#linkml-source","title":"LinkML Source","text":"
name: proposal_rna\ntitle: RNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"protein_spectral_count/","title":"Slot: protein_spectral_count","text":"

sum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file

URI: nmdc:protein_spectral_count

"},{"location":"protein_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_spectral_count/#properties","title":"Properties","text":""},{"location":"protein_spectral_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protein_spectral_count/#schema-source","title":"Schema Source","text":""},{"location":"protein_spectral_count/#linkml-source","title":"LinkML Source","text":"
name: protein_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the best protein within\n  a given LC-MS/MS data file\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_spectral_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\n
"},{"location":"protein_sum_masic_abundance/","title":"Slot: protein_sum_masic_abundance","text":"

combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool

URI: nmdc:protein_sum_masic_abundance

"},{"location":"protein_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_sum_masic_abundance/#properties","title":"Properties","text":""},{"location":"protein_sum_masic_abundance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protein_sum_masic_abundance/#schema-source","title":"Schema Source","text":""},{"location":"protein_sum_masic_abundance/#linkml-source","title":"LinkML Source","text":"
name: protein_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n  with the best protein from a given LC-MS/MS data file using the MASIC tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_sum_masic_abundance\ndomain_of:\n- ProteinQuantification\nrange: integer\n\n
"},{"location":"protocol_execution_category/","title":"Slot: protocol_execution_category","text":"

URI: nmdc:protocol_execution_category

"},{"location":"protocol_execution_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProtocolExecution A PlannedProces that has PlannedProcess parts no"},{"location":"protocol_execution_category/#properties","title":"Properties","text":""},{"location":"protocol_execution_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protocol_execution_category/#schema-source","title":"Schema Source","text":""},{"location":"protocol_execution_category/#linkml-source","title":"LinkML Source","text":"
name: protocol_execution_category\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_execution_category\ndomain_of:\n- ProtocolExecution\nrange: ProtocolCategoryEnum\nrequired: true\n\n
"},{"location":"protocol_execution_set/","title":"Slot: protocol_execution_set","text":"

This property links a database object to the set of protocol executions within it.

URI: nmdc:protocol_execution_set

"},{"location":"protocol_execution_set/#inheritance","title":"Inheritance","text":""},{"location":"protocol_execution_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"protocol_execution_set/#properties","title":"Properties","text":""},{"location":"protocol_execution_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protocol_execution_set/#schema-source","title":"Schema Source","text":""},{"location":"protocol_execution_set/#linkml-source","title":"LinkML Source","text":"
name: protocol_execution_set\ndescription: This property links a database object to the set of protocol executions\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: protocol_execution_set\ndomain_of:\n- Database\nrange: ProtocolExecution\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"protocol_link/","title":"Slot: protocol_link","text":"

URI: nmdc:protocol_link

"},{"location":"protocol_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... no WorkflowExecution Represents an instance of an execution of a particular workflow no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetabolomicsAnalysis no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAssembly no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no LibraryPreparation no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no Study A study summarizes the overall goal of a research initiative and outlines the... yes StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"protocol_link/#properties","title":"Properties","text":""},{"location":"protocol_link/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protocol_link/#schema-source","title":"Schema Source","text":""},{"location":"protocol_link/#linkml-source","title":"LinkML Source","text":"
name: protocol_link\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_link\ndomain_of:\n- PlannedProcess\n- Study\nrange: Protocol\n\n
"},{"location":"qc_comment/","title":"Slot: qc_comment","text":"

Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).

URI: nmdc:qc_comment

"},{"location":"qc_comment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... no WorkflowExecution Represents an instance of an execution of a particular workflow no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetabolomicsAnalysis no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAssembly no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no LibraryPreparation no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"qc_comment/#properties","title":"Properties","text":""},{"location":"qc_comment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"qc_comment/#schema-source","title":"Schema Source","text":""},{"location":"qc_comment/#linkml-source","title":"LinkML Source","text":"
name: qc_comment\ndescription: Slot to store additional comments about laboratory or workflow output.\n  For workflow output it may describe the particular workflow stage that failed. (ie\n  Failed at call-stage due to a malformed fastq file).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_comment\ndomain_of:\n- PlannedProcess\nrange: string\n\n
"},{"location":"qc_failure_what/","title":"Slot: qc_failure_what","text":"

Provides a summary about what caused a lab or workflow process to fail

URI: nmdc:qc_failure_what

"},{"location":"qc_failure_what/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FailureCategorization no"},{"location":"qc_failure_what/#properties","title":"Properties","text":""},{"location":"qc_failure_what/#comments","title":"Comments","text":""},{"location":"qc_failure_what/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"qc_failure_what/#schema-source","title":"Schema Source","text":""},{"location":"qc_failure_what/#linkml-source","title":"LinkML Source","text":"
name: qc_failure_what\ndescription: Provides a summary about what caused a lab or workflow process to fail\ncomments:\n- For example, low read count from a sequencer, malformed fastq files, etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_failure_what\ndomain_of:\n- FailureCategorization\nrange: FailureWhatEnum\n\n
"},{"location":"qc_failure_where/","title":"Slot: qc_failure_where","text":"

Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results.

URI: nmdc:qc_failure_where

"},{"location":"qc_failure_where/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FailureCategorization no"},{"location":"qc_failure_where/#properties","title":"Properties","text":""},{"location":"qc_failure_where/#comments","title":"Comments","text":""},{"location":"qc_failure_where/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"qc_failure_where/#schema-source","title":"Schema Source","text":""},{"location":"qc_failure_where/#linkml-source","title":"LinkML Source","text":"
name: qc_failure_where\ndescription: Describes the nmdc schema class that corresonds to where the failure\n  occurred. Most commonly this would be the same as Class that generated the results.\ncomments:\n- If the assembly size was too small to proceed to annotation failure_where would\n  be MetagenomeAssembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_failure_where\ndomain_of:\n- FailureCategorization\nrange: FailureWhereEnum\n\n
"},{"location":"qc_status/","title":"Slot: qc_status","text":"

Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)

URI: nmdc:qc_status

"},{"location":"qc_status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... no WorkflowExecution Represents an instance of an execution of a particular workflow no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetabolomicsAnalysis no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAssembly no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no LibraryPreparation no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"qc_status/#properties","title":"Properties","text":""},{"location":"qc_status/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"qc_status/#schema-source","title":"Schema Source","text":""},{"location":"qc_status/#linkml-source","title":"LinkML Source","text":"
name: qc_status\ndescription: Stores information about the result of a process (ie the process of sequencing\n  a library may have for qc_status of 'fail' if not enough data was generated)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_status\ndomain_of:\n- PlannedProcess\nrange: StatusEnum\n\n
"},{"location":"quad_pos/","title":"Slot: quadrant position (quad_pos)","text":"

The quadrant position of the sampling room within the building

URI: MIXS:0000820

"},{"location":"quad_pos/#inheritance","title":"Inheritance","text":""},{"location":"quad_pos/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"quad_pos/#properties","title":"Properties","text":""},{"location":"quad_pos/#aliases","title":"Aliases","text":""},{"location":"quad_pos/#examples","title":"Examples","text":"Value West side"},{"location":"quad_pos/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"quad_pos/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"quad_pos/#schema-source","title":"Schema Source","text":""},{"location":"quad_pos/#linkml-source","title":"LinkML Source","text":"
name: quad_pos\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The quadrant position of the sampling room within the building\ntitle: quadrant position\nexamples:\n- value: West side\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- quadrant position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000820\nalias: quad_pos\ndomain_of:\n- Biosample\nrange: quad_pos_enum\nmultivalued: false\n\n
"},{"location":"radiation_regm/","title":"Slot: radiation regimen (radiation_regm)","text":"

Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens

URI: MIXS:0000575

"},{"location":"radiation_regm/#inheritance","title":"Inheritance","text":""},{"location":"radiation_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"radiation_regm/#properties","title":"Properties","text":""},{"location":"radiation_regm/#aliases","title":"Aliases","text":""},{"location":"radiation_regm/#examples","title":"Examples","text":"Value gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"radiation_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"radiation_regm/#annotations","title":"Annotations","text":"property value expected_value radiation type name;radiation amount;treatment interval and duration"},{"location":"radiation_regm/#schema-source","title":"Schema Source","text":""},{"location":"radiation_regm/#linkml-source","title":"LinkML Source","text":"
name: radiation_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: radiation type name;radiation amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: rad, gray\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving exposure of plant or a plant part\n  to a particular radiation regimen; should include the radiation type, amount or\n  intensity administered, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include multiple radiation regimens\ntitle: radiation regimen\nexamples:\n- value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- radiation regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000575\nalias: radiation_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"rainfall_regm/","title":"Slot: rainfall regimen (rainfall_regm)","text":"

Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000576

"},{"location":"rainfall_regm/#inheritance","title":"Inheritance","text":""},{"location":"rainfall_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rainfall_regm/#properties","title":"Properties","text":""},{"location":"rainfall_regm/#aliases","title":"Aliases","text":""},{"location":"rainfall_regm/#examples","title":"Examples","text":"Value 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"rainfall_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rainfall_regm/#annotations","title":"Annotations","text":"property value expected_value measurement value;treatment interval and duration"},{"location":"rainfall_regm/#schema-source","title":"Schema Source","text":""},{"location":"rainfall_regm/#linkml-source","title":"LinkML Source","text":"
name: rainfall_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to a given amount of\n  rainfall, treatment regimen including how many times the treatment was repeated,\n  how long each treatment lasted, and the start and end time of the entire treatment;\n  can include multiple regimens\ntitle: rainfall regimen\nexamples:\n- value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rainfall regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000576\nalias: rainfall_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"reactor_type/","title":"Slot: reactor type (reactor_type)","text":"

Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage

URI: MIXS:0000350

"},{"location":"reactor_type/#inheritance","title":"Inheritance","text":""},{"location":"reactor_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"reactor_type/#properties","title":"Properties","text":""},{"location":"reactor_type/#aliases","title":"Aliases","text":""},{"location":"reactor_type/#examples","title":"Examples","text":"Value"},{"location":"reactor_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reactor_type/#annotations","title":"Annotations","text":"property value expected_value reactor type name"},{"location":"reactor_type/#schema-source","title":"Schema Source","text":""},{"location":"reactor_type/#linkml-source","title":"LinkML Source","text":"
name: reactor_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: reactor type name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Anaerobic digesters can be designed and engineered to operate using a\n  number of different process configurations, as batch or continuous, mesophilic,\n  high solid or low solid, and single stage or multistage\ntitle: reactor type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reactor type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000350\nalias: reactor_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"read_qc_analysis_statistic/","title":"Slot: read_qc_analysis_statistic","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:read_qc_analysis_statistic

"},{"location":"read_qc_analysis_statistic/#inheritance","title":"Inheritance","text":""},{"location":"read_qc_analysis_statistic/#properties","title":"Properties","text":""},{"location":"read_qc_analysis_statistic/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"read_qc_analysis_statistic/#schema-source","title":"Schema Source","text":""},{"location":"read_qc_analysis_statistic/#linkml-source","title":"LinkML Source","text":"
name: read_qc_analysis_statistic\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: read_qc_analysis_statistic\nrange: string\n\n
"},{"location":"redox_potential/","title":"Slot: redox potential (redox_potential)","text":"

Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential

URI: MIXS:0000182

"},{"location":"redox_potential/#inheritance","title":"Inheritance","text":""},{"location":"redox_potential/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"redox_potential/#properties","title":"Properties","text":""},{"location":"redox_potential/#aliases","title":"Aliases","text":""},{"location":"redox_potential/#examples","title":"Examples","text":"Value 300 millivolt"},{"location":"redox_potential/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"redox_potential/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"redox_potential/#schema-source","title":"Schema Source","text":""},{"location":"redox_potential/#linkml-source","title":"LinkML Source","text":"
name: redox_potential\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millivolt\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Redox potential, measured relative to a hydrogen cell, indicating oxidation\n  or reduction potential\ntitle: redox potential\nexamples:\n- value: 300 millivolt\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- redox potential\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000182\nalias: redox_potential\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"rel_air_humidity/","title":"Slot: relative air humidity (rel_air_humidity)","text":"

Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air

URI: MIXS:0000121

"},{"location":"rel_air_humidity/#inheritance","title":"Inheritance","text":""},{"location":"rel_air_humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rel_air_humidity/#properties","title":"Properties","text":""},{"location":"rel_air_humidity/#aliases","title":"Aliases","text":""},{"location":"rel_air_humidity/#examples","title":"Examples","text":"Value 80%"},{"location":"rel_air_humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rel_air_humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"rel_air_humidity/#schema-source","title":"Schema Source","text":""},{"location":"rel_air_humidity/#linkml-source","title":"LinkML Source","text":"
name: rel_air_humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Partial vapor and air pressure, density of the vapor and air, or by the\n  actual mass of the vapor and air\ntitle: relative air humidity\nexamples:\n- value: 80%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000121\nalias: rel_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"rel_humidity_out/","title":"Slot: outside relative humidity (rel_humidity_out)","text":"

The recorded outside relative humidity value at the time of sampling

URI: MIXS:0000188

"},{"location":"rel_humidity_out/#inheritance","title":"Inheritance","text":""},{"location":"rel_humidity_out/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rel_humidity_out/#properties","title":"Properties","text":""},{"location":"rel_humidity_out/#aliases","title":"Aliases","text":""},{"location":"rel_humidity_out/#examples","title":"Examples","text":"Value 12 per kilogram of air"},{"location":"rel_humidity_out/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rel_humidity_out/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"rel_humidity_out/#schema-source","title":"Schema Source","text":""},{"location":"rel_humidity_out/#linkml-source","title":"LinkML Source","text":"
name: rel_humidity_out\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram of air, kilogram of air\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The recorded outside relative humidity value at the time of sampling\ntitle: outside relative humidity\nexamples:\n- value: 12 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- outside relative humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000188\nalias: rel_humidity_out\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"rel_samp_loc/","title":"Slot: relative sampling location (rel_samp_loc)","text":"

The sampling location within the train car

URI: MIXS:0000821

"},{"location":"rel_samp_loc/#inheritance","title":"Inheritance","text":""},{"location":"rel_samp_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rel_samp_loc/#properties","title":"Properties","text":""},{"location":"rel_samp_loc/#aliases","title":"Aliases","text":""},{"location":"rel_samp_loc/#examples","title":"Examples","text":"Value center of car"},{"location":"rel_samp_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rel_samp_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"rel_samp_loc/#schema-source","title":"Schema Source","text":""},{"location":"rel_samp_loc/#linkml-source","title":"LinkML Source","text":"
name: rel_samp_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The sampling location within the train car\ntitle: relative sampling location\nexamples:\n- value: center of car\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative sampling location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000821\nalias: rel_samp_loc\ndomain_of:\n- Biosample\nrange: rel_samp_loc_enum\nmultivalued: false\n\n
"},{"location":"related_identifiers/","title":"Slot: Related Identifiers (related_identifiers)","text":"

Identifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation.

URI: nmdc:related_identifiers

"},{"location":"related_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"related_identifiers/#properties","title":"Properties","text":""},{"location":"related_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"related_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"related_identifiers/#linkml-source","title":"LinkML Source","text":"
name: related_identifiers\ndescription: Identifiers assigned to a thing that is similar to that which is represented\n  in NMDC. Related identifier are not an identical match and may have some variation.\ntitle: Related Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: related_identifiers\ndomain_of:\n- Study\nrange: string\n\n
"},{"location":"replicate_number/","title":"Slot: replicate number (replicate_number)","text":"

If sending biological replicates, indicate the rep number here.

URI: nmdc:replicate_number

"},{"location":"replicate_number/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"replicate_number/#properties","title":"Properties","text":""},{"location":"replicate_number/#comments","title":"Comments","text":""},{"location":"replicate_number/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"replicate_number/#schema-source","title":"Schema Source","text":""},{"location":"replicate_number/#linkml-source","title":"LinkML Source","text":"
name: replicate_number\ndescription: If sending biological replicates, indicate the rep number here.\ntitle: replicate number\ncomments:\n- This will guide staff in ensuring your samples are blocked & randomized correctly\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{integer}'\nalias: replicate_number\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"reservoir/","title":"Slot: reservoir name (reservoir)","text":"

Name of the reservoir (e.g. Carapebus)

URI: MIXS:0000303

"},{"location":"reservoir/#inheritance","title":"Inheritance","text":""},{"location":"reservoir/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"reservoir/#properties","title":"Properties","text":""},{"location":"reservoir/#aliases","title":"Aliases","text":""},{"location":"reservoir/#examples","title":"Examples","text":"Value"},{"location":"reservoir/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reservoir/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"reservoir/#schema-source","title":"Schema Source","text":""},{"location":"reservoir/#linkml-source","title":"LinkML Source","text":"
name: reservoir\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of the reservoir (e.g. Carapebus)\ntitle: reservoir name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reservoir name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000303\nalias: reservoir\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"resins_pc/","title":"Slot: resins wt% (resins_pc)","text":"

Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)

URI: MIXS:0000134

"},{"location":"resins_pc/#inheritance","title":"Inheritance","text":""},{"location":"resins_pc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"resins_pc/#properties","title":"Properties","text":""},{"location":"resins_pc/#aliases","title":"Aliases","text":""},{"location":"resins_pc/#examples","title":"Examples","text":"Value"},{"location":"resins_pc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"resins_pc/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"resins_pc/#schema-source","title":"Schema Source","text":""},{"location":"resins_pc/#linkml-source","title":"LinkML Source","text":"
name: resins_pc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n  that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n  There are three main methods to obtain SARA results. The most popular one is known\n  as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: resins wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- resins wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000134\nalias: resins_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"resolution_categories/","title":"Slot: resolution_categories","text":"

The relative resolution at which spectra were collected.

URI: nmdc:resolution_categories

"},{"location":"resolution_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"resolution_categories/#properties","title":"Properties","text":""},{"location":"resolution_categories/#examples","title":"Examples","text":"Value ['high', 'low']"},{"location":"resolution_categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"resolution_categories/#schema-source","title":"Schema Source","text":""},{"location":"resolution_categories/#linkml-source","title":"LinkML Source","text":"
name: resolution_categories\ndescription: The relative resolution at which spectra were collected.\nexamples:\n- value: '[''high'', ''low'']'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: resolution_categories\ndomain_of:\n- MassSpectrometryConfiguration\nrange: ResolutionCategoryEnum\nmultivalued: true\n\n
"},{"location":"rna_absorb1/","title":"Slot: RNA absorbance 260/280 (rna_absorb1)","text":"

260/280 measurement of RNA sample purity

URI: nmdc:rna_absorb1

"},{"location":"rna_absorb1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_absorb1/#properties","title":"Properties","text":""},{"location":"rna_absorb1/#examples","title":"Examples","text":"Value 2.02"},{"location":"rna_absorb1/#comments","title":"Comments","text":""},{"location":"rna_absorb1/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_absorb1/#schema-source","title":"Schema Source","text":""},{"location":"rna_absorb1/#linkml-source","title":"LinkML Source","text":"
name: rna_absorb1\ndescription: 260/280 measurement of RNA sample purity\ntitle: RNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nstring_serialization: '{float}'\nalias: rna_absorb1\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\n
"},{"location":"rna_absorb2/","title":"Slot: RNA absorbance 260/230 (rna_absorb2)","text":"

260/230 measurement of RNA sample purity

URI: nmdc:rna_absorb2

"},{"location":"rna_absorb2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_absorb2/#properties","title":"Properties","text":""},{"location":"rna_absorb2/#examples","title":"Examples","text":"Value 2.02"},{"location":"rna_absorb2/#comments","title":"Comments","text":""},{"location":"rna_absorb2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_absorb2/#schema-source","title":"Schema Source","text":""},{"location":"rna_absorb2/#linkml-source","title":"LinkML Source","text":"
name: rna_absorb2\ndescription: 260/230 measurement of RNA sample purity\ntitle: RNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nstring_serialization: '{float}'\nalias: rna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\n
"},{"location":"rna_collect_site/","title":"Slot: RNA collection site (rna_collect_site)","text":"

Provide information on the site your RNA sample was collected from

URI: nmdc:rna_collect_site

"},{"location":"rna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_collect_site/#properties","title":"Properties","text":""},{"location":"rna_collect_site/#examples","title":"Examples","text":"Value untreated pond water"},{"location":"rna_collect_site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_collect_site/#schema-source","title":"Schema Source","text":""},{"location":"rna_collect_site/#linkml-source","title":"LinkML Source","text":"
name: rna_collect_site\ndescription: Provide information on the site your RNA sample was collected from\ntitle: RNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: rna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_concentration/","title":"Slot: RNA concentration in ng/ul (rna_concentration)","text":"

URI: nmdc:rna_concentration

"},{"location":"rna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_concentration/#properties","title":"Properties","text":""},{"location":"rna_concentration/#examples","title":"Examples","text":"Value 100"},{"location":"rna_concentration/#comments","title":"Comments","text":""},{"location":"rna_concentration/#see-also","title":"See Also","text":""},{"location":"rna_concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_concentration/#schema-source","title":"Schema Source","text":""},{"location":"rna_concentration/#linkml-source","title":"LinkML Source","text":"
name: rna_concentration\ntitle: RNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n  a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nstring_serialization: '{float}'\nalias: rna_concentration\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\n
"},{"location":"rna_cont_type/","title":"Slot: RNA container type (rna_cont_type)","text":"

Tube or plate (96-well)

URI: nmdc:rna_cont_type

"},{"location":"rna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_type/#properties","title":"Properties","text":""},{"location":"rna_cont_type/#examples","title":"Examples","text":"Value plate"},{"location":"rna_cont_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_cont_type/#schema-source","title":"Schema Source","text":""},{"location":"rna_cont_type/#linkml-source","title":"LinkML Source","text":"
name: rna_cont_type\ndescription: Tube or plate (96-well)\ntitle: RNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: rna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: JgiContTypeEnum\nrecommended: true\n\n
"},{"location":"rna_cont_well/","title":"Slot: RNA plate position (rna_cont_well)","text":"

URI: nmdc:rna_cont_well

"},{"location":"rna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_well/#properties","title":"Properties","text":""},{"location":"rna_cont_well/#examples","title":"Examples","text":"Value B2"},{"location":"rna_cont_well/#comments","title":"Comments","text":""},{"location":"rna_cont_well/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_cont_well/#schema-source","title":"Schema Source","text":""},{"location":"rna_cont_well/#linkml-source","title":"LinkML Source","text":"
name: rna_cont_well\ntitle: RNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n  validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: rna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\npattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n\n
"},{"location":"rna_container_id/","title":"Slot: RNA container label (rna_container_id)","text":"

URI: nmdc:rna_container_id

"},{"location":"rna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_container_id/#properties","title":"Properties","text":""},{"location":"rna_container_id/#examples","title":"Examples","text":"Value Pond_MT_041618"},{"location":"rna_container_id/#comments","title":"Comments","text":""},{"location":"rna_container_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_container_id/#schema-source","title":"Schema Source","text":""},{"location":"rna_container_id/#linkml-source","title":"LinkML Source","text":"
name: rna_container_id\ntitle: RNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n  plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: rna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_isolate_meth/","title":"Slot: RNA isolation method (rna_isolate_meth)","text":"

Describe the method/protocol/kit used to extract DNA/RNA.

URI: nmdc:rna_isolate_meth

"},{"location":"rna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_isolate_meth/#properties","title":"Properties","text":""},{"location":"rna_isolate_meth/#aliases","title":"Aliases","text":""},{"location":"rna_isolate_meth/#examples","title":"Examples","text":"Value phenol/chloroform extraction"},{"location":"rna_isolate_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_isolate_meth/#schema-source","title":"Schema Source","text":""},{"location":"rna_isolate_meth/#linkml-source","title":"LinkML Source","text":"
name: rna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: RNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Sample Isolation Method\nrank: 16\nstring_serialization: '{text}'\nalias: rna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_organisms/","title":"Slot: RNA expected organisms (rna_organisms)","text":"

List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.

URI: nmdc:rna_organisms

"},{"location":"rna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_organisms/#properties","title":"Properties","text":""},{"location":"rna_organisms/#examples","title":"Examples","text":"Value expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)"},{"location":"rna_organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_organisms/#schema-source","title":"Schema Source","text":""},{"location":"rna_organisms/#linkml-source","title":"LinkML Source","text":"
name: rna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n  as estimated % of the organism in that culture.\ntitle: RNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: rna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_project_contact/","title":"Slot: RNA seq project contact (rna_project_contact)","text":"

URI: nmdc:rna_project_contact

"},{"location":"rna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_project_contact/#properties","title":"Properties","text":""},{"location":"rna_project_contact/#examples","title":"Examples","text":"Value John Jones"},{"location":"rna_project_contact/#comments","title":"Comments","text":""},{"location":"rna_project_contact/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_project_contact/#schema-source","title":"Schema Source","text":""},{"location":"rna_project_contact/#linkml-source","title":"LinkML Source","text":"
name: rna_project_contact\ntitle: RNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: rna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_samp_id/","title":"Slot: RNA sample ID (rna_samp_id)","text":"

URI: nmdc:rna_samp_id

"},{"location":"rna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_samp_id/#properties","title":"Properties","text":""},{"location":"rna_samp_id/#examples","title":"Examples","text":"Value 187654"},{"location":"rna_samp_id/#comments","title":"Comments","text":""},{"location":"rna_samp_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_samp_id/#schema-source","title":"Schema Source","text":""},{"location":"rna_samp_id/#linkml-source","title":"LinkML Source","text":"
name: rna_samp_id\ntitle: RNA sample ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: rna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_sample_format/","title":"Slot: RNA sample format (rna_sample_format)","text":"

Solution in which the RNA sample has been suspended

URI: nmdc:rna_sample_format

"},{"location":"rna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_format/#properties","title":"Properties","text":""},{"location":"rna_sample_format/#examples","title":"Examples","text":"Value Water"},{"location":"rna_sample_format/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_sample_format/#schema-source","title":"Schema Source","text":""},{"location":"rna_sample_format/#linkml-source","title":"LinkML Source","text":"
name: rna_sample_format\ndescription: Solution in which the RNA sample has been suspended\ntitle: RNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: rna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: RNASampleFormatEnum\nrecommended: true\n\n
"},{"location":"rna_sample_name/","title":"Slot: RNA sample name (rna_sample_name)","text":"

Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.

URI: nmdc:rna_sample_name

"},{"location":"rna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_name/#properties","title":"Properties","text":""},{"location":"rna_sample_name/#examples","title":"Examples","text":"Value JGI_pond_041618"},{"location":"rna_sample_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_sample_name/#schema-source","title":"Schema Source","text":""},{"location":"rna_sample_name/#linkml-source","title":"LinkML Source","text":"
name: rna_sample_name\ndescription: Give the RNA sample a name that is meaningful to you. Sample names must\n  be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: RNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: rna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\n
"},{"location":"rna_seq_project/","title":"Slot: RNA seq project ID (rna_seq_project)","text":"

URI: nmdc:rna_seq_project

"},{"location":"rna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project/#properties","title":"Properties","text":""},{"location":"rna_seq_project/#aliases","title":"Aliases","text":""},{"location":"rna_seq_project/#examples","title":"Examples","text":"Value 1191234"},{"location":"rna_seq_project/#comments","title":"Comments","text":""},{"location":"rna_seq_project/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_seq_project/#schema-source","title":"Schema Source","text":""},{"location":"rna_seq_project/#linkml-source","title":"LinkML Source","text":"
name: rna_seq_project\ntitle: RNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Seq Project ID\nrank: 1\nstring_serialization: '{text}'\nalias: rna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_seq_project_name/","title":"Slot: RNA seq project name (rna_seq_project_name)","text":"

URI: nmdc:rna_seq_project_name

"},{"location":"rna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_name/#properties","title":"Properties","text":""},{"location":"rna_seq_project_name/#examples","title":"Examples","text":"Value JGI Pond metatranscriptomics"},{"location":"rna_seq_project_name/#comments","title":"Comments","text":""},{"location":"rna_seq_project_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_seq_project_name/#schema-source","title":"Schema Source","text":""},{"location":"rna_seq_project_name/#linkml-source","title":"LinkML Source","text":"
name: rna_seq_project_name\ntitle: RNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: JGI Pond metatranscriptomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: rna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_seq_project_pi/","title":"Slot: RNA seq project PI (rna_seq_project_pi)","text":"

URI: nmdc:rna_seq_project_pi

"},{"location":"rna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_pi/#properties","title":"Properties","text":""},{"location":"rna_seq_project_pi/#examples","title":"Examples","text":"Value Jane Johnson"},{"location":"rna_seq_project_pi/#comments","title":"Comments","text":""},{"location":"rna_seq_project_pi/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_seq_project_pi/#schema-source","title":"Schema Source","text":""},{"location":"rna_seq_project_pi/#linkml-source","title":"LinkML Source","text":"
name: rna_seq_project_pi\ntitle: RNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: rna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_volume/","title":"Slot: RNA volume in ul (rna_volume)","text":"

URI: nmdc:rna_volume

"},{"location":"rna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_volume/#properties","title":"Properties","text":""},{"location":"rna_volume/#examples","title":"Examples","text":"Value 25"},{"location":"rna_volume/#comments","title":"Comments","text":""},{"location":"rna_volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_volume/#schema-source","title":"Schema Source","text":""},{"location":"rna_volume/#linkml-source","title":"LinkML Source","text":"
name: rna_volume\ntitle: RNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n  accepts values < 25, but JGI may refuse to process them unless permission has been\n  granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: rna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\n
"},{"location":"room_air_exch_rate/","title":"Slot: room air exchange rate (room_air_exch_rate)","text":"

The rate at which outside air replaces indoor air in a given space

URI: MIXS:0000169

"},{"location":"room_air_exch_rate/#inheritance","title":"Inheritance","text":""},{"location":"room_air_exch_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_air_exch_rate/#properties","title":"Properties","text":""},{"location":"room_air_exch_rate/#aliases","title":"Aliases","text":""},{"location":"room_air_exch_rate/#examples","title":"Examples","text":"Value"},{"location":"room_air_exch_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_air_exch_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_air_exch_rate/#schema-source","title":"Schema Source","text":""},{"location":"room_air_exch_rate/#linkml-source","title":"LinkML Source","text":"
name: room_air_exch_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: liter per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The rate at which outside air replaces indoor air in a given space\ntitle: room air exchange rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room air exchange rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000169\nalias: room_air_exch_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"room_architec_elem/","title":"Slot: room architectural elements (room_architec_elem)","text":"

The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure

URI: MIXS:0000233

"},{"location":"room_architec_elem/#inheritance","title":"Inheritance","text":""},{"location":"room_architec_elem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_architec_elem/#properties","title":"Properties","text":""},{"location":"room_architec_elem/#aliases","title":"Aliases","text":""},{"location":"room_architec_elem/#examples","title":"Examples","text":"Value"},{"location":"room_architec_elem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_architec_elem/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"room_architec_elem/#schema-source","title":"Schema Source","text":""},{"location":"room_architec_elem/#linkml-source","title":"LinkML Source","text":"
name: room_architec_elem\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The unique details and component parts that, together, form the architecture\n  of a distinguisahable space within a built structure\ntitle: room architectural elements\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room architectural elements\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000233\nalias: room_architec_elem\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"room_condt/","title":"Slot: room condition (room_condt)","text":"

The condition of the room at the time of sampling

URI: MIXS:0000822

"},{"location":"room_condt/#inheritance","title":"Inheritance","text":""},{"location":"room_condt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_condt/#properties","title":"Properties","text":""},{"location":"room_condt/#aliases","title":"Aliases","text":""},{"location":"room_condt/#examples","title":"Examples","text":"Value new"},{"location":"room_condt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_condt/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_condt/#schema-source","title":"Schema Source","text":""},{"location":"room_condt/#linkml-source","title":"LinkML Source","text":"
name: room_condt\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The condition of the room at the time of sampling\ntitle: room condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000822\nalias: room_condt\ndomain_of:\n- Biosample\nrange: room_condt_enum\nmultivalued: false\n\n
"},{"location":"room_connected/","title":"Slot: rooms connected by a doorway (room_connected)","text":"

List of rooms connected to the sampling room by a doorway

URI: MIXS:0000826

"},{"location":"room_connected/#inheritance","title":"Inheritance","text":""},{"location":"room_connected/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_connected/#properties","title":"Properties","text":""},{"location":"room_connected/#aliases","title":"Aliases","text":""},{"location":"room_connected/#examples","title":"Examples","text":"Value office"},{"location":"room_connected/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_connected/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_connected/#schema-source","title":"Schema Source","text":""},{"location":"room_connected/#linkml-source","title":"LinkML Source","text":"
name: room_connected\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of rooms connected to the sampling room by a doorway\ntitle: rooms connected by a doorway\nexamples:\n- value: office\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms connected by a doorway\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000826\nalias: room_connected\ndomain_of:\n- Biosample\nrange: room_connected_enum\nmultivalued: false\n\n
"},{"location":"room_count/","title":"Slot: room count (room_count)","text":"

The total count of rooms in the built structure including all room types

URI: MIXS:0000234

"},{"location":"room_count/#inheritance","title":"Inheritance","text":""},{"location":"room_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_count/#properties","title":"Properties","text":""},{"location":"room_count/#aliases","title":"Aliases","text":""},{"location":"room_count/#examples","title":"Examples","text":"Value"},{"location":"room_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"room_count/#schema-source","title":"Schema Source","text":""},{"location":"room_count/#linkml-source","title":"LinkML Source","text":"
name: room_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The total count of rooms in the built structure including all room types\ntitle: room count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000234\nalias: room_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_dim/","title":"Slot: room dimensions (room_dim)","text":"

The length, width and height of sampling room

URI: MIXS:0000192

"},{"location":"room_dim/#inheritance","title":"Inheritance","text":""},{"location":"room_dim/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_dim/#properties","title":"Properties","text":""},{"location":"room_dim/#aliases","title":"Aliases","text":""},{"location":"room_dim/#examples","title":"Examples","text":"Value"},{"location":"room_dim/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_dim/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_dim/#schema-source","title":"Schema Source","text":""},{"location":"room_dim/#linkml-source","title":"LinkML Source","text":"
name: room_dim\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The length, width and height of sampling room\ntitle: room dimensions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room dimensions\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\nslot_uri: MIXS:0000192\nalias: room_dim\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_door_dist/","title":"Slot: room door distance (room_door_dist)","text":"

Distance between doors (meters) in the hallway between the sampling room and adjacent rooms

URI: MIXS:0000193

"},{"location":"room_door_dist/#inheritance","title":"Inheritance","text":""},{"location":"room_door_dist/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_door_dist/#properties","title":"Properties","text":""},{"location":"room_door_dist/#aliases","title":"Aliases","text":""},{"location":"room_door_dist/#examples","title":"Examples","text":"Value"},{"location":"room_door_dist/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_door_dist/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_door_dist/#schema-source","title":"Schema Source","text":""},{"location":"room_door_dist/#linkml-source","title":"LinkML Source","text":"
name: room_door_dist\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Distance between doors (meters) in the hallway between the sampling room\n  and adjacent rooms\ntitle: room door distance\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room door distance\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000193\nalias: room_door_dist\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_door_share/","title":"Slot: rooms that share a door with sampling room (room_door_share)","text":"

List of room(s) (room number, room name) sharing a door with the sampling room

URI: MIXS:0000242

"},{"location":"room_door_share/#inheritance","title":"Inheritance","text":""},{"location":"room_door_share/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_door_share/#properties","title":"Properties","text":""},{"location":"room_door_share/#aliases","title":"Aliases","text":""},{"location":"room_door_share/#examples","title":"Examples","text":"Value"},{"location":"room_door_share/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_door_share/#annotations","title":"Annotations","text":"property value expected_value room name;room number"},{"location":"room_door_share/#schema-source","title":"Schema Source","text":""},{"location":"room_door_share/#linkml-source","title":"LinkML Source","text":"
name: room_door_share\nannotations:\n  expected_value:\n    tag: expected_value\n    value: room name;room number\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of room(s) (room number, room name) sharing a door with the sampling\n  room\ntitle: rooms that share a door with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a door with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000242\nalias: room_door_share\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_hallway/","title":"Slot: rooms that are on the same hallway (room_hallway)","text":"

List of room(s) (room number, room name) located in the same hallway as sampling room

URI: MIXS:0000238

"},{"location":"room_hallway/#inheritance","title":"Inheritance","text":""},{"location":"room_hallway/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_hallway/#properties","title":"Properties","text":""},{"location":"room_hallway/#aliases","title":"Aliases","text":""},{"location":"room_hallway/#examples","title":"Examples","text":"Value"},{"location":"room_hallway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_hallway/#annotations","title":"Annotations","text":"property value expected_value room name;room number"},{"location":"room_hallway/#schema-source","title":"Schema Source","text":""},{"location":"room_hallway/#linkml-source","title":"LinkML Source","text":"
name: room_hallway\nannotations:\n  expected_value:\n    tag: expected_value\n    value: room name;room number\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of room(s) (room number, room name) located in the same hallway\n  as sampling room\ntitle: rooms that are on the same hallway\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that are on the same hallway\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000238\nalias: room_hallway\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_loc/","title":"Slot: room location in building (room_loc)","text":"

The position of the room within the building

URI: MIXS:0000823

"},{"location":"room_loc/#inheritance","title":"Inheritance","text":""},{"location":"room_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_loc/#properties","title":"Properties","text":""},{"location":"room_loc/#aliases","title":"Aliases","text":""},{"location":"room_loc/#examples","title":"Examples","text":"Value interior room"},{"location":"room_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_loc/#schema-source","title":"Schema Source","text":""},{"location":"room_loc/#linkml-source","title":"LinkML Source","text":"
name: room_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The position of the room within the building\ntitle: room location in building\nexamples:\n- value: interior room\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room location in building\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000823\nalias: room_loc\ndomain_of:\n- Biosample\nrange: room_loc_enum\nmultivalued: false\n\n
"},{"location":"room_moist_dam_hist/","title":"Slot: room moisture damage or mold history (room_moist_dam_hist)","text":"

The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed

URI: MIXS:0000235

"},{"location":"room_moist_dam_hist/#inheritance","title":"Inheritance","text":""},{"location":"room_moist_dam_hist/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_moist_dam_hist/#properties","title":"Properties","text":""},{"location":"room_moist_dam_hist/#aliases","title":"Aliases","text":""},{"location":"room_moist_dam_hist/#examples","title":"Examples","text":"Value"},{"location":"room_moist_dam_hist/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_moist_dam_hist/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"room_moist_dam_hist/#schema-source","title":"Schema Source","text":""},{"location":"room_moist_dam_hist/#linkml-source","title":"LinkML Source","text":"
name: room_moist_dam_hist\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The history of moisture damage or mold in the past 12 months. Number\n  of events of moisture damage or mold observed\ntitle: room moisture damage or mold history\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room moisture damage or mold history\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000235\nalias: room_moist_dam_hist\ndomain_of:\n- Biosample\nrange: integer\nmultivalued: false\n\n
"},{"location":"room_net_area/","title":"Slot: room net area (room_net_area)","text":"

The net floor area of sampling room. Net area excludes wall thicknesses

URI: MIXS:0000194

"},{"location":"room_net_area/#inheritance","title":"Inheritance","text":""},{"location":"room_net_area/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_net_area/#properties","title":"Properties","text":""},{"location":"room_net_area/#aliases","title":"Aliases","text":""},{"location":"room_net_area/#examples","title":"Examples","text":"Value"},{"location":"room_net_area/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_net_area/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_net_area/#schema-source","title":"Schema Source","text":""},{"location":"room_net_area/#linkml-source","title":"LinkML Source","text":"
name: room_net_area\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square feet, square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The net floor area of sampling room. Net area excludes wall thicknesses\ntitle: room net area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room net area\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000194\nalias: room_net_area\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_occup/","title":"Slot: room occupancy (room_occup)","text":"

Count of room occupancy at time of sampling

URI: MIXS:0000236

"},{"location":"room_occup/#inheritance","title":"Inheritance","text":""},{"location":"room_occup/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_occup/#properties","title":"Properties","text":""},{"location":"room_occup/#aliases","title":"Aliases","text":""},{"location":"room_occup/#examples","title":"Examples","text":"Value"},{"location":"room_occup/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_occup/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_occup/#schema-source","title":"Schema Source","text":""},{"location":"room_occup/#linkml-source","title":"LinkML Source","text":"
name: room_occup\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Count of room occupancy at time of sampling\ntitle: room occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000236\nalias: room_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"room_samp_pos/","title":"Slot: room sampling position (room_samp_pos)","text":"

The horizontal sampling position in the room relative to architectural elements

URI: MIXS:0000824

"},{"location":"room_samp_pos/#inheritance","title":"Inheritance","text":""},{"location":"room_samp_pos/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_samp_pos/#properties","title":"Properties","text":""},{"location":"room_samp_pos/#aliases","title":"Aliases","text":""},{"location":"room_samp_pos/#examples","title":"Examples","text":"Value south corner"},{"location":"room_samp_pos/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_samp_pos/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_samp_pos/#schema-source","title":"Schema Source","text":""},{"location":"room_samp_pos/#linkml-source","title":"LinkML Source","text":"
name: room_samp_pos\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The horizontal sampling position in the room relative to architectural\n  elements\ntitle: room sampling position\nexamples:\n- value: south corner\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room sampling position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000824\nalias: room_samp_pos\ndomain_of:\n- Biosample\nrange: room_samp_pos_enum\nmultivalued: false\n\n
"},{"location":"room_type/","title":"Slot: room type (room_type)","text":"

The main purpose or activity of the sampling room. A room is any distinguishable space within a structure

URI: MIXS:0000825

"},{"location":"room_type/#inheritance","title":"Inheritance","text":""},{"location":"room_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_type/#properties","title":"Properties","text":""},{"location":"room_type/#aliases","title":"Aliases","text":""},{"location":"room_type/#examples","title":"Examples","text":"Value bathroom"},{"location":"room_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_type/#schema-source","title":"Schema Source","text":""},{"location":"room_type/#linkml-source","title":"LinkML Source","text":"
name: room_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The main purpose or activity of the sampling room. A room is any distinguishable\n  space within a structure\ntitle: room type\nexamples:\n- value: bathroom\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000825\nalias: room_type\ndomain_of:\n- Biosample\nrange: room_type_enum\nmultivalued: false\n\n
"},{"location":"room_vol/","title":"Slot: room volume (room_vol)","text":"

Volume of sampling room

URI: MIXS:0000195

"},{"location":"room_vol/#inheritance","title":"Inheritance","text":""},{"location":"room_vol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_vol/#properties","title":"Properties","text":""},{"location":"room_vol/#aliases","title":"Aliases","text":""},{"location":"room_vol/#examples","title":"Examples","text":"Value"},{"location":"room_vol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_vol/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_vol/#schema-source","title":"Schema Source","text":""},{"location":"room_vol/#linkml-source","title":"LinkML Source","text":"
name: room_vol\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic feet, cubic meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Volume of sampling room\ntitle: room volume\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room volume\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000195\nalias: room_vol\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_wall_share/","title":"Slot: rooms that share a wall with sampling room (room_wall_share)","text":"

List of room(s) (room number, room name) sharing a wall with the sampling room

URI: MIXS:0000243

"},{"location":"room_wall_share/#inheritance","title":"Inheritance","text":""},{"location":"room_wall_share/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_wall_share/#properties","title":"Properties","text":""},{"location":"room_wall_share/#aliases","title":"Aliases","text":""},{"location":"room_wall_share/#examples","title":"Examples","text":"Value"},{"location":"room_wall_share/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_wall_share/#annotations","title":"Annotations","text":"property value expected_value room name;room number"},{"location":"room_wall_share/#schema-source","title":"Schema Source","text":""},{"location":"room_wall_share/#linkml-source","title":"LinkML Source","text":"
name: room_wall_share\nannotations:\n  expected_value:\n    tag: expected_value\n    value: room name;room number\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of room(s) (room number, room name) sharing a wall with the sampling\n  room\ntitle: rooms that share a wall with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a wall with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000243\nalias: room_wall_share\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_window_count/","title":"Slot: room window count (room_window_count)","text":"

Number of windows in the room

URI: MIXS:0000237

"},{"location":"room_window_count/#inheritance","title":"Inheritance","text":""},{"location":"room_window_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_window_count/#properties","title":"Properties","text":""},{"location":"room_window_count/#aliases","title":"Aliases","text":""},{"location":"room_window_count/#examples","title":"Examples","text":"Value"},{"location":"room_window_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_window_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"room_window_count/#schema-source","title":"Schema Source","text":""},{"location":"room_window_count/#linkml-source","title":"LinkML Source","text":"
name: room_window_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Number of windows in the room\ntitle: room window count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room window count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000237\nalias: room_window_count\ndomain_of:\n- Biosample\nrange: integer\nmultivalued: false\n\n
"},{"location":"root_cond/","title":"Slot: rooting conditions (root_cond)","text":"

Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.

URI: MIXS:0001061

"},{"location":"root_cond/#inheritance","title":"Inheritance","text":""},{"location":"root_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_cond/#properties","title":"Properties","text":""},{"location":"root_cond/#aliases","title":"Aliases","text":""},{"location":"root_cond/#examples","title":"Examples","text":"Value http://himedialabs.com/TD/PT158.pdf"},{"location":"root_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_cond/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url or free text"},{"location":"root_cond/#schema-source","title":"Schema Source","text":""},{"location":"root_cond/#linkml-source","title":"LinkML Source","text":"
name: root_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url or free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Relevant rooting conditions such as field plot size, sowing density,\n  container dimensions, number of plants per container.\ntitle: rooting conditions\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001061\nalias: root_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_carbon/","title":"Slot: rooting medium carbon (root_med_carbon)","text":"

Source of organic carbon in the culture rooting medium; e.g. sucrose.

URI: MIXS:0000577

"},{"location":"root_med_carbon/#inheritance","title":"Inheritance","text":""},{"location":"root_med_carbon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_carbon/#properties","title":"Properties","text":""},{"location":"root_med_carbon/#aliases","title":"Aliases","text":""},{"location":"root_med_carbon/#examples","title":"Examples","text":"Value sucrose"},{"location":"root_med_carbon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_carbon/#annotations","title":"Annotations","text":"property value expected_value carbon source name;measurement value"},{"location":"root_med_carbon/#schema-source","title":"Schema Source","text":""},{"location":"root_med_carbon/#linkml-source","title":"LinkML Source","text":"
name: root_med_carbon\nannotations:\n  expected_value:\n    tag: expected_value\n    value: carbon source name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Source of organic carbon in the culture rooting medium; e.g. sucrose.\ntitle: rooting medium carbon\nexamples:\n- value: sucrose\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium carbon\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000577\nalias: root_med_carbon\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_macronutr/","title":"Slot: rooting medium macronutrients (root_med_macronutr)","text":"

Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).

URI: MIXS:0000578

"},{"location":"root_med_macronutr/#inheritance","title":"Inheritance","text":""},{"location":"root_med_macronutr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_macronutr/#properties","title":"Properties","text":""},{"location":"root_med_macronutr/#aliases","title":"Aliases","text":""},{"location":"root_med_macronutr/#examples","title":"Examples","text":"Value KH2PO4;170\u00ac\u2020milligram per liter"},{"location":"root_med_macronutr/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_macronutr/#annotations","title":"Annotations","text":"property value expected_value macronutrient name;measurement value"},{"location":"root_med_macronutr/#schema-source","title":"Schema Source","text":""},{"location":"root_med_macronutr/#linkml-source","title":"LinkML Source","text":"
name: root_med_macronutr\nannotations:\n  expected_value:\n    tag: expected_value\n    value: macronutrient name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of the culture rooting medium macronutrients (N,P, K, Ca,\n  Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\ntitle: rooting medium macronutrients\nexamples:\n- value: KH2PO4;170\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium macronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000578\nalias: root_med_macronutr\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_micronutr/","title":"Slot: rooting medium micronutrients (root_med_micronutr)","text":"

Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).

URI: MIXS:0000579

"},{"location":"root_med_micronutr/#inheritance","title":"Inheritance","text":""},{"location":"root_med_micronutr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_micronutr/#properties","title":"Properties","text":""},{"location":"root_med_micronutr/#aliases","title":"Aliases","text":""},{"location":"root_med_micronutr/#examples","title":"Examples","text":"Value H3BO3;6.2\u00ac\u2020milligram per liter"},{"location":"root_med_micronutr/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_micronutr/#annotations","title":"Annotations","text":"property value expected_value micronutrient name;measurement value"},{"location":"root_med_micronutr/#schema-source","title":"Schema Source","text":""},{"location":"root_med_micronutr/#linkml-source","title":"LinkML Source","text":"
name: root_med_micronutr\nannotations:\n  expected_value:\n    tag: expected_value\n    value: micronutrient name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn,\n  B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\ntitle: rooting medium micronutrients\nexamples:\n- value: H3BO3;6.2\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium micronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000579\nalias: root_med_micronutr\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_ph/","title":"Slot: rooting medium pH (root_med_ph)","text":"

pH measurement of the culture rooting medium; e.g. 5.5.

URI: MIXS:0001062

"},{"location":"root_med_ph/#inheritance","title":"Inheritance","text":""},{"location":"root_med_ph/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_ph/#properties","title":"Properties","text":""},{"location":"root_med_ph/#aliases","title":"Aliases","text":""},{"location":"root_med_ph/#examples","title":"Examples","text":"Value 7.5"},{"location":"root_med_ph/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_ph/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"root_med_ph/#schema-source","title":"Schema Source","text":""},{"location":"root_med_ph/#linkml-source","title":"LinkML Source","text":"
name: root_med_ph\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: pH measurement of the culture rooting medium; e.g. 5.5.\ntitle: rooting medium pH\nexamples:\n- value: '7.5'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001062\nalias: root_med_ph\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"root_med_regl/","title":"Slot: rooting medium regulators (root_med_regl)","text":"

Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.

URI: MIXS:0000581

"},{"location":"root_med_regl/#inheritance","title":"Inheritance","text":""},{"location":"root_med_regl/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_regl/#properties","title":"Properties","text":""},{"location":"root_med_regl/#aliases","title":"Aliases","text":""},{"location":"root_med_regl/#examples","title":"Examples","text":"Value abscisic acid;0.75 milligram per liter"},{"location":"root_med_regl/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_regl/#annotations","title":"Annotations","text":"property value expected_value regulator name;measurement value"},{"location":"root_med_regl/#schema-source","title":"Schema Source","text":""},{"location":"root_med_regl/#linkml-source","title":"LinkML Source","text":"
name: root_med_regl\nannotations:\n  expected_value:\n    tag: expected_value\n    value: regulator name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Growth regulators in the culture rooting medium such as cytokinins, auxins,\n  gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\ntitle: rooting medium regulators\nexamples:\n- value: abscisic acid;0.75 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium regulators\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000581\nalias: root_med_regl\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_solid/","title":"Slot: rooting medium solidifier (root_med_solid)","text":"

Specification of the solidifying agent in the culture rooting medium; e.g. agar.

URI: MIXS:0001063

"},{"location":"root_med_solid/#inheritance","title":"Inheritance","text":""},{"location":"root_med_solid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_solid/#properties","title":"Properties","text":""},{"location":"root_med_solid/#aliases","title":"Aliases","text":""},{"location":"root_med_solid/#examples","title":"Examples","text":"Value agar"},{"location":"root_med_solid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_solid/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"root_med_solid/#schema-source","title":"Schema Source","text":""},{"location":"root_med_solid/#linkml-source","title":"LinkML Source","text":"
name: root_med_solid\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Specification of the solidifying agent in the culture rooting medium;\n  e.g. agar.\ntitle: rooting medium solidifier\nexamples:\n- value: agar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium solidifier\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001063\nalias: root_med_solid\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_suppl/","title":"Slot: rooting medium organic supplements (root_med_suppl)","text":"

Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5\u00ac\u2020mg/L).

URI: MIXS:0000580

"},{"location":"root_med_suppl/#inheritance","title":"Inheritance","text":""},{"location":"root_med_suppl/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_suppl/#properties","title":"Properties","text":""},{"location":"root_med_suppl/#aliases","title":"Aliases","text":""},{"location":"root_med_suppl/#examples","title":"Examples","text":"Value nicotinic acid;0.5 milligram per liter"},{"location":"root_med_suppl/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_suppl/#annotations","title":"Annotations","text":"property value expected_value supplement name;measurement value"},{"location":"root_med_suppl/#schema-source","title":"Schema Source","text":""},{"location":"root_med_suppl/#linkml-source","title":"LinkML Source","text":"
name: root_med_suppl\nannotations:\n  expected_value:\n    tag: expected_value\n    value: supplement name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Organic supplements of the culture rooting medium, such as vitamins,\n  amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n  (0.5\u00ac\u2020mg/L).\ntitle: rooting medium organic supplements\nexamples:\n- value: nicotinic acid;0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium organic supplements\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000580\nalias: root_med_suppl\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"salinity/","title":"Slot: salinity (salinity)","text":"

The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.

URI: MIXS:0000183

"},{"location":"salinity/#inheritance","title":"Inheritance","text":""},{"location":"salinity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salinity/#properties","title":"Properties","text":""},{"location":"salinity/#aliases","title":"Aliases","text":""},{"location":"salinity/#examples","title":"Examples","text":"Value 25 practical salinity unit"},{"location":"salinity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"salinity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"salinity/#schema-source","title":"Schema Source","text":""},{"location":"salinity/#linkml-source","title":"LinkML Source","text":"
name: salinity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: practical salinity unit, percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The total concentration of all dissolved salts in a liquid or solid sample.\n  While salinity can be measured by a complete chemical analysis, this method is difficult\n  and time consuming. More often, it is instead derived from the conductivity measurement.\n  This is known as practical salinity. These derivations compare the specific conductance\n  of the sample to a salinity standard such as seawater.\ntitle: salinity\nexamples:\n- value: 25 practical salinity unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000183\nalias: salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"salinity_category/","title":"Slot: salinity_category","text":"

Categorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline

URI: nmdc:salinity_category

"},{"location":"salinity_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salinity_category/#properties","title":"Properties","text":""},{"location":"salinity_category/#see-also","title":"See Also","text":""},{"location":"salinity_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"salinity_category/#schema-source","title":"Schema Source","text":""},{"location":"salinity_category/#linkml-source","title":"LinkML Source","text":"
name: salinity_category\ndescription: 'Categorical description of the sample''s salinity. Examples: halophile,\n  halotolerant, hypersaline, huryhaline'\nnotes:\n- maps to gold:salinity\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-metadata/pull/297\nrank: 1000\nalias: salinity_category\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"salinity_meth/","title":"Slot: salinity method (salinity_meth)","text":"

Reference or method used in determining salinity

URI: MIXS:0000341

"},{"location":"salinity_meth/#inheritance","title":"Inheritance","text":""},{"location":"salinity_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"salinity_meth/#properties","title":"Properties","text":""},{"location":"salinity_meth/#aliases","title":"Aliases","text":""},{"location":"salinity_meth/#examples","title":"Examples","text":"Value"},{"location":"salinity_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"salinity_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"salinity_meth/#schema-source","title":"Schema Source","text":""},{"location":"salinity_meth/#linkml-source","title":"LinkML Source","text":"
name: salinity_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining salinity\ntitle: salinity method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000341\nalias: salinity_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"salt_regm/","title":"Slot: salt regimen (salt_regm)","text":"

Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens

URI: MIXS:0000582

"},{"location":"salt_regm/#inheritance","title":"Inheritance","text":""},{"location":"salt_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salt_regm/#properties","title":"Properties","text":""},{"location":"salt_regm/#aliases","title":"Aliases","text":""},{"location":"salt_regm/#examples","title":"Examples","text":"Value NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"salt_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"salt_regm/#annotations","title":"Annotations","text":"property value expected_value salt name;salt amount;treatment interval and duration"},{"location":"salt_regm/#schema-source","title":"Schema Source","text":""},{"location":"salt_regm/#linkml-source","title":"LinkML Source","text":"
name: salt_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: salt name;salt amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, microgram, mole per liter, gram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of salts as supplement to liquid\n  and soil growth media; should include the name of salt, amount administered, treatment\n  regimen including how many times the treatment was repeated, how long each treatment\n  lasted, and the start and end time of the entire treatment; can include multiple\n  salt regimens\ntitle: salt regimen\nexamples:\n- value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salt regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000582\nalias: salt_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"samp_capt_status/","title":"Slot: sample capture status (samp_capt_status)","text":"

Reason for the sample

URI: MIXS:0000860

"},{"location":"samp_capt_status/#inheritance","title":"Inheritance","text":""},{"location":"samp_capt_status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_capt_status/#properties","title":"Properties","text":""},{"location":"samp_capt_status/#aliases","title":"Aliases","text":""},{"location":"samp_capt_status/#examples","title":"Examples","text":"Value farm sample"},{"location":"samp_capt_status/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_capt_status/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_capt_status/#schema-source","title":"Schema Source","text":""},{"location":"samp_capt_status/#linkml-source","title":"LinkML Source","text":"
name: samp_capt_status\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reason for the sample\ntitle: sample capture status\nexamples:\n- value: farm sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample capture status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000860\nalias: samp_capt_status\ndomain_of:\n- Biosample\nrange: samp_capt_status_enum\nmultivalued: false\n\n
"},{"location":"samp_collec_device/","title":"Slot: sample collection device (samp_collec_device)","text":"

The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).

URI: MIXS:0000002

"},{"location":"samp_collec_device/#inheritance","title":"Inheritance","text":""},{"location":"samp_collec_device/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_collec_device/#properties","title":"Properties","text":""},{"location":"samp_collec_device/#aliases","title":"Aliases","text":""},{"location":"samp_collec_device/#examples","title":"Examples","text":"Value swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]"},{"location":"samp_collec_device/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_collec_device/#annotations","title":"Annotations","text":"property value expected_value device name"},{"location":"samp_collec_device/#schema-source","title":"Schema Source","text":""},{"location":"samp_collec_device/#linkml-source","title":"LinkML Source","text":"
name: samp_collec_device\nannotations:\n  expected_value:\n    tag: expected_value\n    value: device name\ndescription: The device used to collect an environmental sample. This field accepts\n  terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n  This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\ntitle: sample collection device\nexamples:\n- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection device\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000002\nalias: samp_collec_device\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"samp_collec_method/","title":"Slot: sample collection method (samp_collec_method)","text":"

The method employed for collecting the sample.

URI: MIXS:0001225

"},{"location":"samp_collec_method/#inheritance","title":"Inheritance","text":""},{"location":"samp_collec_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_collec_method/#properties","title":"Properties","text":""},{"location":"samp_collec_method/#aliases","title":"Aliases","text":""},{"location":"samp_collec_method/#examples","title":"Examples","text":"Value swabbing"},{"location":"samp_collec_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_collec_method/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url , or text"},{"location":"samp_collec_method/#schema-source","title":"Schema Source","text":""},{"location":"samp_collec_method/#linkml-source","title":"LinkML Source","text":"
name: samp_collec_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url , or text\ndescription: The method employed for collecting the sample.\ntitle: sample collection method\nexamples:\n- value: swabbing\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection method\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001225\nalias: samp_collec_method\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"samp_collect_point/","title":"Slot: sample collection point (samp_collect_point)","text":"

Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0001015

"},{"location":"samp_collect_point/#inheritance","title":"Inheritance","text":""},{"location":"samp_collect_point/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_collect_point/#properties","title":"Properties","text":""},{"location":"samp_collect_point/#aliases","title":"Aliases","text":""},{"location":"samp_collect_point/#examples","title":"Examples","text":"Value well"},{"location":"samp_collect_point/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_collect_point/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_collect_point/#schema-source","title":"Schema Source","text":""},{"location":"samp_collect_point/#linkml-source","title":"LinkML Source","text":"
name: samp_collect_point\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sampling point on the asset were sample was collected (e.g. Wellhead,\n  storage tank, separator, etc). If \"other\" is specified, please propose entry in\n  \"additional info\" field\ntitle: sample collection point\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001015\nalias: samp_collect_point\ndomain_of:\n- Biosample\nrange: samp_collect_point_enum\nmultivalued: false\n\n
"},{"location":"samp_dis_stage/","title":"Slot: sample disease stage (samp_dis_stage)","text":"

Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.

URI: MIXS:0000249

"},{"location":"samp_dis_stage/#inheritance","title":"Inheritance","text":""},{"location":"samp_dis_stage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_dis_stage/#properties","title":"Properties","text":""},{"location":"samp_dis_stage/#aliases","title":"Aliases","text":""},{"location":"samp_dis_stage/#examples","title":"Examples","text":"Value infection"},{"location":"samp_dis_stage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_dis_stage/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_dis_stage/#schema-source","title":"Schema Source","text":""},{"location":"samp_dis_stage/#linkml-source","title":"LinkML Source","text":"
name: samp_dis_stage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Stage of the disease at the time of sample collection, e.g. inoculation,\n  penetration, infection, growth and reproduction, dissemination of pathogen.\ntitle: sample disease stage\nexamples:\n- value: infection\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample disease stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000249\nalias: samp_dis_stage\ndomain_of:\n- Biosample\nrange: samp_dis_stage_enum\nmultivalued: false\n\n
"},{"location":"samp_floor/","title":"Slot: sampling floor (samp_floor)","text":"

The floor of the building, where the sampling room is located

URI: MIXS:0000828

"},{"location":"samp_floor/#inheritance","title":"Inheritance","text":""},{"location":"samp_floor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_floor/#properties","title":"Properties","text":""},{"location":"samp_floor/#aliases","title":"Aliases","text":""},{"location":"samp_floor/#examples","title":"Examples","text":"Value 4th floor"},{"location":"samp_floor/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_floor/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_floor/#schema-source","title":"Schema Source","text":""},{"location":"samp_floor/#linkml-source","title":"LinkML Source","text":"
name: samp_floor\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The floor of the building, where the sampling room is located\ntitle: sampling floor\nexamples:\n- value: 4th floor\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling floor\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000828\nalias: samp_floor\ndomain_of:\n- Biosample\nrange: samp_floor_enum\nmultivalued: false\n\n
"},{"location":"samp_loc_corr_rate/","title":"Slot: corrosion rate at sample location (samp_loc_corr_rate)","text":"

Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays

URI: MIXS:0000136

"},{"location":"samp_loc_corr_rate/#inheritance","title":"Inheritance","text":""},{"location":"samp_loc_corr_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_loc_corr_rate/#properties","title":"Properties","text":""},{"location":"samp_loc_corr_rate/#aliases","title":"Aliases","text":""},{"location":"samp_loc_corr_rate/#examples","title":"Examples","text":"Value"},{"location":"samp_loc_corr_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_loc_corr_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value range"},{"location":"samp_loc_corr_rate/#schema-source","title":"Schema Source","text":""},{"location":"samp_loc_corr_rate/#linkml-source","title":"LinkML Source","text":"
name: samp_loc_corr_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter per year\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Metal corrosion rate is the speed of metal deterioration due to environmental\n  conditions. As environmental conditions change corrosion rates change accordingly.\n  Therefore, long term corrosion rates are generally more informative than short term\n  rates and for that reason they are preferred during reporting. In the case of suspected\n  MIC, corrosion rate measurements at the time of sampling might provide insights\n  into the involvement of certain microbial community members in MIC as well as potential\n  microbial interplays\ntitle: corrosion rate at sample location\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- corrosion rate at sample location\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000136\nalias: samp_loc_corr_rate\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_mat_process/","title":"Slot: sample material processing (samp_mat_process)","text":"

A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.

URI: MIXS:0000016

"},{"location":"samp_mat_process/#inheritance","title":"Inheritance","text":""},{"location":"samp_mat_process/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_mat_process/#properties","title":"Properties","text":""},{"location":"samp_mat_process/#aliases","title":"Aliases","text":""},{"location":"samp_mat_process/#examples","title":"Examples","text":"Value filtering of seawater, storing samples in ethanol"},{"location":"samp_mat_process/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_mat_process/#annotations","title":"Annotations","text":"property value expected_value text"},{"location":"samp_mat_process/#schema-source","title":"Schema Source","text":""},{"location":"samp_mat_process/#linkml-source","title":"LinkML Source","text":"
name: samp_mat_process\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text\ndescription: A brief description of any processing applied to the sample during or\n  after retrieving the sample from environment, or a link to the relevant protocol(s)\n  performed.\ntitle: sample material processing\nexamples:\n- value: filtering of seawater, storing samples in ethanol\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample material processing\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000016\nalias: samp_mat_process\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"samp_md/","title":"Slot: sample measured depth (samp_md)","text":"

In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000413

"},{"location":"samp_md/#inheritance","title":"Inheritance","text":""},{"location":"samp_md/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_md/#properties","title":"Properties","text":""},{"location":"samp_md/#aliases","title":"Aliases","text":""},{"location":"samp_md/#examples","title":"Examples","text":"Value 1534 meter;MSL"},{"location":"samp_md/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_md/#annotations","title":"Annotations","text":"property value expected_value measurement value;enumeration"},{"location":"samp_md/#schema-source","title":"Schema Source","text":""},{"location":"samp_md/#linkml-source","title":"LinkML Source","text":"
name: samp_md\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;enumeration\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: In non deviated well, measured depth is equal to the true vertical depth,\n  TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the\n  MD is the length of trajectory of the borehole measured from the same reference\n  or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary\n  table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified,\n  please propose entry in \"additional info\" field\ntitle: sample measured depth\nexamples:\n- value: 1534 meter;MSL\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample measured depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000413\nalias: samp_md\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"samp_name/","title":"Slot: sample name (samp_name)","text":"

A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.

URI: MIXS:0001107

"},{"location":"samp_name/#inheritance","title":"Inheritance","text":""},{"location":"samp_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_name/#properties","title":"Properties","text":""},{"location":"samp_name/#aliases","title":"Aliases","text":""},{"location":"samp_name/#examples","title":"Examples","text":"Value ISDsoil1"},{"location":"samp_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_name/#annotations","title":"Annotations","text":"property value expected_value text"},{"location":"samp_name/#schema-source","title":"Schema Source","text":""},{"location":"samp_name/#linkml-source","title":"LinkML Source","text":"
name: samp_name\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text\ndescription: A local identifier or name that for the material sample used for extracting\n  nucleic acids, and subsequent sequencing. It can refer either to the original material\n  collected or to any derived sub-samples. It can have any format, but we suggest\n  that you make it concise, unique and consistent within your lab, and as informative\n  as possible. INSDC requires every sample name from a single Submitter to be unique.\n  Use of a globally unique identifier for the field source_mat_id is recommended in\n  addition to sample_name.\ntitle: sample name\nexamples:\n- value: ISDsoil1\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample name\nrank: 1000\nis_a: investigation field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001107\nalias: samp_name\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"samp_preserv/","title":"Slot: preservative added to sample (samp_preserv)","text":"

Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)

URI: MIXS:0000463

"},{"location":"samp_preserv/#inheritance","title":"Inheritance","text":""},{"location":"samp_preserv/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_preserv/#properties","title":"Properties","text":""},{"location":"samp_preserv/#aliases","title":"Aliases","text":""},{"location":"samp_preserv/#examples","title":"Examples","text":"Value"},{"location":"samp_preserv/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_preserv/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"samp_preserv/#schema-source","title":"Schema Source","text":""},{"location":"samp_preserv/#linkml-source","title":"LinkML Source","text":"
name: samp_preserv\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milliliter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n  etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\ntitle: preservative added to sample\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- preservative added to sample\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000463\nalias: samp_preserv\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_room_id/","title":"Slot: sampling room ID or name (samp_room_id)","text":"

Sampling room number. This ID should be consistent with the designations on the building floor plans

URI: MIXS:0000244

"},{"location":"samp_room_id/#inheritance","title":"Inheritance","text":""},{"location":"samp_room_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_room_id/#properties","title":"Properties","text":""},{"location":"samp_room_id/#aliases","title":"Aliases","text":""},{"location":"samp_room_id/#examples","title":"Examples","text":"Value"},{"location":"samp_room_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_room_id/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"samp_room_id/#schema-source","title":"Schema Source","text":""},{"location":"samp_room_id/#linkml-source","title":"LinkML Source","text":"
name: samp_room_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sampling room number. This ID should be consistent with the designations\n  on the building floor plans\ntitle: sampling room ID or name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling room ID or name\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000244\nalias: samp_room_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_size/","title":"Slot: amount or size of sample collected (samp_size)","text":"

The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.

URI: MIXS:0000001

"},{"location":"samp_size/#inheritance","title":"Inheritance","text":""},{"location":"samp_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_size/#properties","title":"Properties","text":""},{"location":"samp_size/#aliases","title":"Aliases","text":""},{"location":"samp_size/#examples","title":"Examples","text":"Value 5 liter"},{"location":"samp_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_size/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"samp_size/#schema-source","title":"Schema Source","text":""},{"location":"samp_size/#linkml-source","title":"LinkML Source","text":"
name: samp_size\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millliter, gram, milligram, liter\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n  collected.\ntitle: amount or size of sample collected\nexamples:\n- value: 5 liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount or size of sample collected\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000001\nalias: samp_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"samp_sort_meth/","title":"Slot: sample size sorting method (samp_sort_meth)","text":"

Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.

URI: MIXS:0000216

"},{"location":"samp_sort_meth/#inheritance","title":"Inheritance","text":""},{"location":"samp_sort_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_sort_meth/#properties","title":"Properties","text":""},{"location":"samp_sort_meth/#aliases","title":"Aliases","text":""},{"location":"samp_sort_meth/#examples","title":"Examples","text":"Value"},{"location":"samp_sort_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_sort_meth/#annotations","title":"Annotations","text":"property value expected_value description of method"},{"location":"samp_sort_meth/#schema-source","title":"Schema Source","text":""},{"location":"samp_sort_meth/#linkml-source","title":"LinkML Source","text":"
name: samp_sort_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: description of method\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Method by which samples are sorted; open face filter collecting total\n  suspended particles, prefilter to remove particles larger than X micrometers in\n  diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade\n  impactor.\ntitle: sample size sorting method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample size sorting method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000216\nalias: samp_sort_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"samp_store_dur/","title":"Slot: sample storage duration (samp_store_dur)","text":"

Duration for which the sample was stored

URI: MIXS:0000116

"},{"location":"samp_store_dur/#inheritance","title":"Inheritance","text":""},{"location":"samp_store_dur/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_store_dur/#properties","title":"Properties","text":""},{"location":"samp_store_dur/#aliases","title":"Aliases","text":""},{"location":"samp_store_dur/#examples","title":"Examples","text":"Value P1Y6M"},{"location":"samp_store_dur/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_store_dur/#annotations","title":"Annotations","text":"property value expected_value duration"},{"location":"samp_store_dur/#schema-source","title":"Schema Source","text":""},{"location":"samp_store_dur/#linkml-source","title":"LinkML Source","text":"
name: samp_store_dur\nannotations:\n  expected_value:\n    tag: expected_value\n    value: duration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Duration for which the sample was stored\ntitle: sample storage duration\nexamples:\n- value: P1Y6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage duration\nrank: 1000\nis_a: core field\nstring_serialization: '{duration}'\nslot_uri: MIXS:0000116\nalias: samp_store_dur\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_store_loc/","title":"Slot: sample storage location (samp_store_loc)","text":"

Location at which sample was stored, usually name of a specific freezer/room

URI: MIXS:0000755

"},{"location":"samp_store_loc/#inheritance","title":"Inheritance","text":""},{"location":"samp_store_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_store_loc/#properties","title":"Properties","text":""},{"location":"samp_store_loc/#aliases","title":"Aliases","text":""},{"location":"samp_store_loc/#examples","title":"Examples","text":"Value Freezer no:5"},{"location":"samp_store_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_store_loc/#annotations","title":"Annotations","text":"property value expected_value location name"},{"location":"samp_store_loc/#schema-source","title":"Schema Source","text":""},{"location":"samp_store_loc/#linkml-source","title":"LinkML Source","text":"
name: samp_store_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: location name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Location at which sample was stored, usually name of a specific freezer/room\ntitle: sample storage location\nexamples:\n- value: Freezer no:5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage location\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000755\nalias: samp_store_loc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_store_temp/","title":"Slot: sample storage temperature (samp_store_temp)","text":"

Temperature at which sample was stored, e.g. -80 degree Celsius

URI: MIXS:0000110

"},{"location":"samp_store_temp/#inheritance","title":"Inheritance","text":""},{"location":"samp_store_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_store_temp/#properties","title":"Properties","text":""},{"location":"samp_store_temp/#aliases","title":"Aliases","text":""},{"location":"samp_store_temp/#examples","title":"Examples","text":"Value -80 degree Celsius"},{"location":"samp_store_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_store_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"samp_store_temp/#schema-source","title":"Schema Source","text":""},{"location":"samp_store_temp/#linkml-source","title":"LinkML Source","text":"
name: samp_store_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Temperature at which sample was stored, e.g. -80 degree Celsius\ntitle: sample storage temperature\nexamples:\n- value: -80 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000110\nalias: samp_store_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"samp_subtype/","title":"Slot: sample subtype (samp_subtype)","text":"

Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000999

"},{"location":"samp_subtype/#inheritance","title":"Inheritance","text":""},{"location":"samp_subtype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_subtype/#properties","title":"Properties","text":""},{"location":"samp_subtype/#aliases","title":"Aliases","text":""},{"location":"samp_subtype/#examples","title":"Examples","text":"Value biofilm"},{"location":"samp_subtype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_subtype/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_subtype/#schema-source","title":"Schema Source","text":""},{"location":"samp_subtype/#linkml-source","title":"LinkML Source","text":"
name: samp_subtype\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of sample sub-type. For example if \"sample type\" is \"Produced Water\"\n  then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please\n  propose entry in \"additional info\" field\ntitle: sample subtype\nexamples:\n- value: biofilm\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample subtype\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000999\nalias: samp_subtype\ndomain_of:\n- Biosample\nrange: samp_subtype_enum\nmultivalued: false\n\n
"},{"location":"samp_taxon_id/","title":"Slot: Taxonomy ID of DNA sample (samp_taxon_id)","text":"

NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample' for negative controls.

URI: MIXS:0001320

"},{"location":"samp_taxon_id/#inheritance","title":"Inheritance","text":""},{"location":"samp_taxon_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_taxon_id/#properties","title":"Properties","text":""},{"location":"samp_taxon_id/#aliases","title":"Aliases","text":""},{"location":"samp_taxon_id/#comments","title":"Comments","text":""},{"location":"samp_taxon_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_taxon_id/#annotations","title":"Annotations","text":"property value expected_value Taxonomy ID"},{"location":"samp_taxon_id/#schema-source","title":"Schema Source","text":""},{"location":"samp_taxon_id/#linkml-source","title":"LinkML Source","text":"
name: samp_taxon_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: Taxonomy ID\ndescription: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa sample.\n  Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample'\n  for negative controls.\ntitle: Taxonomy ID of DNA sample\ncomments:\n- coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Taxonomy ID of DNA sample\nrank: 1000\nis_a: investigation field\nslot_uri: MIXS:0001320\nalias: samp_taxon_id\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"samp_time_out/","title":"Slot: sampling time outside (samp_time_out)","text":"

The recent and long term history of outside sampling

URI: MIXS:0000196

"},{"location":"samp_time_out/#inheritance","title":"Inheritance","text":""},{"location":"samp_time_out/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_time_out/#properties","title":"Properties","text":""},{"location":"samp_time_out/#aliases","title":"Aliases","text":""},{"location":"samp_time_out/#examples","title":"Examples","text":"Value"},{"location":"samp_time_out/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_time_out/#annotations","title":"Annotations","text":"property value expected_value time"},{"location":"samp_time_out/#schema-source","title":"Schema Source","text":""},{"location":"samp_time_out/#linkml-source","title":"LinkML Source","text":"
name: samp_time_out\nannotations:\n  expected_value:\n    tag: expected_value\n    value: time\n  preferred_unit:\n    tag: preferred_unit\n    value: hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The recent and long term history of outside sampling\ntitle: sampling time outside\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling time outside\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000196\nalias: samp_time_out\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_transport_cond/","title":"Slot: sample transport conditions (samp_transport_cond)","text":"

Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)

URI: MIXS:0000410

"},{"location":"samp_transport_cond/#inheritance","title":"Inheritance","text":""},{"location":"samp_transport_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_transport_cond/#properties","title":"Properties","text":""},{"location":"samp_transport_cond/#aliases","title":"Aliases","text":""},{"location":"samp_transport_cond/#examples","title":"Examples","text":"Value 5 days;-20 degree Celsius"},{"location":"samp_transport_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_transport_cond/#annotations","title":"Annotations","text":"property value expected_value measurement value;measurement value"},{"location":"samp_transport_cond/#schema-source","title":"Schema Source","text":""},{"location":"samp_transport_cond/#linkml-source","title":"LinkML Source","text":"
name: samp_transport_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: days;degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sample transport duration (in days or hrs) and temperature the sample\n  was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\ntitle: sample transport conditions\nexamples:\n- value: 5 days;-20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample transport conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000410\nalias: samp_transport_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_tvdss/","title":"Slot: sample true vertical depth subsea (samp_tvdss)","text":"

Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m

URI: MIXS:0000409

"},{"location":"samp_tvdss/#inheritance","title":"Inheritance","text":""},{"location":"samp_tvdss/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_tvdss/#properties","title":"Properties","text":""},{"location":"samp_tvdss/#aliases","title":"Aliases","text":""},{"location":"samp_tvdss/#examples","title":"Examples","text":"Value"},{"location":"samp_tvdss/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_tvdss/#annotations","title":"Annotations","text":"property value expected_value measurement value or measurement value range"},{"location":"samp_tvdss/#schema-source","title":"Schema Source","text":""},{"location":"samp_tvdss/#linkml-source","title":"LinkML Source","text":"
name: samp_tvdss\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value or measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Depth of the sample i.e. The vertical distance between the sea level\n  and the sampled position in the subsurface. Depth can be reported as an interval\n  for subsurface samples e.g. 1325.75-1362.25 m\ntitle: sample true vertical depth subsea\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample true vertical depth subsea\nrank: 1000\nis_a: core field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000409\nalias: samp_tvdss\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_type/","title":"Slot: sample type (samp_type)","text":"

The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).

URI: MIXS:0000998

"},{"location":"samp_type/#inheritance","title":"Inheritance","text":""},{"location":"samp_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_type/#properties","title":"Properties","text":""},{"location":"samp_type/#aliases","title":"Aliases","text":""},{"location":"samp_type/#examples","title":"Examples","text":"Value built environment sample [GENEPIO:0001248]"},{"location":"samp_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_type/#annotations","title":"Annotations","text":"property value expected_value GENEPIO:0001246"},{"location":"samp_type/#schema-source","title":"Schema Source","text":""},{"location":"samp_type/#linkml-source","title":"LinkML Source","text":"
name: samp_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: GENEPIO:0001246\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of material from which the sample was obtained. For the Hydrocarbon\n  package, samples include types like core, rock trimmings, drill cuttings, piping\n  section, coupon, pigging debris, solid deposit, produced fluid, produced water,\n  injected water, swabs, etc. For the Food Package, samples are usually categorized\n  as food, body products or tissues, or environmental material. This field accepts\n  terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\ntitle: sample type\nexamples:\n- value: built environment sample [GENEPIO:0001248]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000998\nalias: samp_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_vol_we_dna_ext/","title":"Slot: sample volume or weight for DNA extraction (samp_vol_we_dna_ext)","text":"

Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).

URI: MIXS:0000111

"},{"location":"samp_vol_we_dna_ext/#inheritance","title":"Inheritance","text":""},{"location":"samp_vol_we_dna_ext/#properties","title":"Properties","text":""},{"location":"samp_vol_we_dna_ext/#aliases","title":"Aliases","text":""},{"location":"samp_vol_we_dna_ext/#examples","title":"Examples","text":"Value 1500 milliliter"},{"location":"samp_vol_we_dna_ext/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_vol_we_dna_ext/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"samp_vol_we_dna_ext/#schema-source","title":"Schema Source","text":""},{"location":"samp_vol_we_dna_ext/#linkml-source","title":"LinkML Source","text":"
name: samp_vol_we_dna_ext\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millliter, gram, milligram, square centimeter\ndescription: 'Volume (ml) or mass (g) of total collected sample processed for DNA\n  extraction. Note: total sample collected should be entered under the term Sample\n  Size (MIXS:0000001).'\ntitle: sample volume or weight for DNA extraction\nexamples:\n- value: 1500 milliliter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample volume or weight for DNA extraction\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000111\nalias: samp_vol_we_dna_ext\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"samp_weather/","title":"Slot: sampling day weather (samp_weather)","text":"

The weather on the sampling day

URI: MIXS:0000827

"},{"location":"samp_weather/#inheritance","title":"Inheritance","text":""},{"location":"samp_weather/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_weather/#properties","title":"Properties","text":""},{"location":"samp_weather/#aliases","title":"Aliases","text":""},{"location":"samp_weather/#examples","title":"Examples","text":"Value foggy"},{"location":"samp_weather/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_weather/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_weather/#schema-source","title":"Schema Source","text":""},{"location":"samp_weather/#linkml-source","title":"LinkML Source","text":"
name: samp_weather\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The weather on the sampling day\ntitle: sampling day weather\nexamples:\n- value: foggy\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling day weather\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000827\nalias: samp_weather\ndomain_of:\n- Biosample\nrange: samp_weather_enum\nmultivalued: false\n\n
"},{"location":"samp_well_name/","title":"Slot: sample well name (samp_well_name)","text":"

Name of the well (e.g. BXA1123) where sample was taken

URI: MIXS:0000296

"},{"location":"samp_well_name/#inheritance","title":"Inheritance","text":""},{"location":"samp_well_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_well_name/#properties","title":"Properties","text":""},{"location":"samp_well_name/#aliases","title":"Aliases","text":""},{"location":"samp_well_name/#examples","title":"Examples","text":"Value"},{"location":"samp_well_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_well_name/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"samp_well_name/#schema-source","title":"Schema Source","text":""},{"location":"samp_well_name/#linkml-source","title":"LinkML Source","text":"
name: samp_well_name\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of the well (e.g. BXA1123) where sample was taken\ntitle: sample well name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample well name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000296\nalias: samp_well_name\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"sample_collection_day/","title":"Slot: sample_collection_day","text":"

URI: nmdc:sample_collection_day

"},{"location":"sample_collection_day/#properties","title":"Properties","text":""},{"location":"sample_collection_day/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_day/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_day/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_day\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_day\nrange: integer\n\n
"},{"location":"sample_collection_hour/","title":"Slot: sample_collection_hour","text":"

URI: nmdc:sample_collection_hour

"},{"location":"sample_collection_hour/#properties","title":"Properties","text":""},{"location":"sample_collection_hour/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_hour/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_hour/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_hour\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_hour\nrange: integer\n\n
"},{"location":"sample_collection_minute/","title":"Slot: sample_collection_minute","text":"

URI: nmdc:sample_collection_minute

"},{"location":"sample_collection_minute/#properties","title":"Properties","text":""},{"location":"sample_collection_minute/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_minute/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_minute/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_minute\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_minute\nrange: integer\n\n
"},{"location":"sample_collection_month/","title":"Slot: sample_collection_month","text":"

URI: nmdc:sample_collection_month

"},{"location":"sample_collection_month/#properties","title":"Properties","text":""},{"location":"sample_collection_month/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_month/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_month/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_month\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_month\nrange: string\n\n
"},{"location":"sample_collection_site/","title":"Slot: sample_collection_site","text":"

URI: nmdc:sample_collection_site

"},{"location":"sample_collection_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_collection_site/#properties","title":"Properties","text":""},{"location":"sample_collection_site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_site/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_site/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_site\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_site\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"sample_collection_year/","title":"Slot: sample_collection_year","text":"

URI: nmdc:sample_collection_year

"},{"location":"sample_collection_year/#properties","title":"Properties","text":""},{"location":"sample_collection_year/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_year/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_year/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_year\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_year\nrange: integer\n\n
"},{"location":"sample_link/","title":"Slot: sample linkage (sample_link)","text":"

A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.

URI: nmdc:sample_link

"},{"location":"sample_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_link/#properties","title":"Properties","text":""},{"location":"sample_link/#examples","title":"Examples","text":"Value IGSN:DSJ0284"},{"location":"sample_link/#comments","title":"Comments","text":""},{"location":"sample_link/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_link/#schema-source","title":"Schema Source","text":""},{"location":"sample_link/#linkml-source","title":"LinkML Source","text":"
name: sample_link\ndescription: A unique identifier to assign parent-child, subsample, or sibling samples.\n  This is relevant when a sample or other material was used to generate the new sample.\ntitle: sample linkage\ncomments:\n- 'This field allows multiple entries separated by ; (Examples: Soil collected from\n  the field will link with the soil used in an incubation. The soil a plant was grown\n  in links to the plant sample. An original culture sample was transferred to a new\n  vial and generated a new sample)'\nexamples:\n- value: IGSN:DSJ0284\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{text}:{text}'\nalias: sample_link\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: string\nrecommended: true\nmultivalued: true\n\n
"},{"location":"sample_shipped/","title":"Slot: sample shipped amount (sample_shipped)","text":"

The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.

URI: nmdc:sample_shipped

"},{"location":"sample_shipped/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_shipped/#properties","title":"Properties","text":""},{"location":"sample_shipped/#examples","title":"Examples","text":"Value 15 g 100 uL 5 mL"},{"location":"sample_shipped/#comments","title":"Comments","text":""},{"location":"sample_shipped/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_shipped/#schema-source","title":"Schema Source","text":""},{"location":"sample_shipped/#linkml-source","title":"LinkML Source","text":"
name: sample_shipped\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n  sent to EMSL.\ntitle: sample shipped amount\ncomments:\n- This field is only required when completing metadata for samples being submitted\n  to EMSL for analyses.\nexamples:\n- value: 15 g\n- value: 100 uL\n- value: 5 mL\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{float} {unit}'\nalias: sample_shipped\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"sample_state_information/","title":"Slot: sample_state_information","text":"

The chemical phase of a pure sample, or the state of a mixed sample

URI: nmdc:sample_state_information

"},{"location":"sample_state_information/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"sample_state_information/#properties","title":"Properties","text":""},{"location":"sample_state_information/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_state_information/#schema-source","title":"Schema Source","text":""},{"location":"sample_state_information/#linkml-source","title":"LinkML Source","text":"
name: sample_state_information\ndescription: The chemical phase of a pure sample, or the state of a mixed sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_state_information\ndomain_of:\n- PortionOfSubstance\nrange: SampleStateEnum\n\n
"},{"location":"sample_type/","title":"Slot: sample type (sample_type)","text":"

Type of sample being submitted

URI: nmdc:sample_type

"},{"location":"sample_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_type/#properties","title":"Properties","text":""},{"location":"sample_type/#examples","title":"Examples","text":"Value water extracted soil"},{"location":"sample_type/#comments","title":"Comments","text":""},{"location":"sample_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_type/#schema-source","title":"Schema Source","text":""},{"location":"sample_type/#linkml-source","title":"LinkML Source","text":"
name: sample_type\ndescription: Type of sample being submitted\ntitle: sample type\ncomments:\n- This can vary from 'environmental package' if the sample is an extraction.\nexamples:\n- value: water extracted soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nalias: sample_type\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: SampleTypeEnum\nrecommended: true\n\n
"},{"location":"sampled_portion/","title":"Slot: sampled_portion","text":"

The portion of the sample that is taken for downstream activity.

URI: nmdc:sampled_portion

"},{"location":"sampled_portion/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no"},{"location":"sampled_portion/#properties","title":"Properties","text":""},{"location":"sampled_portion/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sampled_portion/#schema-source","title":"Schema Source","text":""},{"location":"sampled_portion/#linkml-source","title":"LinkML Source","text":"
name: sampled_portion\ndescription: The portion of the sample that is taken for downstream activity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sampled_portion\ndomain_of:\n- SubSamplingProcess\nrange: SamplePortionEnum\nmultivalued: true\n\n
"},{"location":"saturates_pc/","title":"Slot: saturates wt% (saturates_pc)","text":"

Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)

URI: MIXS:0000131

"},{"location":"saturates_pc/#inheritance","title":"Inheritance","text":""},{"location":"saturates_pc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"saturates_pc/#properties","title":"Properties","text":""},{"location":"saturates_pc/#aliases","title":"Aliases","text":""},{"location":"saturates_pc/#examples","title":"Examples","text":"Value"},{"location":"saturates_pc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"saturates_pc/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"saturates_pc/#schema-source","title":"Schema Source","text":""},{"location":"saturates_pc/#linkml-source","title":"LinkML Source","text":"
name: saturates_pc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n  that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n  There are three main methods to obtain SARA results. The most popular one is known\n  as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: saturates wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- saturates wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000131\nalias: saturates_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"scaf_bp/","title":"Slot: scaf_bp","text":"

Total size in bp of all scaffolds.

URI: nmdc:scaf_bp

"},{"location":"scaf_bp/#inheritance","title":"Inheritance","text":""},{"location":"scaf_bp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_bp/#properties","title":"Properties","text":""},{"location":"scaf_bp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_bp/#schema-source","title":"Schema Source","text":""},{"location":"scaf_bp/#linkml-source","title":"LinkML Source","text":"
name: scaf_bp\ndescription: Total size in bp of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_l50/","title":"Slot: scaf_l50","text":"

Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.

URI: nmdc:scaf_l50

"},{"location":"scaf_l50/#inheritance","title":"Inheritance","text":""},{"location":"scaf_l50/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_l50/#properties","title":"Properties","text":""},{"location":"scaf_l50/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_l50/#schema-source","title":"Schema Source","text":""},{"location":"scaf_l50/#linkml-source","title":"LinkML Source","text":"
name: scaf_l50\ndescription: Given a set of scaffolds, the L50 is defined as the sequence length of\n  the shortest scaffold at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_l90/","title":"Slot: scaf_l90","text":"

The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.

URI: nmdc:scaf_l90

"},{"location":"scaf_l90/#inheritance","title":"Inheritance","text":""},{"location":"scaf_l90/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_l90/#properties","title":"Properties","text":""},{"location":"scaf_l90/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_l90/#schema-source","title":"Schema Source","text":""},{"location":"scaf_l90/#linkml-source","title":"LinkML Source","text":"
name: scaf_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n  length for which the collection of all scaffolds of that length or longer contains\n  at least 90% of the sum of the lengths of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_l_gt50k/","title":"Slot: scaf_l_gt50k","text":"

Total size in bp of all scaffolds greater than 50 KB.

URI: nmdc:scaf_l_gt50k

"},{"location":"scaf_l_gt50k/#inheritance","title":"Inheritance","text":""},{"location":"scaf_l_gt50k/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_l_gt50k/#properties","title":"Properties","text":""},{"location":"scaf_l_gt50k/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_l_gt50k/#schema-source","title":"Schema Source","text":""},{"location":"scaf_l_gt50k/#linkml-source","title":"LinkML Source","text":"
name: scaf_l_gt50k\ndescription: Total size in bp of all scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_logsum/","title":"Slot: scaf_logsum","text":"

The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase

URI: nmdc:scaf_logsum

"},{"location":"scaf_logsum/#inheritance","title":"Inheritance","text":""},{"location":"scaf_logsum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_logsum/#properties","title":"Properties","text":""},{"location":"scaf_logsum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_logsum/#schema-source","title":"Schema Source","text":""},{"location":"scaf_logsum/#linkml-source","title":"LinkML Source","text":"
name: scaf_logsum\ndescription: The sum of the (length*log(length)) of all scaffolds, times some constant.  Increase\n  the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_max/","title":"Slot: scaf_max","text":"

Maximum scaffold length.

URI: nmdc:scaf_max

"},{"location":"scaf_max/#inheritance","title":"Inheritance","text":""},{"location":"scaf_max/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_max/#properties","title":"Properties","text":""},{"location":"scaf_max/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_max/#schema-source","title":"Schema Source","text":""},{"location":"scaf_max/#linkml-source","title":"LinkML Source","text":"
name: scaf_max\ndescription: Maximum scaffold length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_n50/","title":"Slot: scaf_n50","text":"

Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.

URI: nmdc:scaf_n50

"},{"location":"scaf_n50/#inheritance","title":"Inheritance","text":""},{"location":"scaf_n50/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_n50/#properties","title":"Properties","text":""},{"location":"scaf_n50/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_n50/#schema-source","title":"Schema Source","text":""},{"location":"scaf_n50/#linkml-source","title":"LinkML Source","text":"
name: scaf_n50\ndescription: Given a set of scaffolds, each with its own length, the N50 count is\n  defined as the smallest number of scaffolds whose length sum makes up half of genome\n  size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_n90/","title":"Slot: scaf_n90","text":"

Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.

URI: nmdc:scaf_n90

"},{"location":"scaf_n90/#inheritance","title":"Inheritance","text":""},{"location":"scaf_n90/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_n90/#properties","title":"Properties","text":""},{"location":"scaf_n90/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_n90/#schema-source","title":"Schema Source","text":""},{"location":"scaf_n90/#linkml-source","title":"LinkML Source","text":"
name: scaf_n90\ndescription: Given a set of scaffolds, each with its own length, the N90 count is\n  defined as the smallest number of scaffolds whose length sum makes up 90% of genome\n  size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_n_gt50k/","title":"Slot: scaf_n_gt50k","text":"

Total sequence count of scaffolds greater than 50 KB.

URI: nmdc:scaf_n_gt50k

"},{"location":"scaf_n_gt50k/#inheritance","title":"Inheritance","text":""},{"location":"scaf_n_gt50k/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_n_gt50k/#properties","title":"Properties","text":""},{"location":"scaf_n_gt50k/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_n_gt50k/#schema-source","title":"Schema Source","text":""},{"location":"scaf_n_gt50k/#linkml-source","title":"LinkML Source","text":"
name: scaf_n_gt50k\ndescription: Total sequence count of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_pct_gt50k/","title":"Slot: scaf_pct_gt50k","text":"

Total sequence size percentage of scaffolds greater than 50 KB.

URI: nmdc:scaf_pct_gt50k

"},{"location":"scaf_pct_gt50k/#inheritance","title":"Inheritance","text":""},{"location":"scaf_pct_gt50k/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_pct_gt50k/#properties","title":"Properties","text":""},{"location":"scaf_pct_gt50k/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_pct_gt50k/#schema-source","title":"Schema Source","text":""},{"location":"scaf_pct_gt50k/#linkml-source","title":"LinkML Source","text":"
name: scaf_pct_gt50k\ndescription: Total sequence size percentage of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_pct_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_powsum/","title":"Slot: scaf_powsum","text":"

Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).

URI: nmdc:scaf_powsum

"},{"location":"scaf_powsum/#inheritance","title":"Inheritance","text":""},{"location":"scaf_powsum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaf_powsum/#properties","title":"Properties","text":""},{"location":"scaf_powsum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_powsum/#schema-source","title":"Schema Source","text":""},{"location":"scaf_powsum/#linkml-source","title":"LinkML Source","text":"
name: scaf_powsum\ndescription: Powersum of all scaffolds is the same as logsum except that it uses the\n  sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaffolds/","title":"Slot: scaffolds","text":"

Total sequence count of all scaffolds.

URI: nmdc:scaffolds

"},{"location":"scaffolds/#inheritance","title":"Inheritance","text":""},{"location":"scaffolds/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no"},{"location":"scaffolds/#properties","title":"Properties","text":""},{"location":"scaffolds/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaffolds/#schema-source","title":"Schema Source","text":""},{"location":"scaffolds/#linkml-source","title":"LinkML Source","text":"
name: scaffolds\ndescription: Total sequence count of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaffolds\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"schema-validation/","title":"Validating data against the nmdc-schema","text":"

The nmdc-schema's preferred on-disk data serializations are YAML, closely followed by JSON. Preferred databases are MongDB and any RDF triplestore.

The nmdc-schema Makefiles use the linkml-validate and linkml-run-examples CLIs for build-time validation of data file, both of which build upon JSON Schema validation. linkml-validate can even validate against TSV, as long as the schema classes that are instantiated can reasonably be expressed in a table. Programmers can learn more about the internals of these tools at https://linkml.io/linkml/data/validating-data.html

We can conceive of validating a data file at two levels

  1. The file should be syntactically correct
  2. The file should conform to the NMDC schema
"},{"location":"schema-validation/#syntactically-correct-yaml-or-json","title":"Syntactically correct YAML or JSON","text":"

All tools, libraries, or scripts generating NMDC data SHOULD instantiate Python data classes from the nmdc-schema PyPI package. It is strongly discouraged to generate Python dicts or JSON by any method other than object instantiation, even using high-quality, standard JSON libraries. That practice may generate valid data files when first tested but is likely to degrade over time. That degradation can be difficult to debug.

Mike Farrah's yq is a system dependency for the nmdc-schema. It can be used to validate legacy YAML and JSON data. If malformed YAML or JSON is presented to linkml-validate, the error messages may not be as helpful as the messages from yq or some other syntactical validator.

"},{"location":"schema-validation/#what-to-do-if-the-data-do-not-validate","title":"What to do if the data do not validate","text":"

Start by reflecting on whether your data may be ahead of what the schema can currently account for.

  1. The data are reasonable, but the schema needs to be extended or modified to account for it
  2. The schema really does provide support for your data, but you are just not adhering to it

For 1, you can make PR on the schema yaml. If you aren't comfortable editing LinkML YAML, then you can get help from one of the schema developers. We recommend filing a new ticket explaining the issue. Please include your error messages.

For 2, we suggest taking a minimal example approach. linkml-validate is very good at identifying schema violations in small, syntactically valid data files. Debugging can be aided in pulling out single data instances and first verifying that they are syntactically valid YAML or JSON. If you don't want to use yq, then you could paste one instance into a website like https://jsonlint.com/. A common issue in multi-instance files is using incorrect syntax for grouping the instances into a YAML or JSON array. Using a small subsample of your data and an online linter as above can aide in debugging this.

"},{"location":"schema-validation/#expectations-of-nmdc-data-producers","title":"Expectations of NMDC data producers","text":"

It is expected that data producers or transformers take the upfront initiative to validate their data.

Currently, not all providers of information to NMDC provide JSON - for example, GOLD is provided as database dumps, and an ETL process transforms this into JSON. In the future, we would like to move towards a situation where all information is provided as JSON.

"},{"location":"schema_element_deprecation_guide/","title":"Deprecating NMDC schema elements","text":"

By deprecating, rather than deleting, schema elements in the NMDC model, we ensure backward compatibility, extend user trust, and provide a valuable historical record, aiding in the understanding of the model's evolution. Therefore, 'deleting' a schema element in NMDC is instead, a two-step (and two-release) deprecation process.

"},{"location":"schema_element_deprecation_guide/#first-release-cycle","title":"First release cycle:","text":" Annotation Value One of: deprecated_element_has_exact_replacement OR deprecated_element_has_possible_replacement * uriorcurie value required deprecated A string explaining the reason for deprecation along with a link to the corresponding issue. last_updated_on modified_by With an ORCID value Deprecation Date Conforms to iso8601/international dates (e.g., # doi_awards deprecated on 2023-11-12 in a class's usage).

* note: If a replacement is not warranted, then using only the deprecated metadata tag with an explanation string and issue link is fine.

"},{"location":"schema_element_deprecation_guide/#second-release-cycle","title":"Second release cycle:","text":"

** note: For a deprecated class, references could be in the is_a or mixin elements of another class, or in the domain or range elements of an existing slot. For deprecated slots, check all classes that reference that slot, etc.

"},{"location":"schema_element_deprecation_guide/#todo-section-on-updating-the-portal-schema-in-the-context-of-deprecation","title":"TODO - section on updating the portal schema in the context of deprecation","text":""},{"location":"season/","title":"Slot: season (season)","text":"

The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).

URI: MIXS:0000829

"},{"location":"season/#inheritance","title":"Inheritance","text":""},{"location":"season/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"season/#properties","title":"Properties","text":""},{"location":"season/#aliases","title":"Aliases","text":""},{"location":"season/#examples","title":"Examples","text":"Value autumn [NCIT:C94733]"},{"location":"season/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season/#annotations","title":"Annotations","text":"property value expected_value NCIT:C94729"},{"location":"season/#schema-source","title":"Schema Source","text":""},{"location":"season/#linkml-source","title":"LinkML Source","text":"
name: season\nannotations:\n  expected_value:\n    tag: expected_value\n    value: NCIT:C94729\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The season when sampling occurred. Any of the four periods into which\n  the year is divided by the equinoxes and solstices. This field accepts terms listed\n  under season (http://purl.obolibrary.org/obo/NCIT_C94729).\ntitle: season\nexamples:\n- value: autumn [NCIT:C94733]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- season\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000829\nalias: season\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"season_environment/","title":"Slot: seasonal environment (season_environment)","text":"

Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment

URI: MIXS:0001068

"},{"location":"season_environment/#inheritance","title":"Inheritance","text":""},{"location":"season_environment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"season_environment/#properties","title":"Properties","text":""},{"location":"season_environment/#aliases","title":"Aliases","text":""},{"location":"season_environment/#examples","title":"Examples","text":"Value rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"season_environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season_environment/#annotations","title":"Annotations","text":"property value expected_value seasonal environment name;treatment interval and duration"},{"location":"season_environment/#schema-source","title":"Schema Source","text":""},{"location":"season_environment/#linkml-source","title":"LinkML Source","text":"
name: season_environment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: seasonal environment name;treatment interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Treatment involving an exposure to a particular season (e.g. Winter,\n  summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment\ntitle: seasonal environment\nexamples:\n- value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001068\nalias: season_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"season_precpt/","title":"Slot: mean seasonal precipitation (season_precpt)","text":"

The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.

URI: MIXS:0000645

"},{"location":"season_precpt/#inheritance","title":"Inheritance","text":""},{"location":"season_precpt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"season_precpt/#properties","title":"Properties","text":""},{"location":"season_precpt/#aliases","title":"Aliases","text":""},{"location":"season_precpt/#examples","title":"Examples","text":"Value"},{"location":"season_precpt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season_precpt/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"season_precpt/#schema-source","title":"Schema Source","text":""},{"location":"season_precpt/#linkml-source","title":"LinkML Source","text":"
name: season_precpt\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average of all seasonal precipitation values known, or an estimated\n  equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean seasonal precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000645\nalias: season_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"season_temp/","title":"Slot: mean seasonal temperature (season_temp)","text":"

Mean seasonal temperature

URI: MIXS:0000643

"},{"location":"season_temp/#inheritance","title":"Inheritance","text":""},{"location":"season_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"season_temp/#properties","title":"Properties","text":""},{"location":"season_temp/#aliases","title":"Aliases","text":""},{"location":"season_temp/#examples","title":"Examples","text":"Value 18 degree Celsius"},{"location":"season_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"season_temp/#schema-source","title":"Schema Source","text":""},{"location":"season_temp/#linkml-source","title":"LinkML Source","text":"
name: season_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Mean seasonal temperature\ntitle: mean seasonal temperature\nexamples:\n- value: 18 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000643\nalias: season_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"season_use/","title":"Slot: seasonal use (season_use)","text":"

The seasons the space is occupied

URI: MIXS:0000830

"},{"location":"season_use/#inheritance","title":"Inheritance","text":""},{"location":"season_use/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"season_use/#properties","title":"Properties","text":""},{"location":"season_use/#aliases","title":"Aliases","text":""},{"location":"season_use/#examples","title":"Examples","text":"Value Winter"},{"location":"season_use/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season_use/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"season_use/#schema-source","title":"Schema Source","text":""},{"location":"season_use/#linkml-source","title":"LinkML Source","text":"
name: season_use\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The seasons the space is occupied\ntitle: seasonal use\nexamples:\n- value: Winter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000830\nalias: season_use\ndomain_of:\n- Biosample\nrange: season_use_enum\nmultivalued: false\n\n
"},{"location":"secondary_treatment/","title":"Slot: secondary treatment (secondary_treatment)","text":"

The process for substantially degrading the biological content of the sewage

URI: MIXS:0000351

"},{"location":"secondary_treatment/#inheritance","title":"Inheritance","text":""},{"location":"secondary_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"secondary_treatment/#properties","title":"Properties","text":""},{"location":"secondary_treatment/#aliases","title":"Aliases","text":""},{"location":"secondary_treatment/#examples","title":"Examples","text":"Value"},{"location":"secondary_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"secondary_treatment/#annotations","title":"Annotations","text":"property value expected_value secondary treatment type"},{"location":"secondary_treatment/#schema-source","title":"Schema Source","text":""},{"location":"secondary_treatment/#linkml-source","title":"LinkML Source","text":"
name: secondary_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: secondary treatment type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The process for substantially degrading the biological content of the\n  sewage\ntitle: secondary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000351\nalias: secondary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"sediment_type/","title":"Slot: sediment type (sediment_type)","text":"

Information about the sediment type based on major constituents

URI: MIXS:0001078

"},{"location":"sediment_type/#inheritance","title":"Inheritance","text":""},{"location":"sediment_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sediment_type/#properties","title":"Properties","text":""},{"location":"sediment_type/#aliases","title":"Aliases","text":""},{"location":"sediment_type/#examples","title":"Examples","text":"Value biogenous"},{"location":"sediment_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sediment_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sediment_type/#schema-source","title":"Schema Source","text":""},{"location":"sediment_type/#linkml-source","title":"LinkML Source","text":"
name: sediment_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information about the sediment type based on major constituents\ntitle: sediment type\nexamples:\n- value: biogenous\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sediment type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001078\nalias: sediment_type\ndomain_of:\n- Biosample\nrange: sediment_type_enum\nmultivalued: false\n\n
"},{"location":"separation_method/","title":"Slot: separation_method","text":"

The method that was used to separate a substance from a solution or mixture.

URI: nmdc:separation_method

"},{"location":"separation_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"separation_method/#properties","title":"Properties","text":""},{"location":"separation_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"separation_method/#schema-source","title":"Schema Source","text":""},{"location":"separation_method/#linkml-source","title":"LinkML Source","text":"
name: separation_method\ndescription: The method that was used to separate a substance from a solution or mixture.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: separation_method\ndomain_of:\n- FiltrationProcess\nrange: SeparationMethodEnum\n\n
"},{"location":"seq_meth/","title":"Slot: sequencing method (seq_meth)","text":"

Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).

URI: MIXS:0000050

"},{"location":"seq_meth/#inheritance","title":"Inheritance","text":""},{"location":"seq_meth/#properties","title":"Properties","text":""},{"location":"seq_meth/#aliases","title":"Aliases","text":""},{"location":"seq_meth/#examples","title":"Examples","text":"Value 454 Genome Sequencer FLX [OBI:0000702]"},{"location":"seq_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"seq_meth/#annotations","title":"Annotations","text":"property value expected_value Text or OBI"},{"location":"seq_meth/#schema-source","title":"Schema Source","text":""},{"location":"seq_meth/#linkml-source","title":"LinkML Source","text":"
name: seq_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: Text or OBI\ndescription: Sequencing machine used. Where possible the term should be taken from\n  the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\ntitle: sequencing method\nexamples:\n- value: 454 Genome Sequencer FLX [OBI:0000702]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequencing method\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000050\nalias: seq_meth\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"seq_quality_check/","title":"Slot: sequence quality check (seq_quality_check)","text":"

Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA

URI: MIXS:0000051

"},{"location":"seq_quality_check/#inheritance","title":"Inheritance","text":""},{"location":"seq_quality_check/#properties","title":"Properties","text":""},{"location":"seq_quality_check/#aliases","title":"Aliases","text":""},{"location":"seq_quality_check/#examples","title":"Examples","text":"Value none"},{"location":"seq_quality_check/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"seq_quality_check/#annotations","title":"Annotations","text":"property value expected_value none or manually edited"},{"location":"seq_quality_check/#schema-source","title":"Schema Source","text":""},{"location":"seq_quality_check/#linkml-source","title":"LinkML Source","text":"
name: seq_quality_check\nannotations:\n  expected_value:\n    tag: expected_value\n    value: none or manually edited\ndescription: Indicate if the sequence has been called by automatic systems (none)\n  or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms).\n  Applied only for sequences that are not submitted to SRA,ENA or DRA\ntitle: sequence quality check\nexamples:\n- value: none\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequence quality check\nrank: 1000\nis_a: sequencing field\nstring_serialization: '[none|manually edited]'\nslot_uri: MIXS:0000051\nalias: seq_quality_check\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"seqid/","title":"Slot: seqid","text":"

The ID of the landmark used to establish the coordinate system for the current feature.

URI: nmdc:seqid

"},{"location":"seqid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"seqid/#properties","title":"Properties","text":""},{"location":"seqid/#todos","title":"TODOs","text":""},{"location":"seqid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"seqid/#schema-source","title":"Schema Source","text":""},{"location":"seqid/#linkml-source","title":"LinkML Source","text":"
name: seqid\ndescription: The ID of the landmark used to establish the coordinate system for the\n  current feature.\ntodos:\n- change range from string to object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: seqid\ndomain_of:\n- GenomeFeature\nrange: string\n\n
"},{"location":"sequencing_field/","title":"Slot: sequencing_field","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:sequencing_field

"},{"location":"sequencing_field/#inheritance","title":"Inheritance","text":""},{"location":"sequencing_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sequencing_field/#properties","title":"Properties","text":""},{"location":"sequencing_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sequencing_field/#schema-source","title":"Schema Source","text":""},{"location":"sequencing_field/#linkml-source","title":"LinkML Source","text":"
name: sequencing field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: sequencing_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"sewage_type/","title":"Slot: sewage type (sewage_type)","text":"

Type of wastewater treatment plant as municipial or industrial

URI: MIXS:0000215

"},{"location":"sewage_type/#inheritance","title":"Inheritance","text":""},{"location":"sewage_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sewage_type/#properties","title":"Properties","text":""},{"location":"sewage_type/#aliases","title":"Aliases","text":""},{"location":"sewage_type/#examples","title":"Examples","text":"Value"},{"location":"sewage_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sewage_type/#annotations","title":"Annotations","text":"property value expected_value sewage type name"},{"location":"sewage_type/#schema-source","title":"Schema Source","text":""},{"location":"sewage_type/#linkml-source","title":"LinkML Source","text":"
name: sewage_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: sewage type name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Type of wastewater treatment plant as municipial or industrial\ntitle: sewage type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sewage type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000215\nalias: sewage_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"shad_dev_water_mold/","title":"Slot: shading device signs of water/mold (shad_dev_water_mold)","text":"

Signs of the presence of mold or mildew on the shading device

URI: MIXS:0000834

"},{"location":"shad_dev_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"shad_dev_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shad_dev_water_mold/#properties","title":"Properties","text":""},{"location":"shad_dev_water_mold/#aliases","title":"Aliases","text":""},{"location":"shad_dev_water_mold/#examples","title":"Examples","text":"Value no presence of mold visible"},{"location":"shad_dev_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shad_dev_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"shad_dev_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"shad_dev_water_mold/#linkml-source","title":"LinkML Source","text":"
name: shad_dev_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on the shading device\ntitle: shading device signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000834\nalias: shad_dev_water_mold\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"shading_device_cond/","title":"Slot: shading device condition (shading_device_cond)","text":"

The physical condition of the shading device at the time of sampling

URI: MIXS:0000831

"},{"location":"shading_device_cond/#inheritance","title":"Inheritance","text":""},{"location":"shading_device_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shading_device_cond/#properties","title":"Properties","text":""},{"location":"shading_device_cond/#aliases","title":"Aliases","text":""},{"location":"shading_device_cond/#examples","title":"Examples","text":"Value new"},{"location":"shading_device_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shading_device_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"shading_device_cond/#schema-source","title":"Schema Source","text":""},{"location":"shading_device_cond/#linkml-source","title":"LinkML Source","text":"
name: shading_device_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the shading device at the time of sampling\ntitle: shading device condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000831\nalias: shading_device_cond\ndomain_of:\n- Biosample\nrange: shading_device_cond_enum\nmultivalued: false\n\n
"},{"location":"shading_device_loc/","title":"Slot: shading device location (shading_device_loc)","text":"

The location of the shading device in relation to the built structure

URI: MIXS:0000832

"},{"location":"shading_device_loc/#inheritance","title":"Inheritance","text":""},{"location":"shading_device_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shading_device_loc/#properties","title":"Properties","text":""},{"location":"shading_device_loc/#aliases","title":"Aliases","text":""},{"location":"shading_device_loc/#examples","title":"Examples","text":"Value exterior"},{"location":"shading_device_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shading_device_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"shading_device_loc/#schema-source","title":"Schema Source","text":""},{"location":"shading_device_loc/#linkml-source","title":"LinkML Source","text":"
name: shading_device_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The location of the shading device in relation to the built structure\ntitle: shading device location\nexamples:\n- value: exterior\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device location\nrank: 1000\nis_a: core field\nstring_serialization: '[exterior|interior]'\nslot_uri: MIXS:0000832\nalias: shading_device_loc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"shading_device_mat/","title":"Slot: shading device material (shading_device_mat)","text":"

The material the shading device is composed of

URI: MIXS:0000245

"},{"location":"shading_device_mat/#inheritance","title":"Inheritance","text":""},{"location":"shading_device_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shading_device_mat/#properties","title":"Properties","text":""},{"location":"shading_device_mat/#aliases","title":"Aliases","text":""},{"location":"shading_device_mat/#examples","title":"Examples","text":"Value"},{"location":"shading_device_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shading_device_mat/#annotations","title":"Annotations","text":"property value expected_value material name"},{"location":"shading_device_mat/#schema-source","title":"Schema Source","text":""},{"location":"shading_device_mat/#linkml-source","title":"LinkML Source","text":"
name: shading_device_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: material name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The material the shading device is composed of\ntitle: shading device material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device material\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000245\nalias: shading_device_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"shading_device_type/","title":"Slot: shading device type (shading_device_type)","text":"

The type of shading device

URI: MIXS:0000835

"},{"location":"shading_device_type/#inheritance","title":"Inheritance","text":""},{"location":"shading_device_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shading_device_type/#properties","title":"Properties","text":""},{"location":"shading_device_type/#aliases","title":"Aliases","text":""},{"location":"shading_device_type/#examples","title":"Examples","text":"Value slatted aluminum awning"},{"location":"shading_device_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shading_device_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"shading_device_type/#schema-source","title":"Schema Source","text":""},{"location":"shading_device_type/#linkml-source","title":"LinkML Source","text":"
name: shading_device_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of shading device\ntitle: shading device type\nexamples:\n- value: slatted aluminum awning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000835\nalias: shading_device_type\ndomain_of:\n- Biosample\nrange: shading_device_type_enum\nmultivalued: false\n\n
"},{"location":"sieving/","title":"Slot: composite design/sieving (sieving)","text":"

Collection design of pooled samples and/or sieve size and amount of sample sieved

URI: MIXS:0000322

"},{"location":"sieving/#inheritance","title":"Inheritance","text":""},{"location":"sieving/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"sieving/#properties","title":"Properties","text":""},{"location":"sieving/#aliases","title":"Aliases","text":""},{"location":"sieving/#examples","title":"Examples","text":"Value"},{"location":"sieving/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sieving/#annotations","title":"Annotations","text":"property value expected_value design name and/or size;amount"},{"location":"sieving/#schema-source","title":"Schema Source","text":""},{"location":"sieving/#linkml-source","title":"LinkML Source","text":"
name: sieving\nannotations:\n  expected_value:\n    tag: expected_value\n    value: design name and/or size;amount\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Collection design of pooled samples and/or sieve size and amount of sample\n  sieved\ntitle: composite design/sieving\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- composite design/sieving\nrank: 1000\nis_a: core field\nstring_serialization: '{{text}|{float} {unit}};{float} {unit}'\nslot_uri: MIXS:0000322\nalias: sieving\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"silicate/","title":"Slot: silicate (silicate)","text":"

Concentration of silicate

URI: MIXS:0000184

"},{"location":"silicate/#inheritance","title":"Inheritance","text":""},{"location":"silicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"silicate/#properties","title":"Properties","text":""},{"location":"silicate/#aliases","title":"Aliases","text":""},{"location":"silicate/#examples","title":"Examples","text":"Value 0.05 micromole per liter"},{"location":"silicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"silicate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"silicate/#schema-source","title":"Schema Source","text":""},{"location":"silicate/#linkml-source","title":"LinkML Source","text":"
name: silicate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of silicate\ntitle: silicate\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- silicate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000184\nalias: silicate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"size_frac/","title":"Slot: size fraction selected (size_frac)","text":"

Filtering pore size used in sample preparation

URI: MIXS:0000017

"},{"location":"size_frac/#inheritance","title":"Inheritance","text":""},{"location":"size_frac/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"size_frac/#properties","title":"Properties","text":""},{"location":"size_frac/#aliases","title":"Aliases","text":""},{"location":"size_frac/#examples","title":"Examples","text":"Value 0-0.22 micrometer"},{"location":"size_frac/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"size_frac/#annotations","title":"Annotations","text":"property value expected_value filter size value range"},{"location":"size_frac/#schema-source","title":"Schema Source","text":""},{"location":"size_frac/#linkml-source","title":"LinkML Source","text":"
name: size_frac\nannotations:\n  expected_value:\n    tag: expected_value\n    value: filter size value range\ndescription: Filtering pore size used in sample preparation\ntitle: size fraction selected\nexamples:\n- value: 0-0.22 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size fraction selected\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000017\nalias: size_frac\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"size_frac_low/","title":"Slot: size-fraction lower threshold (size_frac_low)","text":"

Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample

URI: MIXS:0000735

"},{"location":"size_frac_low/#inheritance","title":"Inheritance","text":""},{"location":"size_frac_low/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"size_frac_low/#properties","title":"Properties","text":""},{"location":"size_frac_low/#aliases","title":"Aliases","text":""},{"location":"size_frac_low/#examples","title":"Examples","text":"Value 0.2 micrometer"},{"location":"size_frac_low/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"size_frac_low/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"size_frac_low/#schema-source","title":"Schema Source","text":""},{"location":"size_frac_low/#linkml-source","title":"LinkML Source","text":"
name: size_frac_low\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: micrometer\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n  Materials larger than the size threshold are excluded from the sample\ntitle: size-fraction lower threshold\nexamples:\n- value: 0.2 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction lower threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000735\nalias: size_frac_low\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"size_frac_up/","title":"Slot: size-fraction upper threshold (size_frac_up)","text":"

Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample

URI: MIXS:0000736

"},{"location":"size_frac_up/#inheritance","title":"Inheritance","text":""},{"location":"size_frac_up/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"size_frac_up/#properties","title":"Properties","text":""},{"location":"size_frac_up/#aliases","title":"Aliases","text":""},{"location":"size_frac_up/#examples","title":"Examples","text":"Value 20 micrometer"},{"location":"size_frac_up/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"size_frac_up/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"size_frac_up/#schema-source","title":"Schema Source","text":""},{"location":"size_frac_up/#linkml-source","title":"LinkML Source","text":"
name: size_frac_up\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: micrometer\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Refers to the mesh/pore size used to retain the sample. Materials smaller\n  than the size threshold are excluded from the sample\ntitle: size-fraction upper threshold\nexamples:\n- value: 20 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction upper threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000736\nalias: size_frac_up\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"slope_aspect/","title":"Slot: slope aspect (slope_aspect)","text":"

The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.

URI: MIXS:0000647

"},{"location":"slope_aspect/#inheritance","title":"Inheritance","text":""},{"location":"slope_aspect/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"slope_aspect/#properties","title":"Properties","text":""},{"location":"slope_aspect/#aliases","title":"Aliases","text":""},{"location":"slope_aspect/#examples","title":"Examples","text":"Value"},{"location":"slope_aspect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"slope_aspect/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"slope_aspect/#schema-source","title":"Schema Source","text":""},{"location":"slope_aspect/#linkml-source","title":"LinkML Source","text":"
name: slope_aspect\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The direction a slope faces. While looking down a slope use a compass\n  to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees.\n  This measure provides an indication of sun and wind exposure that will influence\n  soil temperature and evapotranspiration.\ntitle: slope aspect\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope aspect\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000647\nalias: slope_aspect\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"slope_gradient/","title":"Slot: slope gradient (slope_gradient)","text":"

Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer

URI: MIXS:0000646

"},{"location":"slope_gradient/#inheritance","title":"Inheritance","text":""},{"location":"slope_gradient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"slope_gradient/#properties","title":"Properties","text":""},{"location":"slope_gradient/#aliases","title":"Aliases","text":""},{"location":"slope_gradient/#examples","title":"Examples","text":"Value"},{"location":"slope_gradient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"slope_gradient/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"slope_gradient/#schema-source","title":"Schema Source","text":""},{"location":"slope_gradient/#linkml-source","title":"LinkML Source","text":"
name: slope_gradient\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Commonly called 'slope'. The angle between ground surface and a horizontal\n  line (in percent). This is the direction that overland water would flow. This measure\n  is usually taken with a hand level meter or clinometer\ntitle: slope gradient\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope gradient\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000646\nalias: slope_gradient\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"sludge_retent_time/","title":"Slot: sludge retention time (sludge_retent_time)","text":"

The time activated sludge remains in reactor

URI: MIXS:0000669

"},{"location":"sludge_retent_time/#inheritance","title":"Inheritance","text":""},{"location":"sludge_retent_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sludge_retent_time/#properties","title":"Properties","text":""},{"location":"sludge_retent_time/#aliases","title":"Aliases","text":""},{"location":"sludge_retent_time/#examples","title":"Examples","text":"Value"},{"location":"sludge_retent_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sludge_retent_time/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sludge_retent_time/#schema-source","title":"Schema Source","text":""},{"location":"sludge_retent_time/#linkml-source","title":"LinkML Source","text":"
name: sludge_retent_time\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: hours\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The time activated sludge remains in reactor\ntitle: sludge retention time\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sludge retention time\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000669\nalias: sludge_retent_time\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"smiles/","title":"Slot: smiles","text":"

A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.

URI: nmdc:smiles

"},{"location":"smiles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"smiles/#properties","title":"Properties","text":""},{"location":"smiles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"smiles/#schema-source","title":"Schema Source","text":""},{"location":"smiles/#linkml-source","title":"LinkML Source","text":"
name: smiles\ndescription: A string encoding of a molecular graph, no chiral or isotopic information.\n  There are usually a large number of valid SMILES which represent a given structure.\n  For example, CCO, OCC and C(O)C all specify the structure of ethanol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: smiles\ndomain_of:\n- ChemicalEntity\nrange: string\nmultivalued: true\n\n
"},{"location":"sodium/","title":"Slot: sodium (sodium)","text":"

Sodium concentration in the sample

URI: MIXS:0000428

"},{"location":"sodium/#inheritance","title":"Inheritance","text":""},{"location":"sodium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sodium/#properties","title":"Properties","text":""},{"location":"sodium/#aliases","title":"Aliases","text":""},{"location":"sodium/#examples","title":"Examples","text":"Value 10.5 milligram per liter"},{"location":"sodium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sodium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sodium/#schema-source","title":"Schema Source","text":""},{"location":"sodium/#linkml-source","title":"LinkML Source","text":"
name: sodium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sodium concentration in the sample\ntitle: sodium\nexamples:\n- value: 10.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sodium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000428\nalias: sodium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"soil_annual_season_temp/","title":"Slot: soil_annual_season_temp","text":"

URI: nmdc:soil_annual_season_temp

"},{"location":"soil_annual_season_temp/#properties","title":"Properties","text":""},{"location":"soil_annual_season_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_annual_season_temp/#schema-source","title":"Schema Source","text":""},{"location":"soil_annual_season_temp/#linkml-source","title":"LinkML Source","text":"
name: soil_annual_season_temp\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soil_annual_season_temp\nrange: string\n\n
"},{"location":"soil_horizon/","title":"Slot: soil horizon (soil_horizon)","text":"

Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath

URI: MIXS:0001082

"},{"location":"soil_horizon/#inheritance","title":"Inheritance","text":""},{"location":"soil_horizon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soil_horizon/#properties","title":"Properties","text":""},{"location":"soil_horizon/#aliases","title":"Aliases","text":""},{"location":"soil_horizon/#examples","title":"Examples","text":"Value A horizon"},{"location":"soil_horizon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_horizon/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"soil_horizon/#schema-source","title":"Schema Source","text":""},{"location":"soil_horizon/#linkml-source","title":"LinkML Source","text":"
name: soil_horizon\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Specific layer in the land area which measures parallel to the soil surface\n  and possesses physical characteristics which differ from the layers above and beneath\ntitle: soil horizon\nexamples:\n- value: A horizon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001082\nalias: soil_horizon\ndomain_of:\n- Biosample\nrange: soil_horizon_enum\nmultivalued: false\n\n
"},{"location":"soil_text_measure/","title":"Slot: soil texture measurement (soil_text_measure)","text":"

The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.

URI: MIXS:0000335

"},{"location":"soil_text_measure/#inheritance","title":"Inheritance","text":""},{"location":"soil_text_measure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soil_text_measure/#properties","title":"Properties","text":""},{"location":"soil_text_measure/#aliases","title":"Aliases","text":""},{"location":"soil_text_measure/#examples","title":"Examples","text":"Value"},{"location":"soil_text_measure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_text_measure/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"soil_text_measure/#schema-source","title":"Schema Source","text":""},{"location":"soil_text_measure/#linkml-source","title":"LinkML Source","text":"
name: soil_text_measure\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The relative proportion of different grain sizes of mineral particles\n  in a soil, as described using a standard system; express as % sand (50 um to 2 mm),\n  silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam)\n  optional.\ntitle: soil texture measurement\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture measurement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000335\nalias: soil_text_measure\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"soil_texture_meth/","title":"Slot: soil texture method (soil_texture_meth)","text":"

Reference or method used in determining soil texture

URI: MIXS:0000336

"},{"location":"soil_texture_meth/#inheritance","title":"Inheritance","text":""},{"location":"soil_texture_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soil_texture_meth/#properties","title":"Properties","text":""},{"location":"soil_texture_meth/#aliases","title":"Aliases","text":""},{"location":"soil_texture_meth/#examples","title":"Examples","text":"Value"},{"location":"soil_texture_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_texture_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"soil_texture_meth/#schema-source","title":"Schema Source","text":""},{"location":"soil_texture_meth/#linkml-source","title":"LinkML Source","text":"
name: soil_texture_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining soil texture\ntitle: soil texture method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000336\nalias: soil_texture_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"soil_type/","title":"Slot: soil type (soil_type)","text":"

Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.

URI: MIXS:0000332

"},{"location":"soil_type/#inheritance","title":"Inheritance","text":""},{"location":"soil_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment no"},{"location":"soil_type/#properties","title":"Properties","text":""},{"location":"soil_type/#aliases","title":"Aliases","text":""},{"location":"soil_type/#examples","title":"Examples","text":"Value plinthosol [ENVO:00002250]"},{"location":"soil_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_type/#annotations","title":"Annotations","text":"property value expected_value ENVO_00001998"},{"location":"soil_type/#schema-source","title":"Schema Source","text":""},{"location":"soil_type/#linkml-source","title":"LinkML Source","text":"
name: soil_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: ENVO_00001998\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Description of the soil type or classification. This field accepts terms\n  under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms can be\n  separated by pipes.\ntitle: soil type\nexamples:\n- value: plinthosol [ENVO:00002250]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000332\nalias: soil_type\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"soil_type_meth/","title":"Slot: soil type method (soil_type_meth)","text":"

Reference or method used in determining soil series name or other lower-level classification

URI: MIXS:0000334

"},{"location":"soil_type_meth/#inheritance","title":"Inheritance","text":""},{"location":"soil_type_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soil_type_meth/#properties","title":"Properties","text":""},{"location":"soil_type_meth/#aliases","title":"Aliases","text":""},{"location":"soil_type_meth/#examples","title":"Examples","text":"Value"},{"location":"soil_type_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_type_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"soil_type_meth/#schema-source","title":"Schema Source","text":""},{"location":"soil_type_meth/#linkml-source","title":"LinkML Source","text":"
name: soil_type_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining soil series name or other lower-level\n  classification\ntitle: soil type method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000334\nalias: soil_type_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"solar_irradiance/","title":"Slot: solar irradiance (solar_irradiance)","text":"

The amount of solar energy that arrives at a specific area of a surface during a specific time interval

URI: MIXS:0000112

"},{"location":"solar_irradiance/#inheritance","title":"Inheritance","text":""},{"location":"solar_irradiance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"solar_irradiance/#properties","title":"Properties","text":""},{"location":"solar_irradiance/#aliases","title":"Aliases","text":""},{"location":"solar_irradiance/#examples","title":"Examples","text":"Value 1.36 kilowatts per square meter per day"},{"location":"solar_irradiance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"solar_irradiance/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"solar_irradiance/#schema-source","title":"Schema Source","text":""},{"location":"solar_irradiance/#linkml-source","title":"LinkML Source","text":"
name: solar_irradiance\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilowatts per square meter per day, ergs per square centimeter per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The amount of solar energy that arrives at a specific area of a surface\n  during a specific time interval\ntitle: solar irradiance\nexamples:\n- value: 1.36 kilowatts per square meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- solar irradiance\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000112\nalias: solar_irradiance\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"soluble_inorg_mat/","title":"Slot: soluble inorganic material (soluble_inorg_mat)","text":"

Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.

URI: MIXS:0000672

"},{"location":"soluble_inorg_mat/#inheritance","title":"Inheritance","text":""},{"location":"soluble_inorg_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_inorg_mat/#properties","title":"Properties","text":""},{"location":"soluble_inorg_mat/#aliases","title":"Aliases","text":""},{"location":"soluble_inorg_mat/#examples","title":"Examples","text":"Value"},{"location":"soluble_inorg_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soluble_inorg_mat/#annotations","title":"Annotations","text":"property value expected_value soluble inorganic material name;measurement value"},{"location":"soluble_inorg_mat/#schema-source","title":"Schema Source","text":""},{"location":"soluble_inorg_mat/#linkml-source","title":"LinkML Source","text":"
name: soluble_inorg_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: soluble inorganic material name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, microgram, mole per liter, gram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide,\n  hydrogen sulfide, thiocyanates, thiosulfates, etc.\ntitle: soluble inorganic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble inorganic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000672\nalias: soluble_inorg_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"soluble_iron_micromol/","title":"Slot: soluble_iron_micromol","text":"

URI: nmdc:soluble_iron_micromol

"},{"location":"soluble_iron_micromol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_iron_micromol/#properties","title":"Properties","text":""},{"location":"soluble_iron_micromol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soluble_iron_micromol/#schema-source","title":"Schema Source","text":""},{"location":"soluble_iron_micromol/#linkml-source","title":"LinkML Source","text":"
name: soluble_iron_micromol\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soluble_iron_micromol\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"soluble_org_mat/","title":"Slot: soluble organic material (soluble_org_mat)","text":"

Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.

URI: MIXS:0000673

"},{"location":"soluble_org_mat/#inheritance","title":"Inheritance","text":""},{"location":"soluble_org_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_org_mat/#properties","title":"Properties","text":""},{"location":"soluble_org_mat/#aliases","title":"Aliases","text":""},{"location":"soluble_org_mat/#examples","title":"Examples","text":"Value"},{"location":"soluble_org_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soluble_org_mat/#annotations","title":"Annotations","text":"property value expected_value soluble organic material name;measurement value"},{"location":"soluble_org_mat/#schema-source","title":"Schema Source","text":""},{"location":"soluble_org_mat/#linkml-source","title":"LinkML Source","text":"
name: soluble_org_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: soluble organic material name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, microgram, mole per liter, gram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of substances such as urea, fruit sugars, soluble proteins,\n  drugs, pharmaceuticals, etc.\ntitle: soluble organic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble organic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000673\nalias: soluble_org_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"soluble_react_phosp/","title":"Slot: soluble reactive phosphorus (soluble_react_phosp)","text":"

Concentration of soluble reactive phosphorus

URI: MIXS:0000738

"},{"location":"soluble_react_phosp/#inheritance","title":"Inheritance","text":""},{"location":"soluble_react_phosp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_react_phosp/#properties","title":"Properties","text":""},{"location":"soluble_react_phosp/#aliases","title":"Aliases","text":""},{"location":"soluble_react_phosp/#examples","title":"Examples","text":"Value 0.1 milligram per liter"},{"location":"soluble_react_phosp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soluble_react_phosp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"soluble_react_phosp/#schema-source","title":"Schema Source","text":""},{"location":"soluble_react_phosp/#linkml-source","title":"LinkML Source","text":"
name: soluble_react_phosp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of soluble reactive phosphorus\ntitle: soluble reactive phosphorus\nexamples:\n- value: 0.1 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble reactive phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000738\nalias: soluble_react_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"source_concentration/","title":"Slot: source_concentration","text":"

When solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in solution A

URI: nmdc:source_concentration

"},{"location":"source_concentration/#inheritance","title":"Inheritance","text":""},{"location":"source_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"source_concentration/#properties","title":"Properties","text":""},{"location":"source_concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"source_concentration/#schema-source","title":"Schema Source","text":""},{"location":"source_concentration/#linkml-source","title":"LinkML Source","text":"
name: source_concentration\ndescription: When solutions A (containing substance X) and B are combined together,\n  this slot captures the concentration of X in solution A\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: concentration\nalias: source_concentration\ndomain_of:\n- PortionOfSubstance\nrange: QuantityValue\n\n
"},{"location":"source_mat_id/","title":"Slot: source material identifiers (source_mat_id)","text":"

A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).

URI: MIXS:0000026

"},{"location":"source_mat_id/#inheritance","title":"Inheritance","text":""},{"location":"source_mat_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"source_mat_id/#properties","title":"Properties","text":""},{"location":"source_mat_id/#aliases","title":"Aliases","text":""},{"location":"source_mat_id/#examples","title":"Examples","text":"Value MPI012345"},{"location":"source_mat_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"source_mat_id/#annotations","title":"Annotations","text":"property value expected_value for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer"},{"location":"source_mat_id/#schema-source","title":"Schema Source","text":""},{"location":"source_mat_id/#linkml-source","title":"LinkML Source","text":"
name: source_mat_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: 'for cultures of microorganisms: identifiers for two culture collections;\n      for other material a unique arbitrary identifer'\ndescription: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID,\n  and as opposed to a particular digital record of a material sample) used for extracting\n  nucleic acids, and subsequent sequencing. The identifier can refer either to the\n  original material collected or to any derived sub-samples. The INSDC qualifiers\n  /specimen_voucher, /bio_material, or /culture_collection may or may not share the\n  same value as the source_mat_id field. For instance, the /specimen_voucher qualifier\n  and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen\n  voucher and sampled tissue with the same identifier. However, the /culture_collection\n  qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id\n  would refer to an identifier from some derived culture from which the nucleic acids\n  were extracted (e.g. xatc123 or ark:/2154/R2).\ntitle: source material identifiers\nexamples:\n- value: MPI012345\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source material identifiers\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000026\nalias: source_mat_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"space_typ_state/","title":"Slot: space typical state (space_typ_state)","text":"

Customary or normal state of the space

URI: MIXS:0000770

"},{"location":"space_typ_state/#inheritance","title":"Inheritance","text":""},{"location":"space_typ_state/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"space_typ_state/#properties","title":"Properties","text":""},{"location":"space_typ_state/#aliases","title":"Aliases","text":""},{"location":"space_typ_state/#examples","title":"Examples","text":"Value typically occupied"},{"location":"space_typ_state/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"space_typ_state/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"space_typ_state/#schema-source","title":"Schema Source","text":""},{"location":"space_typ_state/#linkml-source","title":"LinkML Source","text":"
name: space_typ_state\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Customary or normal state of the space\ntitle: space typical state\nexamples:\n- value: typically occupied\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- space typical state\nrank: 1000\nis_a: core field\nstring_serialization: '[typically occupied|typically unoccupied]'\nslot_uri: MIXS:0000770\nalias: space_typ_state\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"specific/","title":"Slot: specifications (specific)","text":"

The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents

URI: MIXS:0000836

"},{"location":"specific/#inheritance","title":"Inheritance","text":""},{"location":"specific/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"specific/#properties","title":"Properties","text":""},{"location":"specific/#aliases","title":"Aliases","text":""},{"location":"specific/#examples","title":"Examples","text":"Value construction"},{"location":"specific/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"specific/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"specific/#schema-source","title":"Schema Source","text":""},{"location":"specific/#linkml-source","title":"LinkML Source","text":"
name: specific\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'The building specifications. If design is chosen, indicate phase: conceptual,\n  schematic, design development, construction documents'\ntitle: specifications\nexamples:\n- value: construction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specifications\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000836\nalias: specific\ndomain_of:\n- Biosample\nrange: specific_enum\nmultivalued: false\n\n
"},{"location":"specific_ecosystem/","title":"Slot: specific_ecosystem","text":"

Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.

URI: nmdc:specific_ecosystem

"},{"location":"specific_ecosystem/#inheritance","title":"Inheritance","text":""},{"location":"specific_ecosystem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"specific_ecosystem/#properties","title":"Properties","text":""},{"location":"specific_ecosystem/#comments","title":"Comments","text":""},{"location":"specific_ecosystem/#see-also","title":"See Also","text":""},{"location":"specific_ecosystem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"specific_ecosystem/#schema-source","title":"Schema Source","text":""},{"location":"specific_ecosystem/#linkml-source","title":"LinkML Source","text":"
name: specific_ecosystem\ndescription: Specific ecosystems represent specific features of the environment like\n  aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific\n  ecosystem is in position 5/5 in a GOLD path.\ncomments:\n- Specific ecosystems help to define samples based on very specific characteristics\n  of an environment under the five-level classification system.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: specific_ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"specific_humidity/","title":"Slot: specific humidity (specific_humidity)","text":"

The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.

URI: MIXS:0000214

"},{"location":"specific_humidity/#inheritance","title":"Inheritance","text":""},{"location":"specific_humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"specific_humidity/#properties","title":"Properties","text":""},{"location":"specific_humidity/#aliases","title":"Aliases","text":""},{"location":"specific_humidity/#examples","title":"Examples","text":"Value 15 per kilogram of air"},{"location":"specific_humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"specific_humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"specific_humidity/#schema-source","title":"Schema Source","text":""},{"location":"specific_humidity/#linkml-source","title":"LinkML Source","text":"
name: specific_humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram of air, kilogram of air\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The mass of water vapour in a unit mass of moist air, usually expressed\n  as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.\ntitle: specific humidity\nexamples:\n- value: 15 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specific humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000214\nalias: specific_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"sr_dep_env/","title":"Slot: source rock depositional environment (sr_dep_env)","text":"

Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000996

"},{"location":"sr_dep_env/#inheritance","title":"Inheritance","text":""},{"location":"sr_dep_env/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sr_dep_env/#properties","title":"Properties","text":""},{"location":"sr_dep_env/#aliases","title":"Aliases","text":""},{"location":"sr_dep_env/#examples","title":"Examples","text":"Value Marine"},{"location":"sr_dep_env/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sr_dep_env/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sr_dep_env/#schema-source","title":"Schema Source","text":""},{"location":"sr_dep_env/#linkml-source","title":"LinkML Source","text":"
name: sr_dep_env\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n  If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock depositional environment\nexamples:\n- value: Marine\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000996\nalias: sr_dep_env\ndomain_of:\n- Biosample\nrange: sr_dep_env_enum\nmultivalued: false\n\n
"},{"location":"sr_geol_age/","title":"Slot: source rock geological age (sr_geol_age)","text":"

Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000997

"},{"location":"sr_geol_age/#inheritance","title":"Inheritance","text":""},{"location":"sr_geol_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sr_geol_age/#properties","title":"Properties","text":""},{"location":"sr_geol_age/#aliases","title":"Aliases","text":""},{"location":"sr_geol_age/#examples","title":"Examples","text":"Value Silurian"},{"location":"sr_geol_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sr_geol_age/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sr_geol_age/#schema-source","title":"Schema Source","text":""},{"location":"sr_geol_age/#linkml-source","title":"LinkML Source","text":"
name: sr_geol_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n  If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: source rock geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000997\nalias: sr_geol_age\ndomain_of:\n- Biosample\nrange: sr_geol_age_enum\nmultivalued: false\n\n
"},{"location":"sr_kerog_type/","title":"Slot: source rock kerogen type (sr_kerog_type)","text":"

Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000994

"},{"location":"sr_kerog_type/#inheritance","title":"Inheritance","text":""},{"location":"sr_kerog_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sr_kerog_type/#properties","title":"Properties","text":""},{"location":"sr_kerog_type/#aliases","title":"Aliases","text":""},{"location":"sr_kerog_type/#examples","title":"Examples","text":"Value Type IV"},{"location":"sr_kerog_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sr_kerog_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sr_kerog_type/#schema-source","title":"Schema Source","text":""},{"location":"sr_kerog_type/#linkml-source","title":"LinkML Source","text":"
name: sr_kerog_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and\n  soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous\n  plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial)\n  (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified,\n  please propose entry in \"additional info\" field'\ntitle: source rock kerogen type\nexamples:\n- value: Type IV\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock kerogen type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000994\nalias: sr_kerog_type\ndomain_of:\n- Biosample\nrange: sr_kerog_type_enum\nmultivalued: false\n\n
"},{"location":"sr_lithology/","title":"Slot: source rock lithology (sr_lithology)","text":"

Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000995

"},{"location":"sr_lithology/#inheritance","title":"Inheritance","text":""},{"location":"sr_lithology/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sr_lithology/#properties","title":"Properties","text":""},{"location":"sr_lithology/#aliases","title":"Aliases","text":""},{"location":"sr_lithology/#examples","title":"Examples","text":"Value Coal"},{"location":"sr_lithology/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sr_lithology/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sr_lithology/#schema-source","title":"Schema Source","text":""},{"location":"sr_lithology/#linkml-source","title":"LinkML Source","text":"
name: sr_lithology\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n  If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock lithology\nexamples:\n- value: Coal\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000995\nalias: sr_lithology\ndomain_of:\n- Biosample\nrange: sr_lithology_enum\nmultivalued: false\n\n
"},{"location":"standing_water_regm/","title":"Slot: standing water regimen (standing_water_regm)","text":"

Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0001069

"},{"location":"standing_water_regm/#inheritance","title":"Inheritance","text":""},{"location":"standing_water_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"standing_water_regm/#properties","title":"Properties","text":""},{"location":"standing_water_regm/#aliases","title":"Aliases","text":""},{"location":"standing_water_regm/#examples","title":"Examples","text":"Value standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"standing_water_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"standing_water_regm/#annotations","title":"Annotations","text":"property value expected_value standing water type;treatment interval and duration"},{"location":"standing_water_regm/#schema-source","title":"Schema Source","text":""},{"location":"standing_water_regm/#linkml-source","title":"LinkML Source","text":"
name: standing_water_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: standing water type;treatment interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Treatment involving an exposure to standing water during a plant's life\n  span, types can be flood water or standing water, treatment regimen including how\n  many times the treatment was repeated, how long each treatment lasted, and the start\n  and end time of the entire treatment; can include multiple regimens\ntitle: standing water regimen\nexamples:\n- value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- standing water regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001069\nalias: standing_water_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"start/","title":"Slot: start","text":"

The start of the feature in positive 1-based integer coordinates

URI: nmdc:start

"},{"location":"start/#inheritance","title":"Inheritance","text":""},{"location":"start/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"start/#properties","title":"Properties","text":""},{"location":"start/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"start/#schema-source","title":"Schema Source","text":""},{"location":"start/#linkml-source","title":"LinkML Source","text":"
name: start\ndescription: The start of the feature in positive 1-based integer coordinates\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:start_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: start\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\n
"},{"location":"start_date/","title":"Slot: start_date","text":"

The date on which any process or activity was started

URI: nmdc:start_date

"},{"location":"start_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no Extraction A material separation in which a desired component of an input material is se... no WorkflowExecution Represents an instance of an execution of a particular workflow no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no NomAnalysis no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetabolomicsAnalysis no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAssembly no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no LibraryPreparation no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"start_date/#properties","title":"Properties","text":""},{"location":"start_date/#comments","title":"Comments","text":""},{"location":"start_date/#todos","title":"TODOs","text":""},{"location":"start_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"start_date/#schema-source","title":"Schema Source","text":""},{"location":"start_date/#linkml-source","title":"LinkML Source","text":"
name: start_date\ndescription: The date on which any process or activity was started\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n  can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: start_date\ndomain_of:\n- PlannedProcess\nrange: string\n\n
"},{"location":"start_date_inc/","title":"Slot: incubation start date (start_date_inc)","text":"

Date the incubation was started. Only relevant for incubation samples.

URI: nmdc:start_date_inc

"},{"location":"start_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_date_inc/#properties","title":"Properties","text":""},{"location":"start_date_inc/#examples","title":"Examples","text":"Value 2021-04-15, 2021-04 and 2021 are all acceptable."},{"location":"start_date_inc/#comments","title":"Comments","text":""},{"location":"start_date_inc/#see-also","title":"See Also","text":""},{"location":"start_date_inc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"start_date_inc/#schema-source","title":"Schema Source","text":""},{"location":"start_date_inc/#linkml-source","title":"LinkML Source","text":"
name: start_date_inc\ndescription: Date the incubation was started. Only relevant for incubation samples.\ntitle: incubation start date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n  date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n  all acceptable.\nexamples:\n- value: 2021-04-15, 2021-04 and 2021 are all acceptable.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 4\nstring_serialization: '{date, arbitrary precision}'\nalias: start_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"start_time_inc/","title":"Slot: incubation start time, GMT (start_time_inc)","text":"

Time the incubation was started. Only relevant for incubation samples.

URI: nmdc:start_time_inc

"},{"location":"start_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_time_inc/#properties","title":"Properties","text":""},{"location":"start_time_inc/#examples","title":"Examples","text":"Value 13:33 or 13:33:55"},{"location":"start_time_inc/#comments","title":"Comments","text":""},{"location":"start_time_inc/#see-also","title":"See Also","text":""},{"location":"start_time_inc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"start_time_inc/#schema-source","title":"Schema Source","text":""},{"location":"start_time_inc/#linkml-source","title":"LinkML Source","text":"
name: start_time_inc\ndescription: Time the incubation was started. Only relevant for incubation samples.\ntitle: incubation start time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n  only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 5\nstring_serialization: '{time, seconds optional}'\nalias: start_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"started_at_time/","title":"Slot: started_at_time","text":"

URI: nmdc:started_at_time

"},{"location":"started_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetaproteomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetatranscriptomeAnnotation no MetatranscriptomeAssembly no"},{"location":"started_at_time/#properties","title":"Properties","text":""},{"location":"started_at_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"started_at_time/#schema-source","title":"Schema Source","text":""},{"location":"started_at_time/#linkml-source","title":"LinkML Source","text":"
name: started_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n  It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:startedAtTime\nrank: 1000\nalias: started_at_time\ndomain_of:\n- WorkflowExecution\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\n
"},{"location":"stationary_phase/","title":"Slot: stationary_phase","text":"

The material the stationary phase is comprised of used in chromatography.

URI: nmdc:stationary_phase

"},{"location":"stationary_phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no"},{"location":"stationary_phase/#properties","title":"Properties","text":""},{"location":"stationary_phase/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"stationary_phase/#schema-source","title":"Schema Source","text":""},{"location":"stationary_phase/#linkml-source","title":"LinkML Source","text":"
name: stationary_phase\ndescription: The material the stationary phase is comprised of used in chromatography.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stationary_phase\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: StationaryPhaseEnum\n\n
"},{"location":"storage_process_set/","title":"Slot: storage_process_set","text":"

This property links a database object to the set of storage processes within it.

URI: nmdc:storage_process_set

"},{"location":"storage_process_set/#inheritance","title":"Inheritance","text":""},{"location":"storage_process_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"storage_process_set/#properties","title":"Properties","text":""},{"location":"storage_process_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"storage_process_set/#schema-source","title":"Schema Source","text":""},{"location":"storage_process_set/#linkml-source","title":"LinkML Source","text":"
name: storage_process_set\ndescription: This property links a database object to the set of storage processes\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: storage_process_set\ndomain_of:\n- Database\nrange: StorageProcess\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"store_cond/","title":"Slot: storage conditions (store_cond)","text":"

Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).

URI: MIXS:0000327

"},{"location":"store_cond/#inheritance","title":"Inheritance","text":""},{"location":"store_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"store_cond/#properties","title":"Properties","text":""},{"location":"store_cond/#aliases","title":"Aliases","text":""},{"location":"store_cond/#examples","title":"Examples","text":"Value -20 degree Celsius freezer;P2Y10D"},{"location":"store_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"store_cond/#annotations","title":"Annotations","text":"property value expected_value storage condition type;duration"},{"location":"store_cond/#schema-source","title":"Schema Source","text":""},{"location":"store_cond/#linkml-source","title":"LinkML Source","text":"
name: store_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: storage condition type;duration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Explain how and for how long the soil sample was stored before DNA extraction\n  (fresh/frozen/other).\ntitle: storage conditions\nexamples:\n- value: -20 degree Celsius freezer;P2Y10D\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- storage conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000327\nalias: store_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"strand/","title":"Slot: strand","text":"

The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).

URI: nmdc:strand

"},{"location":"strand/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"strand/#properties","title":"Properties","text":""},{"location":"strand/#todos","title":"TODOs","text":""},{"location":"strand/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"strand/#schema-source","title":"Schema Source","text":""},{"location":"strand/#linkml-source","title":"LinkML Source","text":"
name: strand\ndescription: The strand on which a feature is located. Has a value of '+' (sense strand\n  or forward strand) or  '-' (anti-sense strand or reverse strand).\ntodos:\n- set the range to an enum?\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:strand\nrank: 1000\nalias: strand\ndomain_of:\n- GenomeFeature\nrange: string\n\n
"},{"location":"stranded_orientation/","title":"Slot: stranded_orientation","text":"

Lists the strand orientiation for a stranded RNA library preparation.

URI: nmdc:stranded_orientation

"},{"location":"stranded_orientation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"stranded_orientation/#properties","title":"Properties","text":""},{"location":"stranded_orientation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"stranded_orientation/#schema-source","title":"Schema Source","text":""},{"location":"stranded_orientation/#linkml-source","title":"LinkML Source","text":"
name: stranded_orientation\ndescription: Lists the strand orientiation for a stranded RNA library preparation.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stranded_orientation\ndomain_of:\n- LibraryPreparation\nrange: StrandedOrientationEnum\n\n
"},{"location":"study_category/","title":"Slot: study_category","text":"

The type of research initiative

URI: nmdc:study_category

"},{"location":"study_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_category/#properties","title":"Properties","text":""},{"location":"study_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"study_category/#schema-source","title":"Schema Source","text":""},{"location":"study_category/#linkml-source","title":"LinkML Source","text":"
name: study_category\ndescription: The type of research initiative\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_category\ndomain_of:\n- Study\nrange: StudyCategoryEnum\nrequired: true\n\n
"},{"location":"study_identifiers/","title":"Slot: study_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:study_identifiers

"},{"location":"study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"study_identifiers/#properties","title":"Properties","text":""},{"location":"study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: study_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"study_image/","title":"Slot: study_image","text":"

Links a study to one or more images.

URI: nmdc:study_image

"},{"location":"study_image/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_image/#properties","title":"Properties","text":""},{"location":"study_image/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"study_image/#schema-source","title":"Schema Source","text":""},{"location":"study_image/#linkml-source","title":"LinkML Source","text":"
name: study_image\ndescription: Links a study to one or more images.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_image\ndomain_of:\n- Study\nrange: ImageValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"study_set/","title":"Slot: study_set","text":"

This property links a database object to the set of studies within it.

URI: nmdc:study_set

"},{"location":"study_set/#inheritance","title":"Inheritance","text":""},{"location":"study_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"study_set/#properties","title":"Properties","text":""},{"location":"study_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"study_set/#schema-source","title":"Schema Source","text":""},{"location":"study_set/#linkml-source","title":"LinkML Source","text":"
name: study_set\ndescription: This property links a database object to the set of studies within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: study_set\ndomain_of:\n- Database\nrange: Study\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"subject/","title":"Slot: subject","text":"

URI: nmdc:subject

"},{"location":"subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e no"},{"location":"subject/#properties","title":"Properties","text":""},{"location":"subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"subject/#schema-source","title":"Schema Source","text":""},{"location":"subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subject\ndomain_of:\n- FunctionalAnnotation\nrange: GeneProduct\n\n
"},{"location":"substance_role/","title":"Slot: substance_role","text":"

The role of a substance in a process

URI: nmdc:substance_role

"},{"location":"substance_role/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"substance_role/#properties","title":"Properties","text":""},{"location":"substance_role/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"substance_role/#schema-source","title":"Schema Source","text":""},{"location":"substance_role/#linkml-source","title":"LinkML Source","text":"
name: substance_role\ndescription: The role of a substance in a process\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substance_role\ndomain_of:\n- PortionOfSubstance\nrange: SubstanceRoleEnum\n\n
"},{"location":"substances_used/","title":"Slot: substances_used","text":"

The substances that are combined to enable a ChemicalConversionProcess.

URI: nmdc:substances_used

"},{"location":"substances_used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... no StorageProcess A planned process with the objective to preserve and protect material entitie... yes MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no"},{"location":"substances_used/#properties","title":"Properties","text":""},{"location":"substances_used/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"substances_used/#schema-source","title":"Schema Source","text":""},{"location":"substances_used/#linkml-source","title":"LinkML Source","text":"
name: substances_used\ndescription: The substances that are combined to enable a ChemicalConversionProcess.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substances_used\ndomain_of:\n- Extraction\n- StorageProcess\n- DissolvingProcess\n- ChemicalConversionProcess\n- MobilePhaseSegment\nrange: PortionOfSubstance\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"substances_volume/","title":"Slot: substances_volume","text":"

The volume of the combined substances that was included in a ChemicalConversionProcess.

URI: nmdc:substances_volume

"},{"location":"substances_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no"},{"location":"substances_volume/#properties","title":"Properties","text":""},{"location":"substances_volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"substances_volume/#schema-source","title":"Schema Source","text":""},{"location":"substances_volume/#linkml-source","title":"LinkML Source","text":"
name: substances_volume\ndescription: The volume of the combined substances that was included in a ChemicalConversionProcess.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substances_volume\ndomain_of:\n- ChemicalConversionProcess\nrange: QuantityValue\n\n
"},{"location":"substructure_type/","title":"Slot: substructure type (substructure_type)","text":"

The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level

URI: MIXS:0000767

"},{"location":"substructure_type/#inheritance","title":"Inheritance","text":""},{"location":"substructure_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"substructure_type/#properties","title":"Properties","text":""},{"location":"substructure_type/#aliases","title":"Aliases","text":""},{"location":"substructure_type/#examples","title":"Examples","text":"Value basement"},{"location":"substructure_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"substructure_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"substructure_type/#schema-source","title":"Schema Source","text":""},{"location":"substructure_type/#linkml-source","title":"LinkML Source","text":"
name: substructure_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: The substructure or under building is that largely hidden section of\n  the building which is built off the foundations to the ground floor level\ntitle: substructure type\nexamples:\n- value: basement\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- substructure type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000767\nalias: substructure_type\ndomain_of:\n- Biosample\nrange: substructure_type_enum\nmultivalued: true\n\n
"},{"location":"subsurface_depth/","title":"Slot: subsurface_depth","text":"

URI: nmdc:subsurface_depth

"},{"location":"subsurface_depth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"subsurface_depth/#properties","title":"Properties","text":""},{"location":"subsurface_depth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"subsurface_depth/#schema-source","title":"Schema Source","text":""},{"location":"subsurface_depth/#linkml-source","title":"LinkML Source","text":"
name: subsurface_depth\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subsurface_depth\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"sulfate/","title":"Slot: sulfate (sulfate)","text":"

Concentration of sulfate in the sample

URI: MIXS:0000423

"},{"location":"sulfate/#inheritance","title":"Inheritance","text":""},{"location":"sulfate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sulfate/#properties","title":"Properties","text":""},{"location":"sulfate/#aliases","title":"Aliases","text":""},{"location":"sulfate/#examples","title":"Examples","text":"Value 5 micromole per liter"},{"location":"sulfate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sulfate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sulfate/#schema-source","title":"Schema Source","text":""},{"location":"sulfate/#linkml-source","title":"LinkML Source","text":"
name: sulfate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of sulfate in the sample\ntitle: sulfate\nexamples:\n- value: 5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000423\nalias: sulfate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"sulfate_fw/","title":"Slot: sulfate in formation water (sulfate_fw)","text":"

Original sulfate concentration in the hydrocarbon resource

URI: MIXS:0000407

"},{"location":"sulfate_fw/#inheritance","title":"Inheritance","text":""},{"location":"sulfate_fw/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sulfate_fw/#properties","title":"Properties","text":""},{"location":"sulfate_fw/#aliases","title":"Aliases","text":""},{"location":"sulfate_fw/#examples","title":"Examples","text":"Value"},{"location":"sulfate_fw/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sulfate_fw/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sulfate_fw/#schema-source","title":"Schema Source","text":""},{"location":"sulfate_fw/#linkml-source","title":"LinkML Source","text":"
name: sulfate_fw\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original sulfate concentration in the hydrocarbon resource\ntitle: sulfate in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000407\nalias: sulfate_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"sulfide/","title":"Slot: sulfide (sulfide)","text":"

Concentration of sulfide in the sample

URI: MIXS:0000424

"},{"location":"sulfide/#inheritance","title":"Inheritance","text":""},{"location":"sulfide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sulfide/#properties","title":"Properties","text":""},{"location":"sulfide/#aliases","title":"Aliases","text":""},{"location":"sulfide/#examples","title":"Examples","text":"Value 2 micromole per liter"},{"location":"sulfide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sulfide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sulfide/#schema-source","title":"Schema Source","text":""},{"location":"sulfide/#linkml-source","title":"LinkML Source","text":"
name: sulfide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of sulfide in the sample\ntitle: sulfide\nexamples:\n- value: 2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000424\nalias: sulfide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"surf_air_cont/","title":"Slot: surface-air contaminant (surf_air_cont)","text":"

Contaminant identified on surface

URI: MIXS:0000759

"},{"location":"surf_air_cont/#inheritance","title":"Inheritance","text":""},{"location":"surf_air_cont/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_air_cont/#properties","title":"Properties","text":""},{"location":"surf_air_cont/#aliases","title":"Aliases","text":""},{"location":"surf_air_cont/#examples","title":"Examples","text":"Value radon"},{"location":"surf_air_cont/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_air_cont/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"surf_air_cont/#schema-source","title":"Schema Source","text":""},{"location":"surf_air_cont/#linkml-source","title":"LinkML Source","text":"
name: surf_air_cont\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Contaminant identified on surface\ntitle: surface-air contaminant\nexamples:\n- value: radon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface-air contaminant\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000759\nalias: surf_air_cont\ndomain_of:\n- Biosample\nrange: surf_air_cont_enum\nmultivalued: true\n\n
"},{"location":"surf_humidity/","title":"Slot: surface humidity (surf_humidity)","text":"

Surfaces: water activity as a function of air and material moisture

URI: MIXS:0000123

"},{"location":"surf_humidity/#inheritance","title":"Inheritance","text":""},{"location":"surf_humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_humidity/#properties","title":"Properties","text":""},{"location":"surf_humidity/#aliases","title":"Aliases","text":""},{"location":"surf_humidity/#examples","title":"Examples","text":"Value 10%"},{"location":"surf_humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"surf_humidity/#schema-source","title":"Schema Source","text":""},{"location":"surf_humidity/#linkml-source","title":"LinkML Source","text":"
name: surf_humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Surfaces: water activity as a function of air and material moisture'\ntitle: surface humidity\nexamples:\n- value: 10%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000123\nalias: surf_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"surf_material/","title":"Slot: surface material (surf_material)","text":"

Surface materials at the point of sampling

URI: MIXS:0000758

"},{"location":"surf_material/#inheritance","title":"Inheritance","text":""},{"location":"surf_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_material/#properties","title":"Properties","text":""},{"location":"surf_material/#aliases","title":"Aliases","text":""},{"location":"surf_material/#examples","title":"Examples","text":"Value wood"},{"location":"surf_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_material/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"surf_material/#schema-source","title":"Schema Source","text":""},{"location":"surf_material/#linkml-source","title":"LinkML Source","text":"
name: surf_material\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Surface materials at the point of sampling\ntitle: surface material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000758\nalias: surf_material\ndomain_of:\n- Biosample\nrange: surf_material_enum\nmultivalued: false\n\n
"},{"location":"surf_moisture/","title":"Slot: surface moisture (surf_moisture)","text":"

Water held on a surface

URI: MIXS:0000128

"},{"location":"surf_moisture/#inheritance","title":"Inheritance","text":""},{"location":"surf_moisture/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_moisture/#properties","title":"Properties","text":""},{"location":"surf_moisture/#aliases","title":"Aliases","text":""},{"location":"surf_moisture/#examples","title":"Examples","text":"Value 0.01 gram per square meter"},{"location":"surf_moisture/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_moisture/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"surf_moisture/#schema-source","title":"Schema Source","text":""},{"location":"surf_moisture/#linkml-source","title":"LinkML Source","text":"
name: surf_moisture\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: parts per million, gram per cubic meter, gram per square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Water held on a surface\ntitle: surface moisture\nexamples:\n- value: 0.01 gram per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000128\nalias: surf_moisture\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"surf_moisture_ph/","title":"Slot: surface moisture pH (surf_moisture_ph)","text":"

ph measurement of surface

URI: MIXS:0000760

"},{"location":"surf_moisture_ph/#inheritance","title":"Inheritance","text":""},{"location":"surf_moisture_ph/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_moisture_ph/#properties","title":"Properties","text":""},{"location":"surf_moisture_ph/#aliases","title":"Aliases","text":""},{"location":"surf_moisture_ph/#examples","title":"Examples","text":"Value 7"},{"location":"surf_moisture_ph/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_moisture_ph/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"surf_moisture_ph/#schema-source","title":"Schema Source","text":""},{"location":"surf_moisture_ph/#linkml-source","title":"LinkML Source","text":"
name: surf_moisture_ph\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: ph measurement of surface\ntitle: surface moisture pH\nexamples:\n- value: '7'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000760\nalias: surf_moisture_ph\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\n
"},{"location":"surf_temp/","title":"Slot: surface temperature (surf_temp)","text":"

Temperature of the surface at the time of sampling

URI: MIXS:0000125

"},{"location":"surf_temp/#inheritance","title":"Inheritance","text":""},{"location":"surf_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_temp/#properties","title":"Properties","text":""},{"location":"surf_temp/#aliases","title":"Aliases","text":""},{"location":"surf_temp/#examples","title":"Examples","text":"Value 15 degree Celsius"},{"location":"surf_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"surf_temp/#schema-source","title":"Schema Source","text":""},{"location":"surf_temp/#linkml-source","title":"LinkML Source","text":"
name: surf_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Temperature of the surface at the time of sampling\ntitle: surface temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000125\nalias: surf_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"suspend_part_matter/","title":"Slot: suspended particulate matter (suspend_part_matter)","text":"

Concentration of suspended particulate matter

URI: MIXS:0000741

"},{"location":"suspend_part_matter/#inheritance","title":"Inheritance","text":""},{"location":"suspend_part_matter/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"suspend_part_matter/#properties","title":"Properties","text":""},{"location":"suspend_part_matter/#aliases","title":"Aliases","text":""},{"location":"suspend_part_matter/#examples","title":"Examples","text":"Value 0.5 milligram per liter"},{"location":"suspend_part_matter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"suspend_part_matter/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"suspend_part_matter/#schema-source","title":"Schema Source","text":""},{"location":"suspend_part_matter/#linkml-source","title":"LinkML Source","text":"
name: suspend_part_matter\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of suspended particulate matter\ntitle: suspended particulate matter\nexamples:\n- value: 0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended particulate matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000741\nalias: suspend_part_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"suspend_solids/","title":"Slot: suspended solids (suspend_solids)","text":"

Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances

URI: MIXS:0000150

"},{"location":"suspend_solids/#inheritance","title":"Inheritance","text":""},{"location":"suspend_solids/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"suspend_solids/#properties","title":"Properties","text":""},{"location":"suspend_solids/#aliases","title":"Aliases","text":""},{"location":"suspend_solids/#examples","title":"Examples","text":"Value"},{"location":"suspend_solids/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"suspend_solids/#annotations","title":"Annotations","text":"property value expected_value suspended solid name;measurement value"},{"location":"suspend_solids/#schema-source","title":"Schema Source","text":""},{"location":"suspend_solids/#linkml-source","title":"LinkML Source","text":"
name: suspend_solids\nannotations:\n  expected_value:\n    tag: expected_value\n    value: suspended solid name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, microgram, milligram per liter, mole per liter, gram per liter, part\n      per million\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of substances including a wide variety of material, such\n  as silt, decaying plant and animal matter; can include multiple substances\ntitle: suspended solids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended solids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000150\nalias: suspend_solids\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"tan/","title":"Slot: total acid number (tan)","text":"

Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)

URI: MIXS:0000120

"},{"location":"tan/#inheritance","title":"Inheritance","text":""},{"location":"tan/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tan/#properties","title":"Properties","text":""},{"location":"tan/#aliases","title":"Aliases","text":""},{"location":"tan/#examples","title":"Examples","text":"Value"},{"location":"tan/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tan/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tan/#schema-source","title":"Schema Source","text":""},{"location":"tan/#linkml-source","title":"LinkML Source","text":"
name: tan\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n  by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n  the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n  oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\ntitle: total acid number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total acid number\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000120\nalias: tan\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"target_gene/","title":"Slot: target gene (target_gene)","text":"

Targeted gene or locus name for marker gene studies

URI: MIXS:0000044

"},{"location":"target_gene/#inheritance","title":"Inheritance","text":""},{"location":"target_gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"target_gene/#properties","title":"Properties","text":""},{"location":"target_gene/#aliases","title":"Aliases","text":""},{"location":"target_gene/#examples","title":"Examples","text":"Value 16S rRNA, 18S rRNA, nif, amoA, rpo"},{"location":"target_gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"target_gene/#annotations","title":"Annotations","text":"property value expected_value gene name"},{"location":"target_gene/#schema-source","title":"Schema Source","text":""},{"location":"target_gene/#linkml-source","title":"LinkML Source","text":"
name: target_gene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gene name\ndescription: Targeted gene or locus name for marker gene studies\ntitle: target gene\nexamples:\n- value: 16S rRNA, 18S rRNA, nif, amoA, rpo\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target gene\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000044\nalias: target_gene\ndomain_of:\n- NucleotideSequencing\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"target_subfragment/","title":"Slot: target subfragment (target_subfragment)","text":"

Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA

URI: MIXS:0000045

"},{"location":"target_subfragment/#inheritance","title":"Inheritance","text":""},{"location":"target_subfragment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"target_subfragment/#properties","title":"Properties","text":""},{"location":"target_subfragment/#aliases","title":"Aliases","text":""},{"location":"target_subfragment/#examples","title":"Examples","text":"Value V6, V9, ITS"},{"location":"target_subfragment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"target_subfragment/#annotations","title":"Annotations","text":"property value expected_value gene fragment name"},{"location":"target_subfragment/#schema-source","title":"Schema Source","text":""},{"location":"target_subfragment/#linkml-source","title":"LinkML Source","text":"
name: target_subfragment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gene fragment name\ndescription: Name of subfragment of a gene or locus. Important to e.g. identify special\n  regions on marker genes like V6 on 16S rRNA\ntitle: target subfragment\nexamples:\n- value: V6, V9, ITS\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target subfragment\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000045\nalias: target_subfragment\ndomain_of:\n- NucleotideSequencing\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"technical_reps/","title":"Slot: number technical replicate (technical_reps)","text":"

If sending technical replicates of the same sample, indicate the replicate count.

URI: nmdc:technical_reps

"},{"location":"technical_reps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"technical_reps/#properties","title":"Properties","text":""},{"location":"technical_reps/#examples","title":"Examples","text":"Value 2"},{"location":"technical_reps/#comments","title":"Comments","text":""},{"location":"technical_reps/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"technical_reps/#schema-source","title":"Schema Source","text":""},{"location":"technical_reps/#linkml-source","title":"LinkML Source","text":"
name: technical_reps\ndescription: If sending technical replicates of the same sample, indicate the replicate\n  count.\ntitle: number technical replicate\ncomments:\n- This field is only required when completing metadata for samples being submitted\n  to EMSL for analyses.\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{integer}'\nalias: technical_reps\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"temp/","title":"Slot: temperature (temp)","text":"

Temperature of the sample at the time of sampling.

URI: MIXS:0000113

"},{"location":"temp/#inheritance","title":"Inheritance","text":""},{"location":"temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"temp/#properties","title":"Properties","text":""},{"location":"temp/#aliases","title":"Aliases","text":""},{"location":"temp/#examples","title":"Examples","text":"Value 25 degree Celsius"},{"location":"temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"temp/#schema-source","title":"Schema Source","text":""},{"location":"temp/#linkml-source","title":"LinkML Source","text":"
name: temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\ndescription: Temperature of the sample at the time of sampling.\ntitle: temperature\nexamples:\n- value: 25 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000113\nalias: temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"temp_out/","title":"Slot: temperature outside house (temp_out)","text":"

The recorded temperature value at sampling time outside

URI: MIXS:0000197

"},{"location":"temp_out/#inheritance","title":"Inheritance","text":""},{"location":"temp_out/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"temp_out/#properties","title":"Properties","text":""},{"location":"temp_out/#aliases","title":"Aliases","text":""},{"location":"temp_out/#examples","title":"Examples","text":"Value 5 degree Celsius"},{"location":"temp_out/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"temp_out/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"temp_out/#schema-source","title":"Schema Source","text":""},{"location":"temp_out/#linkml-source","title":"LinkML Source","text":"
name: temp_out\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The recorded temperature value at sampling time outside\ntitle: temperature outside house\nexamples:\n- value: 5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature outside house\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000197\nalias: temp_out\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"temperature/","title":"Slot: temperature","text":"

The value of a temperature measurement or temperature used in a process.

URI: nmdc:temperature

"},{"location":"temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no"},{"location":"temperature/#properties","title":"Properties","text":""},{"location":"temperature/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"temperature/#schema-source","title":"Schema Source","text":""},{"location":"temperature/#linkml-source","title":"LinkML Source","text":"
name: temperature\ndescription: The value of a temperature measurement or temperature used in a process.\nnotes:\n- Not to be confused with the MIXS:0000113\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: temperature\ndomain_of:\n- ChromatographyConfiguration\n- SubSamplingProcess\n- StorageProcess\n- ChromatographicSeparationProcess\n- DissolvingProcess\n- ChemicalConversionProcess\nrange: QuantityValue\n\n
"},{"location":"term/","title":"Slot: term","text":"

pointer to an ontology class

URI: nmdc:term

"},{"location":"term/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ControlledTermValue A controlled term or class from an ontology no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... yes"},{"location":"term/#properties","title":"Properties","text":""},{"location":"term/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"term/#schema-source","title":"Schema Source","text":""},{"location":"term/#linkml-source","title":"LinkML Source","text":"
name: term\ndescription: pointer to an ontology class\nnotes:\n- 'removed ''slot_uri: rdf:type'''\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: term\ndomain_of:\n- ControlledTermValue\nrange: OntologyClass\ninlined: true\n\n
"},{"location":"tertiary_treatment/","title":"Slot: tertiary treatment (tertiary_treatment)","text":"

The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment

URI: MIXS:0000352

"},{"location":"tertiary_treatment/#inheritance","title":"Inheritance","text":""},{"location":"tertiary_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tertiary_treatment/#properties","title":"Properties","text":""},{"location":"tertiary_treatment/#aliases","title":"Aliases","text":""},{"location":"tertiary_treatment/#examples","title":"Examples","text":"Value"},{"location":"tertiary_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tertiary_treatment/#annotations","title":"Annotations","text":"property value expected_value tertiary treatment type"},{"location":"tertiary_treatment/#schema-source","title":"Schema Source","text":""},{"location":"tertiary_treatment/#linkml-source","title":"LinkML Source","text":"
name: tertiary_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: tertiary treatment type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The process providing a final treatment stage to raise the effluent quality\n  before it is discharged to the receiving environment\ntitle: tertiary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tertiary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000352\nalias: tertiary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"tidal_stage/","title":"Slot: tidal stage (tidal_stage)","text":"

Stage of tide

URI: MIXS:0000750

"},{"location":"tidal_stage/#inheritance","title":"Inheritance","text":""},{"location":"tidal_stage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tidal_stage/#properties","title":"Properties","text":""},{"location":"tidal_stage/#aliases","title":"Aliases","text":""},{"location":"tidal_stage/#examples","title":"Examples","text":"Value high tide"},{"location":"tidal_stage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tidal_stage/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"tidal_stage/#schema-source","title":"Schema Source","text":""},{"location":"tidal_stage/#linkml-source","title":"LinkML Source","text":"
name: tidal_stage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Stage of tide\ntitle: tidal stage\nexamples:\n- value: high tide\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tidal stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000750\nalias: tidal_stage\ndomain_of:\n- Biosample\nrange: tidal_stage_enum\nmultivalued: false\n\n
"},{"location":"tillage/","title":"Slot: history/tillage (tillage)","text":"

Note method(s) used for tilling

URI: MIXS:0001081

"},{"location":"tillage/#inheritance","title":"Inheritance","text":""},{"location":"tillage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tillage/#properties","title":"Properties","text":""},{"location":"tillage/#aliases","title":"Aliases","text":""},{"location":"tillage/#examples","title":"Examples","text":"Value chisel"},{"location":"tillage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tillage/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"tillage/#schema-source","title":"Schema Source","text":""},{"location":"tillage/#linkml-source","title":"LinkML Source","text":"
name: tillage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Note method(s) used for tilling\ntitle: history/tillage\nexamples:\n- value: chisel\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/tillage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001081\nalias: tillage\ndomain_of:\n- Biosample\nrange: tillage_enum\nmultivalued: true\n\n
"},{"location":"tiss_cult_growth_med/","title":"Slot: tissue culture growth media (tiss_cult_growth_med)","text":"

Description of plant tissue culture growth media used

URI: MIXS:0001070

"},{"location":"tiss_cult_growth_med/#inheritance","title":"Inheritance","text":""},{"location":"tiss_cult_growth_med/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tiss_cult_growth_med/#properties","title":"Properties","text":""},{"location":"tiss_cult_growth_med/#aliases","title":"Aliases","text":""},{"location":"tiss_cult_growth_med/#examples","title":"Examples","text":"Value https://link.springer.com/content/pdf/10.1007/BF02796489.pdf"},{"location":"tiss_cult_growth_med/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tiss_cult_growth_med/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url or free text"},{"location":"tiss_cult_growth_med/#schema-source","title":"Schema Source","text":""},{"location":"tiss_cult_growth_med/#linkml-source","title":"LinkML Source","text":"
name: tiss_cult_growth_med\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url or free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Description of plant tissue culture growth media used\ntitle: tissue culture growth media\nexamples:\n- value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tissue culture growth media\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001070\nalias: tiss_cult_growth_med\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"title/","title":"Slot: title","text":"

A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.

URI: nmdc:title

"},{"location":"title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"title/#properties","title":"Properties","text":""},{"location":"title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"title/#schema-source","title":"Schema Source","text":""},{"location":"title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: A name given to the entity that differs from the name/label programmatically\n  assigned to it. For example, when extracting study information for GOLD, the GOLD\n  system has assigned a name/label. However, for display purposes, we may also wish\n  the capture the title of the proposal that was used to fund the study.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:title\nrank: 1000\nalias: title\ndomain_of:\n- Study\nrange: string\n\n
"},{"location":"toluene/","title":"Slot: toluene (toluene)","text":"

Concentration of toluene in the sample

URI: MIXS:0000154

"},{"location":"toluene/#inheritance","title":"Inheritance","text":""},{"location":"toluene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"toluene/#properties","title":"Properties","text":""},{"location":"toluene/#aliases","title":"Aliases","text":""},{"location":"toluene/#examples","title":"Examples","text":"Value"},{"location":"toluene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"toluene/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"toluene/#schema-source","title":"Schema Source","text":""},{"location":"toluene/#linkml-source","title":"LinkML Source","text":"
name: toluene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of toluene in the sample\ntitle: toluene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- toluene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000154\nalias: toluene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"too_short_contig_num/","title":"Slot: too_short_contig_num","text":"

URI: nmdc:too_short_contig_num

"},{"location":"too_short_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"too_short_contig_num/#properties","title":"Properties","text":""},{"location":"too_short_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"too_short_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"too_short_contig_num/#linkml-source","title":"LinkML Source","text":"
name: too_short_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: too_short_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"tot_carb/","title":"Slot: total carbon (tot_carb)","text":"

Total carbon content

URI: MIXS:0000525

"},{"location":"tot_carb/#inheritance","title":"Inheritance","text":""},{"location":"tot_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_carb/#properties","title":"Properties","text":""},{"location":"tot_carb/#aliases","title":"Aliases","text":""},{"location":"tot_carb/#examples","title":"Examples","text":"Value"},{"location":"tot_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_carb/#schema-source","title":"Schema Source","text":""},{"location":"tot_carb/#linkml-source","title":"LinkML Source","text":"
name: tot_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total carbon content\ntitle: total carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000525\nalias: tot_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_depth_water_col/","title":"Slot: total depth of water column (tot_depth_water_col)","text":"

Measurement of total depth of water column

URI: MIXS:0000634

"},{"location":"tot_depth_water_col/#inheritance","title":"Inheritance","text":""},{"location":"tot_depth_water_col/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_depth_water_col/#properties","title":"Properties","text":""},{"location":"tot_depth_water_col/#aliases","title":"Aliases","text":""},{"location":"tot_depth_water_col/#examples","title":"Examples","text":"Value 500 meter"},{"location":"tot_depth_water_col/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_depth_water_col/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_depth_water_col/#schema-source","title":"Schema Source","text":""},{"location":"tot_depth_water_col/#linkml-source","title":"LinkML Source","text":"
name: tot_depth_water_col\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of total depth of water column\ntitle: total depth of water column\nexamples:\n- value: 500 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total depth of water column\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000634\nalias: tot_depth_water_col\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_diss_nitro/","title":"Slot: total dissolved nitrogen (tot_diss_nitro)","text":"

Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen

URI: MIXS:0000744

"},{"location":"tot_diss_nitro/#inheritance","title":"Inheritance","text":""},{"location":"tot_diss_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_diss_nitro/#properties","title":"Properties","text":""},{"location":"tot_diss_nitro/#aliases","title":"Aliases","text":""},{"location":"tot_diss_nitro/#examples","title":"Examples","text":"Value 40 microgram per liter"},{"location":"tot_diss_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_diss_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_diss_nitro/#schema-source","title":"Schema Source","text":""},{"location":"tot_diss_nitro/#linkml-source","title":"LinkML Source","text":"
name: tot_diss_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n  by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\ntitle: total dissolved nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total dissolved nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000744\nalias: tot_diss_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_inorg_nitro/","title":"Slot: total inorganic nitrogen (tot_inorg_nitro)","text":"

Total inorganic nitrogen content

URI: MIXS:0000745

"},{"location":"tot_inorg_nitro/#inheritance","title":"Inheritance","text":""},{"location":"tot_inorg_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_inorg_nitro/#properties","title":"Properties","text":""},{"location":"tot_inorg_nitro/#aliases","title":"Aliases","text":""},{"location":"tot_inorg_nitro/#examples","title":"Examples","text":"Value 40 microgram per liter"},{"location":"tot_inorg_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_inorg_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_inorg_nitro/#schema-source","title":"Schema Source","text":""},{"location":"tot_inorg_nitro/#linkml-source","title":"LinkML Source","text":"
name: tot_inorg_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total inorganic nitrogen content\ntitle: total inorganic nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000745\nalias: tot_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_iron/","title":"Slot: total iron (tot_iron)","text":"

Concentration of total iron in the sample

URI: MIXS:0000105

"},{"location":"tot_iron/#inheritance","title":"Inheritance","text":""},{"location":"tot_iron/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_iron/#properties","title":"Properties","text":""},{"location":"tot_iron/#aliases","title":"Aliases","text":""},{"location":"tot_iron/#examples","title":"Examples","text":"Value"},{"location":"tot_iron/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_iron/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_iron/#schema-source","title":"Schema Source","text":""},{"location":"tot_iron/#linkml-source","title":"LinkML Source","text":"
name: tot_iron\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, milligram per kilogram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of total iron in the sample\ntitle: total iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000105\nalias: tot_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_nitro/","title":"Slot: total nitrogen concentration (tot_nitro)","text":"

Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen

URI: MIXS:0000102

"},{"location":"tot_nitro/#inheritance","title":"Inheritance","text":""},{"location":"tot_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_nitro/#properties","title":"Properties","text":""},{"location":"tot_nitro/#aliases","title":"Aliases","text":""},{"location":"tot_nitro/#examples","title":"Examples","text":"Value 50 micromole per liter"},{"location":"tot_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_nitro/#schema-source","title":"Schema Source","text":""},{"location":"tot_nitro/#linkml-source","title":"LinkML Source","text":"
name: tot_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Total nitrogen concentration of water samples, calculated by: total\n  nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n  without filtering, reported as nitrogen'\ntitle: total nitrogen concentration\nexamples:\n- value: 50 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen concentration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000102\nalias: tot_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_nitro_cont_meth/","title":"Slot: total nitrogen content method (tot_nitro_cont_meth)","text":"

Reference or method used in determining the total nitrogen

URI: MIXS:0000338

"},{"location":"tot_nitro_cont_meth/#inheritance","title":"Inheritance","text":""},{"location":"tot_nitro_cont_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_nitro_cont_meth/#properties","title":"Properties","text":""},{"location":"tot_nitro_cont_meth/#aliases","title":"Aliases","text":""},{"location":"tot_nitro_cont_meth/#examples","title":"Examples","text":"Value"},{"location":"tot_nitro_cont_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_nitro_cont_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"tot_nitro_cont_meth/#schema-source","title":"Schema Source","text":""},{"location":"tot_nitro_cont_meth/#linkml-source","title":"LinkML Source","text":"
name: tot_nitro_cont_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining the total nitrogen\ntitle: total nitrogen content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000338\nalias: tot_nitro_cont_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"tot_nitro_content/","title":"Slot: total nitrogen content (tot_nitro_content)","text":"

Total nitrogen content of the sample

URI: MIXS:0000530

"},{"location":"tot_nitro_content/#inheritance","title":"Inheritance","text":""},{"location":"tot_nitro_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_nitro_content/#properties","title":"Properties","text":""},{"location":"tot_nitro_content/#aliases","title":"Aliases","text":""},{"location":"tot_nitro_content/#examples","title":"Examples","text":"Value"},{"location":"tot_nitro_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_nitro_content/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_nitro_content/#schema-source","title":"Schema Source","text":""},{"location":"tot_nitro_content/#linkml-source","title":"LinkML Source","text":"
name: tot_nitro_content\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total nitrogen content of the sample\ntitle: total nitrogen content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000530\nalias: tot_nitro_content\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_org_c_meth/","title":"Slot: total organic carbon method (tot_org_c_meth)","text":"

Reference or method used in determining total organic carbon

URI: MIXS:0000337

"},{"location":"tot_org_c_meth/#inheritance","title":"Inheritance","text":""},{"location":"tot_org_c_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_org_c_meth/#properties","title":"Properties","text":""},{"location":"tot_org_c_meth/#aliases","title":"Aliases","text":""},{"location":"tot_org_c_meth/#examples","title":"Examples","text":"Value"},{"location":"tot_org_c_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_org_c_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"tot_org_c_meth/#schema-source","title":"Schema Source","text":""},{"location":"tot_org_c_meth/#linkml-source","title":"LinkML Source","text":"
name: tot_org_c_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining total organic carbon\ntitle: total organic carbon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000337\nalias: tot_org_c_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"tot_org_carb/","title":"Slot: total organic carbon (tot_org_carb)","text":"

Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content

URI: MIXS:0000533

"},{"location":"tot_org_carb/#inheritance","title":"Inheritance","text":""},{"location":"tot_org_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_org_carb/#properties","title":"Properties","text":""},{"location":"tot_org_carb/#aliases","title":"Aliases","text":""},{"location":"tot_org_carb/#examples","title":"Examples","text":"Value"},{"location":"tot_org_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_org_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_org_carb/#schema-source","title":"Schema Source","text":""},{"location":"tot_org_carb/#linkml-source","title":"LinkML Source","text":"
name: tot_org_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram Carbon per kilogram sample material\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Definition for soil: total organic carbon content of the soil, definition\n  otherwise: total organic carbon content'\ntitle: total organic carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000533\nalias: tot_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_part_carb/","title":"Slot: total particulate carbon (tot_part_carb)","text":"

Total particulate carbon content

URI: MIXS:0000747

"},{"location":"tot_part_carb/#inheritance","title":"Inheritance","text":""},{"location":"tot_part_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_part_carb/#properties","title":"Properties","text":""},{"location":"tot_part_carb/#aliases","title":"Aliases","text":""},{"location":"tot_part_carb/#examples","title":"Examples","text":"Value 35 micromole per liter"},{"location":"tot_part_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_part_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_part_carb/#schema-source","title":"Schema Source","text":""},{"location":"tot_part_carb/#linkml-source","title":"LinkML Source","text":"
name: tot_part_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total particulate carbon content\ntitle: total particulate carbon\nexamples:\n- value: 35 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total particulate carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000747\nalias: tot_part_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_phosp/","title":"Slot: total phosphorus (tot_phosp)","text":"

Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus

URI: MIXS:0000117

"},{"location":"tot_phosp/#inheritance","title":"Inheritance","text":""},{"location":"tot_phosp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_phosp/#properties","title":"Properties","text":""},{"location":"tot_phosp/#aliases","title":"Aliases","text":""},{"location":"tot_phosp/#examples","title":"Examples","text":"Value 0.03 milligram per liter"},{"location":"tot_phosp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_phosp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_phosp/#schema-source","title":"Schema Source","text":""},{"location":"tot_phosp/#linkml-source","title":"LinkML Source","text":"
name: tot_phosp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Total phosphorus concentration in the sample, calculated by: total phosphorus\n  = total dissolved phosphorus + particulate phosphorus'\ntitle: total phosphorus\nexamples:\n- value: 0.03 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000117\nalias: tot_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_phosphate/","title":"Slot: total phosphate (tot_phosphate)","text":"

Total amount or concentration of phosphate

URI: MIXS:0000689

"},{"location":"tot_phosphate/#inheritance","title":"Inheritance","text":""},{"location":"tot_phosphate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_phosphate/#properties","title":"Properties","text":""},{"location":"tot_phosphate/#aliases","title":"Aliases","text":""},{"location":"tot_phosphate/#examples","title":"Examples","text":"Value"},{"location":"tot_phosphate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_phosphate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_phosphate/#schema-source","title":"Schema Source","text":""},{"location":"tot_phosphate/#linkml-source","title":"LinkML Source","text":"
name: tot_phosphate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total amount or concentration of phosphate\ntitle: total phosphate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000689\nalias: tot_phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_sulfur/","title":"Slot: total sulfur (tot_sulfur)","text":"

Concentration of total sulfur in the sample

URI: MIXS:0000419

"},{"location":"tot_sulfur/#inheritance","title":"Inheritance","text":""},{"location":"tot_sulfur/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_sulfur/#properties","title":"Properties","text":""},{"location":"tot_sulfur/#aliases","title":"Aliases","text":""},{"location":"tot_sulfur/#examples","title":"Examples","text":"Value"},{"location":"tot_sulfur/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_sulfur/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_sulfur/#schema-source","title":"Schema Source","text":""},{"location":"tot_sulfur/#linkml-source","title":"LinkML Source","text":"
name: tot_sulfur\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of total sulfur in the sample\ntitle: total sulfur\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total sulfur\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000419\nalias: tot_sulfur\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"total_bases/","title":"Slot: total_bases","text":"

URI: nmdc:total_bases

"},{"location":"total_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"total_bases/#properties","title":"Properties","text":""},{"location":"total_bases/#todos","title":"TODOs","text":""},{"location":"total_bases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"total_bases/#schema-source","title":"Schema Source","text":""},{"location":"total_bases/#linkml-source","title":"LinkML Source","text":"
name: total_bases\ntodos:\n- this slot needs some basic textual annotations and constraints\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: total_bases\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"train_line/","title":"Slot: train line (train_line)","text":"

The subway line name

URI: MIXS:0000837

"},{"location":"train_line/#inheritance","title":"Inheritance","text":""},{"location":"train_line/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"train_line/#properties","title":"Properties","text":""},{"location":"train_line/#aliases","title":"Aliases","text":""},{"location":"train_line/#examples","title":"Examples","text":"Value red"},{"location":"train_line/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"train_line/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"train_line/#schema-source","title":"Schema Source","text":""},{"location":"train_line/#linkml-source","title":"LinkML Source","text":"
name: train_line\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The subway line name\ntitle: train line\nexamples:\n- value: red\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train line\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000837\nalias: train_line\ndomain_of:\n- Biosample\nrange: train_line_enum\nmultivalued: false\n\n
"},{"location":"train_stat_loc/","title":"Slot: train station collection location (train_stat_loc)","text":"

The train station collection location

URI: MIXS:0000838

"},{"location":"train_stat_loc/#inheritance","title":"Inheritance","text":""},{"location":"train_stat_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"train_stat_loc/#properties","title":"Properties","text":""},{"location":"train_stat_loc/#aliases","title":"Aliases","text":""},{"location":"train_stat_loc/#examples","title":"Examples","text":"Value forest hills"},{"location":"train_stat_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"train_stat_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"train_stat_loc/#schema-source","title":"Schema Source","text":""},{"location":"train_stat_loc/#linkml-source","title":"LinkML Source","text":"
name: train_stat_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The train station collection location\ntitle: train station collection location\nexamples:\n- value: forest hills\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train station collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000838\nalias: train_stat_loc\ndomain_of:\n- Biosample\nrange: train_stat_loc_enum\nmultivalued: false\n\n
"},{"location":"train_stop_loc/","title":"Slot: train stop collection location (train_stop_loc)","text":"

The train stop collection location

URI: MIXS:0000839

"},{"location":"train_stop_loc/#inheritance","title":"Inheritance","text":""},{"location":"train_stop_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"train_stop_loc/#properties","title":"Properties","text":""},{"location":"train_stop_loc/#aliases","title":"Aliases","text":""},{"location":"train_stop_loc/#examples","title":"Examples","text":"Value end"},{"location":"train_stop_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"train_stop_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"train_stop_loc/#schema-source","title":"Schema Source","text":""},{"location":"train_stop_loc/#linkml-source","title":"LinkML Source","text":"
name: train_stop_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The train stop collection location\ntitle: train stop collection location\nexamples:\n- value: end\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train stop collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000839\nalias: train_stop_loc\ndomain_of:\n- Biosample\nrange: train_stop_loc_enum\nmultivalued: false\n\n
"},{"location":"turbidity/","title":"Slot: turbidity (turbidity)","text":"

Measure of the amount of cloudiness or haziness in water caused by individual particles

URI: MIXS:0000191

"},{"location":"turbidity/#inheritance","title":"Inheritance","text":""},{"location":"turbidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"turbidity/#properties","title":"Properties","text":""},{"location":"turbidity/#aliases","title":"Aliases","text":""},{"location":"turbidity/#examples","title":"Examples","text":"Value 0.3 nephelometric turbidity units"},{"location":"turbidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"turbidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"turbidity/#schema-source","title":"Schema Source","text":""},{"location":"turbidity/#linkml-source","title":"LinkML Source","text":"
name: turbidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: formazin turbidity unit, formazin nephelometric units\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measure of the amount of cloudiness or haziness in water caused by individual\n  particles\ntitle: turbidity\nexamples:\n- value: 0.3 nephelometric turbidity units\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- turbidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000191\nalias: turbidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tvdss_of_hcr_press/","title":"Slot: depth (TVDSS) of hydrocarbon resource pressure (tvdss_of_hcr_press)","text":"

True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).

URI: MIXS:0000397

"},{"location":"tvdss_of_hcr_press/#inheritance","title":"Inheritance","text":""},{"location":"tvdss_of_hcr_press/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tvdss_of_hcr_press/#properties","title":"Properties","text":""},{"location":"tvdss_of_hcr_press/#aliases","title":"Aliases","text":""},{"location":"tvdss_of_hcr_press/#examples","title":"Examples","text":"Value"},{"location":"tvdss_of_hcr_press/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tvdss_of_hcr_press/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tvdss_of_hcr_press/#schema-source","title":"Schema Source","text":""},{"location":"tvdss_of_hcr_press/#linkml-source","title":"LinkML Source","text":"
name: tvdss_of_hcr_press\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n  the original pressure was measured (e.g. 1578 m).\ntitle: depth (TVDSS) of hydrocarbon resource pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000397\nalias: tvdss_of_hcr_press\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tvdss_of_hcr_temp/","title":"Slot: depth (TVDSS) of hydrocarbon resource temperature (tvdss_of_hcr_temp)","text":"

True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).

URI: MIXS:0000394

"},{"location":"tvdss_of_hcr_temp/#inheritance","title":"Inheritance","text":""},{"location":"tvdss_of_hcr_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tvdss_of_hcr_temp/#properties","title":"Properties","text":""},{"location":"tvdss_of_hcr_temp/#aliases","title":"Aliases","text":""},{"location":"tvdss_of_hcr_temp/#examples","title":"Examples","text":"Value"},{"location":"tvdss_of_hcr_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tvdss_of_hcr_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tvdss_of_hcr_temp/#schema-source","title":"Schema Source","text":""},{"location":"tvdss_of_hcr_temp/#linkml-source","title":"LinkML Source","text":"
name: tvdss_of_hcr_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n  the original temperature was measured (e.g. 1345 m).\ntitle: depth (TVDSS) of hydrocarbon resource temperature\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000394\nalias: tvdss_of_hcr_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"typ_occup_density/","title":"Slot: typical occupant density (typ_occup_density)","text":"

Customary or normal density of occupants

URI: MIXS:0000771

"},{"location":"typ_occup_density/#inheritance","title":"Inheritance","text":""},{"location":"typ_occup_density/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"typ_occup_density/#properties","title":"Properties","text":""},{"location":"typ_occup_density/#aliases","title":"Aliases","text":""},{"location":"typ_occup_density/#examples","title":"Examples","text":"Value 25"},{"location":"typ_occup_density/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"typ_occup_density/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"typ_occup_density/#schema-source","title":"Schema Source","text":""},{"location":"typ_occup_density/#linkml-source","title":"LinkML Source","text":"
name: typ_occup_density\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Customary or normal density of occupants\ntitle: typical occupant density\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- typical occupant density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000771\nalias: typ_occup_density\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\n
"},{"location":"type/","title":"Slot: type","text":"

the class_uri of the class that has been instantiated

URI: rdf:type

"},{"location":"type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TimestampValue A value that is a timestamp no PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no MetaproteomicsAnalysis no ImageValue An attribute value representing an image no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no NamedThing a databased entity or concept/class no Extraction A material separation in which a desired component of an input material is se... no AttributeValue The value for any value of a attribute for a sample no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no WorkflowExecution Represents an instance of an execution of a particular workflow no Biosample Biological source material which can be characterized by an experiment no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no Configuration A set of parameters that define the actions of a process and is shared among ... no PersonValue An attribute value representing a person no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no FunctionalAnnotation An assignment of a function term (e no CreditAssociation This class supports binding associated researchers to studies no CollectingBiosamplesFromSite no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no Site no TextValue A basic string value no ControlledTermValue A controlled term or class from an ontology no NomAnalysis no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no MetabolomicsAnalysis no ProcessedSample no OntologyClass no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no MagBin no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no Doi A centrally registered identifier symbol used to uniquely identify objects gi... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no GeneProduct A molecule encoded by a gene that has an evolved function no FailureCategorization no DataObject An object that primarily consists of symbols that represent information no FunctionalAnnotationAggMember no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no QuantityValue A simple quantity, e no Instrument A material entity that is designed to perform a function in a scientific inve... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no FiltrationProcess The process of segregation of phases; e no MetatranscriptomeAssembly no EnvironmentalMaterialTerm no GenomeFeature A feature localized to an interval along a genome no LibraryPreparation no GeolocationValue A normalized value for a location on the earth's surface no MetagenomeSequencing Initial sequencing activity that precedes any analysis no Pooling physical combination of several instances of like material no MaterialEntity no CalibrationInformation A calibration object that is associated with a process no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no DataGeneration The methods and processes used to generate omics data from a biosample or org... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no OrthologyGroup A set of genes or gene products in which all members are orthologous no PlannedProcess no Protocol no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no Study A study summarizes the overall goal of a research initiative and outlines the... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no Manifest no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"type/#properties","title":"Properties","text":""},{"location":"type/#examples","title":"Examples","text":"Value nmdc:Biosample nmdc:Study"},{"location":"type/#see-also","title":"See Also","text":""},{"location":"type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"type/#schema-source","title":"Schema Source","text":""},{"location":"type/#linkml-source","title":"LinkML Source","text":"
name: type\ndescription: the class_uri of the class that has been instantiated\nnotes:\n- replaces legacy nmdc:type slot\n- makes it easier to read example data files\n- required for polymorphic MongoDB collections\nexamples:\n- value: nmdc:Biosample\n- value: nmdc:Study\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-schema/issues/1048\n- https://github.com/microbiomedata/nmdc-schema/issues/1233\n- https://github.com/microbiomedata/nmdc-schema/issues/248\nrank: 1000\nslot_uri: rdf:type\ndesignates_type: true\nalias: type\ndomain_of:\n- EukEval\n- FunctionalAnnotationAggMember\n- MobilePhaseSegment\n- PortionOfSubstance\n- MagBin\n- MetaboliteIdentification\n- PeptideQuantification\n- ProteinQuantification\n- GenomeFeature\n- FunctionalAnnotation\n- AttributeValue\n- NamedThing\n- FailureCategorization\n- Protocol\n- CreditAssociation\n- Doi\nrange: uriorcurie\nrequired: true\n\n
"},{"location":"unbinned_contig_num/","title":"Slot: unbinned_contig_num","text":"

URI: nmdc:unbinned_contig_num

"},{"location":"unbinned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"unbinned_contig_num/#properties","title":"Properties","text":""},{"location":"unbinned_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"unbinned_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"unbinned_contig_num/#linkml-source","title":"LinkML Source","text":"
name: unbinned_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: unbinned_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"url/","title":"Slot: url","text":"

URI: nmdc:url

"},{"location":"url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Protocol no ImageValue An attribute value representing an image no DataObject An object that primarily consists of symbols that represent information no"},{"location":"url/#properties","title":"Properties","text":""},{"location":"url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"url/#schema-source","title":"Schema Source","text":""},{"location":"url/#linkml-source","title":"LinkML Source","text":"
name: url\nnotes:\n- See issue 207 - this clashes with the mixs field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: url\ndomain_of:\n- ImageValue\n- Protocol\n- DataObject\nrange: string\n\n
"},{"location":"value/","title":"Slot: value","text":"

URI: nmdc:value

"},{"location":"value/#properties","title":"Properties","text":""},{"location":"value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"value/#schema-source","title":"Schema Source","text":""},{"location":"value/#linkml-source","title":"LinkML Source","text":"
name: value\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: value\nrange: QuantityValue\n\n
"},{"location":"vendor/","title":"Slot: vendor","text":"

URI: nmdc:vendor

"},{"location":"vendor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Instrument A material entity that is designed to perform a function in a scientific inve... no"},{"location":"vendor/#properties","title":"Properties","text":""},{"location":"vendor/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"vendor/#schema-source","title":"Schema Source","text":""},{"location":"vendor/#linkml-source","title":"LinkML Source","text":"
name: vendor\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: vendor\ndomain_of:\n- Instrument\nrange: InstrumentVendorEnum\n\n
"},{"location":"ventilation_rate/","title":"Slot: ventilation rate (ventilation_rate)","text":"

Ventilation rate of the system in the sampled premises

URI: MIXS:0000114

"},{"location":"ventilation_rate/#inheritance","title":"Inheritance","text":""},{"location":"ventilation_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ventilation_rate/#properties","title":"Properties","text":""},{"location":"ventilation_rate/#aliases","title":"Aliases","text":""},{"location":"ventilation_rate/#examples","title":"Examples","text":"Value 750 cubic meter per minute"},{"location":"ventilation_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ventilation_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ventilation_rate/#schema-source","title":"Schema Source","text":""},{"location":"ventilation_rate/#linkml-source","title":"LinkML Source","text":"
name: ventilation_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic meter per minute, liters per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Ventilation rate of the system in the sampled premises\ntitle: ventilation rate\nexamples:\n- value: 750 cubic meter per minute\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000114\nalias: ventilation_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ventilation_type/","title":"Slot: ventilation type (ventilation_type)","text":"

Ventilation system used in the sampled premises

URI: MIXS:0000756

"},{"location":"ventilation_type/#inheritance","title":"Inheritance","text":""},{"location":"ventilation_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ventilation_type/#properties","title":"Properties","text":""},{"location":"ventilation_type/#aliases","title":"Aliases","text":""},{"location":"ventilation_type/#examples","title":"Examples","text":"Value Operable windows"},{"location":"ventilation_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ventilation_type/#annotations","title":"Annotations","text":"property value expected_value ventilation type name"},{"location":"ventilation_type/#schema-source","title":"Schema Source","text":""},{"location":"ventilation_type/#linkml-source","title":"LinkML Source","text":"
name: ventilation_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: ventilation type name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Ventilation system used in the sampled premises\ntitle: ventilation type\nexamples:\n- value: Operable windows\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000756\nalias: ventilation_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"version/","title":"Slot: version","text":"

URI: nmdc:version

"},{"location":"version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetaproteomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetatranscriptomeAnnotation no MetatranscriptomeAssembly no"},{"location":"version/#properties","title":"Properties","text":""},{"location":"version/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"version/#schema-source","title":"Schema Source","text":""},{"location":"version/#linkml-source","title":"LinkML Source","text":"
name: version\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: version\ndomain_of:\n- WorkflowExecution\nrange: string\n\n
"},{"location":"vfa/","title":"Slot: volatile fatty acids (vfa)","text":"

Concentration of Volatile Fatty Acids in the sample

URI: MIXS:0000152

"},{"location":"vfa/#inheritance","title":"Inheritance","text":""},{"location":"vfa/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"vfa/#properties","title":"Properties","text":""},{"location":"vfa/#aliases","title":"Aliases","text":""},{"location":"vfa/#examples","title":"Examples","text":"Value"},{"location":"vfa/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"vfa/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"vfa/#schema-source","title":"Schema Source","text":""},{"location":"vfa/#linkml-source","title":"LinkML Source","text":"
name: vfa\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of Volatile Fatty Acids in the sample\ntitle: volatile fatty acids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile fatty acids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000152\nalias: vfa\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"vfa_fw/","title":"Slot: vfa in formation water (vfa_fw)","text":"

Original volatile fatty acid concentration in the hydrocarbon resource

URI: MIXS:0000408

"},{"location":"vfa_fw/#inheritance","title":"Inheritance","text":""},{"location":"vfa_fw/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"vfa_fw/#properties","title":"Properties","text":""},{"location":"vfa_fw/#aliases","title":"Aliases","text":""},{"location":"vfa_fw/#examples","title":"Examples","text":"Value"},{"location":"vfa_fw/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"vfa_fw/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"vfa_fw/#schema-source","title":"Schema Source","text":""},{"location":"vfa_fw/#linkml-source","title":"LinkML Source","text":"
name: vfa_fw\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original volatile fatty acid concentration in the hydrocarbon resource\ntitle: vfa in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- vfa in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000408\nalias: vfa_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"vis_media/","title":"Slot: visual media (vis_media)","text":"

The building visual media

URI: MIXS:0000840

"},{"location":"vis_media/#inheritance","title":"Inheritance","text":""},{"location":"vis_media/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"vis_media/#properties","title":"Properties","text":""},{"location":"vis_media/#aliases","title":"Aliases","text":""},{"location":"vis_media/#examples","title":"Examples","text":"Value 3D scans"},{"location":"vis_media/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"vis_media/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"vis_media/#schema-source","title":"Schema Source","text":""},{"location":"vis_media/#linkml-source","title":"LinkML Source","text":"
name: vis_media\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The building visual media\ntitle: visual media\nexamples:\n- value: 3D scans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- visual media\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000840\nalias: vis_media\ndomain_of:\n- Biosample\nrange: vis_media_enum\nmultivalued: false\n\n
"},{"location":"viscosity/","title":"Slot: viscosity (viscosity)","text":"

A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)

URI: MIXS:0000126

"},{"location":"viscosity/#inheritance","title":"Inheritance","text":""},{"location":"viscosity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"viscosity/#properties","title":"Properties","text":""},{"location":"viscosity/#aliases","title":"Aliases","text":""},{"location":"viscosity/#examples","title":"Examples","text":"Value"},{"location":"viscosity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"viscosity/#annotations","title":"Annotations","text":"property value expected_value measurement value;measurement value"},{"location":"viscosity/#schema-source","title":"Schema Source","text":""},{"location":"viscosity/#linkml-source","title":"LinkML Source","text":"
name: viscosity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cP at degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n  stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\ntitle: viscosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- viscosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000126\nalias: viscosity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"volatile_org_comp/","title":"Slot: volatile organic compounds (volatile_org_comp)","text":"

Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound

URI: MIXS:0000115

"},{"location":"volatile_org_comp/#inheritance","title":"Inheritance","text":""},{"location":"volatile_org_comp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"volatile_org_comp/#properties","title":"Properties","text":""},{"location":"volatile_org_comp/#aliases","title":"Aliases","text":""},{"location":"volatile_org_comp/#examples","title":"Examples","text":"Value formaldehyde;500 nanogram per liter"},{"location":"volatile_org_comp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"volatile_org_comp/#annotations","title":"Annotations","text":"property value expected_value volatile organic compound name;measurement value"},{"location":"volatile_org_comp/#schema-source","title":"Schema Source","text":""},{"location":"volatile_org_comp/#linkml-source","title":"LinkML Source","text":"
name: volatile_org_comp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: volatile organic compound name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per cubic meter, parts per million, nanogram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of carbon-based chemicals that easily evaporate at room\n  temperature; can report multiple volatile organic compounds by entering numeric\n  values preceded by name of compound\ntitle: volatile organic compounds\nexamples:\n- value: formaldehyde;500 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile organic compounds\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000115\nalias: volatile_org_comp\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"volume/","title":"Slot: volume","text":"

The volume of a substance.

URI: nmdc:volume

"},{"location":"volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e yes PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no Extraction A material separation in which a desired component of an input material is se... yes MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes"},{"location":"volume/#properties","title":"Properties","text":""},{"location":"volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"volume/#schema-source","title":"Schema Source","text":""},{"location":"volume/#linkml-source","title":"LinkML Source","text":"
name: volume\ndescription: The volume of a substance.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: volume\ndomain_of:\n- Extraction\n- SubSamplingProcess\n- FiltrationProcess\n- MobilePhaseSegment\n- PortionOfSubstance\nrange: QuantityValue\n\n
"},{"location":"wall_area/","title":"Slot: wall area (wall_area)","text":"

The total area of the sampled room's walls

URI: MIXS:0000198

"},{"location":"wall_area/#inheritance","title":"Inheritance","text":""},{"location":"wall_area/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_area/#properties","title":"Properties","text":""},{"location":"wall_area/#aliases","title":"Aliases","text":""},{"location":"wall_area/#examples","title":"Examples","text":"Value"},{"location":"wall_area/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_area/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"wall_area/#schema-source","title":"Schema Source","text":""},{"location":"wall_area/#linkml-source","title":"LinkML Source","text":"
name: wall_area\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The total area of the sampled room's walls\ntitle: wall area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000198\nalias: wall_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"wall_const_type/","title":"Slot: wall construction type (wall_const_type)","text":"

The building class of the wall defined by the composition of the building elements and fire-resistance rating.

URI: MIXS:0000841

"},{"location":"wall_const_type/#inheritance","title":"Inheritance","text":""},{"location":"wall_const_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_const_type/#properties","title":"Properties","text":""},{"location":"wall_const_type/#aliases","title":"Aliases","text":""},{"location":"wall_const_type/#examples","title":"Examples","text":"Value fire resistive"},{"location":"wall_const_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_const_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_const_type/#schema-source","title":"Schema Source","text":""},{"location":"wall_const_type/#linkml-source","title":"LinkML Source","text":"
name: wall_const_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The building class of the wall defined by the composition of the building\n  elements and fire-resistance rating.\ntitle: wall construction type\nexamples:\n- value: fire resistive\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall construction type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000841\nalias: wall_const_type\ndomain_of:\n- Biosample\nrange: wall_const_type_enum\nmultivalued: false\n\n
"},{"location":"wall_finish_mat/","title":"Slot: wall finish material (wall_finish_mat)","text":"

The material utilized to finish the outer most layer of the wall

URI: MIXS:0000842

"},{"location":"wall_finish_mat/#inheritance","title":"Inheritance","text":""},{"location":"wall_finish_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_finish_mat/#properties","title":"Properties","text":""},{"location":"wall_finish_mat/#aliases","title":"Aliases","text":""},{"location":"wall_finish_mat/#examples","title":"Examples","text":"Value wood"},{"location":"wall_finish_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_finish_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_finish_mat/#schema-source","title":"Schema Source","text":""},{"location":"wall_finish_mat/#linkml-source","title":"LinkML Source","text":"
name: wall_finish_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The material utilized to finish the outer most layer of the wall\ntitle: wall finish material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000842\nalias: wall_finish_mat\ndomain_of:\n- Biosample\nrange: wall_finish_mat_enum\nmultivalued: false\n\n
"},{"location":"wall_height/","title":"Slot: wall height (wall_height)","text":"

The average height of the walls in the sampled room

URI: MIXS:0000221

"},{"location":"wall_height/#inheritance","title":"Inheritance","text":""},{"location":"wall_height/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_height/#properties","title":"Properties","text":""},{"location":"wall_height/#aliases","title":"Aliases","text":""},{"location":"wall_height/#examples","title":"Examples","text":"Value"},{"location":"wall_height/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_height/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"wall_height/#schema-source","title":"Schema Source","text":""},{"location":"wall_height/#linkml-source","title":"LinkML Source","text":"
name: wall_height\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average height of the walls in the sampled room\ntitle: wall height\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000221\nalias: wall_height\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"wall_loc/","title":"Slot: wall location (wall_loc)","text":"

The relative location of the wall within the room

URI: MIXS:0000843

"},{"location":"wall_loc/#inheritance","title":"Inheritance","text":""},{"location":"wall_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_loc/#properties","title":"Properties","text":""},{"location":"wall_loc/#aliases","title":"Aliases","text":""},{"location":"wall_loc/#examples","title":"Examples","text":"Value north"},{"location":"wall_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_loc/#schema-source","title":"Schema Source","text":""},{"location":"wall_loc/#linkml-source","title":"LinkML Source","text":"
name: wall_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The relative location of the wall within the room\ntitle: wall location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000843\nalias: wall_loc\ndomain_of:\n- Biosample\nrange: wall_loc_enum\nmultivalued: false\n\n
"},{"location":"wall_surf_treatment/","title":"Slot: wall surface treatment (wall_surf_treatment)","text":"

The surface treatment of interior wall

URI: MIXS:0000845

"},{"location":"wall_surf_treatment/#inheritance","title":"Inheritance","text":""},{"location":"wall_surf_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_surf_treatment/#properties","title":"Properties","text":""},{"location":"wall_surf_treatment/#aliases","title":"Aliases","text":""},{"location":"wall_surf_treatment/#examples","title":"Examples","text":"Value paneling"},{"location":"wall_surf_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_surf_treatment/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_surf_treatment/#schema-source","title":"Schema Source","text":""},{"location":"wall_surf_treatment/#linkml-source","title":"LinkML Source","text":"
name: wall_surf_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The surface treatment of interior wall\ntitle: wall surface treatment\nexamples:\n- value: paneling\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall surface treatment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000845\nalias: wall_surf_treatment\ndomain_of:\n- Biosample\nrange: wall_surf_treatment_enum\nmultivalued: false\n\n
"},{"location":"wall_texture/","title":"Slot: wall texture (wall_texture)","text":"

The feel, appearance, or consistency of a wall surface

URI: MIXS:0000846

"},{"location":"wall_texture/#inheritance","title":"Inheritance","text":""},{"location":"wall_texture/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_texture/#properties","title":"Properties","text":""},{"location":"wall_texture/#aliases","title":"Aliases","text":""},{"location":"wall_texture/#examples","title":"Examples","text":"Value popcorn"},{"location":"wall_texture/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_texture/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_texture/#schema-source","title":"Schema Source","text":""},{"location":"wall_texture/#linkml-source","title":"LinkML Source","text":"
name: wall_texture\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The feel, appearance, or consistency of a wall surface\ntitle: wall texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000846\nalias: wall_texture\ndomain_of:\n- Biosample\nrange: wall_texture_enum\nmultivalued: false\n\n
"},{"location":"wall_thermal_mass/","title":"Slot: wall thermal mass (wall_thermal_mass)","text":"

The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint

URI: MIXS:0000222

"},{"location":"wall_thermal_mass/#inheritance","title":"Inheritance","text":""},{"location":"wall_thermal_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_thermal_mass/#properties","title":"Properties","text":""},{"location":"wall_thermal_mass/#aliases","title":"Aliases","text":""},{"location":"wall_thermal_mass/#examples","title":"Examples","text":"Value"},{"location":"wall_thermal_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_thermal_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"wall_thermal_mass/#schema-source","title":"Schema Source","text":""},{"location":"wall_thermal_mass/#linkml-source","title":"LinkML Source","text":"
name: wall_thermal_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: joule per degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The ability of the wall to provide inertia against temperature fluctuations.\n  Generally this means concrete or concrete block that is either exposed or covered\n  only with paint\ntitle: wall thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000222\nalias: wall_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"wall_water_mold/","title":"Slot: wall signs of water/mold (wall_water_mold)","text":"

Signs of the presence of mold or mildew on a wall

URI: MIXS:0000844

"},{"location":"wall_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"wall_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_water_mold/#properties","title":"Properties","text":""},{"location":"wall_water_mold/#aliases","title":"Aliases","text":""},{"location":"wall_water_mold/#examples","title":"Examples","text":"Value no presence of mold visible"},{"location":"wall_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"wall_water_mold/#linkml-source","title":"LinkML Source","text":"
name: wall_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on a wall\ntitle: wall signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000844\nalias: wall_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"was_generated_by/","title":"Slot: was_generated_by","text":"

URI: nmdc:was_generated_by

"},{"location":"was_generated_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e yes DataObject An object that primarily consists of symbols that represent information yes"},{"location":"was_generated_by/#properties","title":"Properties","text":""},{"location":"was_generated_by/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"was_generated_by/#schema-source","title":"Schema Source","text":""},{"location":"was_generated_by/#linkml-source","title":"LinkML Source","text":"
name: was_generated_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasGeneratedBy\nrank: 1000\nalias: was_generated_by\ndomain_of:\n- FunctionalAnnotation\n- DataObject\nrange: WorkflowExecution\nany_of:\n- range: WorkflowExecution\n- range: DataGeneration\n\n
"},{"location":"was_informed_by/","title":"Slot: was_informed_by","text":"

URI: nmdc:was_informed_by

"},{"location":"was_informed_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes MetaproteomicsAnalysis yes NomAnalysis yes ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... yes MetabolomicsAnalysis yes WorkflowExecution Represents an instance of an execution of a particular workflow yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes MetagenomeSequencing Initial sequencing activity that precedes any analysis yes MetatranscriptomeAnnotation yes MetatranscriptomeAssembly yes"},{"location":"was_informed_by/#properties","title":"Properties","text":""},{"location":"was_informed_by/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"was_informed_by/#schema-source","title":"Schema Source","text":""},{"location":"was_informed_by/#linkml-source","title":"LinkML Source","text":"
name: was_informed_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasInformedBy\nrank: 1000\nalias: was_informed_by\ndomain_of:\n- WorkflowExecution\nrange: DataGeneration\n\n
"},{"location":"wastewater_type/","title":"Slot: wastewater type (wastewater_type)","text":"

The origin of wastewater such as human waste, rainfall, storm drains, etc.

URI: MIXS:0000353

"},{"location":"wastewater_type/#inheritance","title":"Inheritance","text":""},{"location":"wastewater_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wastewater_type/#properties","title":"Properties","text":""},{"location":"wastewater_type/#aliases","title":"Aliases","text":""},{"location":"wastewater_type/#examples","title":"Examples","text":"Value"},{"location":"wastewater_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wastewater_type/#annotations","title":"Annotations","text":"property value expected_value wastewater type name"},{"location":"wastewater_type/#schema-source","title":"Schema Source","text":""},{"location":"wastewater_type/#linkml-source","title":"LinkML Source","text":"
name: wastewater_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: wastewater type name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The origin of wastewater such as human waste, rainfall, storm drains,\n  etc.\ntitle: wastewater type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wastewater type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000353\nalias: wastewater_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"water_cont_soil_meth/","title":"Slot: water content method (water_cont_soil_meth)","text":"

Reference or method used in determining the water content of soil

URI: MIXS:0000323

"},{"location":"water_cont_soil_meth/#inheritance","title":"Inheritance","text":""},{"location":"water_cont_soil_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"water_cont_soil_meth/#properties","title":"Properties","text":""},{"location":"water_cont_soil_meth/#aliases","title":"Aliases","text":""},{"location":"water_cont_soil_meth/#examples","title":"Examples","text":"Value"},{"location":"water_cont_soil_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_cont_soil_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"water_cont_soil_meth/#schema-source","title":"Schema Source","text":""},{"location":"water_cont_soil_meth/#linkml-source","title":"LinkML Source","text":"
name: water_cont_soil_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining the water content of soil\ntitle: water content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000323\nalias: water_cont_soil_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"water_content/","title":"Slot: water content (water_content)","text":"

Water content measurement

URI: MIXS:0000185

"},{"location":"water_content/#inheritance","title":"Inheritance","text":""},{"location":"water_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"water_content/#properties","title":"Properties","text":""},{"location":"water_content/#aliases","title":"Aliases","text":""},{"location":"water_content/#examples","title":"Examples","text":"Value"},{"location":"water_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_content/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_content/#schema-source","title":"Schema Source","text":""},{"location":"water_content/#linkml-source","title":"LinkML Source","text":"
name: water_content\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per gram or cubic centimeter per cubic centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Water content measurement\ntitle: water content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000185\nalias: water_content\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"water_current/","title":"Slot: water current (water_current)","text":"

Measurement of magnitude and direction of flow within a fluid

URI: MIXS:0000203

"},{"location":"water_current/#inheritance","title":"Inheritance","text":""},{"location":"water_current/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_current/#properties","title":"Properties","text":""},{"location":"water_current/#aliases","title":"Aliases","text":""},{"location":"water_current/#examples","title":"Examples","text":"Value 10 cubic meter per second"},{"location":"water_current/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_current/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_current/#schema-source","title":"Schema Source","text":""},{"location":"water_current/#linkml-source","title":"LinkML Source","text":"
name: water_current\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic meter per second, knots\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of magnitude and direction of flow within a fluid\ntitle: water current\nexamples:\n- value: 10 cubic meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water current\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000203\nalias: water_current\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"water_cut/","title":"Slot: water cut (water_cut)","text":"

Current amount of water (%) in a produced fluid stream; or the average of the combined streams

URI: MIXS:0000454

"},{"location":"water_cut/#inheritance","title":"Inheritance","text":""},{"location":"water_cut/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_cut/#properties","title":"Properties","text":""},{"location":"water_cut/#aliases","title":"Aliases","text":""},{"location":"water_cut/#examples","title":"Examples","text":"Value"},{"location":"water_cut/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_cut/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_cut/#schema-source","title":"Schema Source","text":""},{"location":"water_cut/#linkml-source","title":"LinkML Source","text":"
name: water_cut\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Current amount of water (%) in a produced fluid stream; or the average\n  of the combined streams\ntitle: water cut\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water cut\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000454\nalias: water_cut\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"water_feat_size/","title":"Slot: water feature size (water_feat_size)","text":"

The size of the water feature

URI: MIXS:0000223

"},{"location":"water_feat_size/#inheritance","title":"Inheritance","text":""},{"location":"water_feat_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_feat_size/#properties","title":"Properties","text":""},{"location":"water_feat_size/#aliases","title":"Aliases","text":""},{"location":"water_feat_size/#examples","title":"Examples","text":"Value"},{"location":"water_feat_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_feat_size/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_feat_size/#schema-source","title":"Schema Source","text":""},{"location":"water_feat_size/#linkml-source","title":"LinkML Source","text":"
name: water_feat_size\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The size of the water feature\ntitle: water feature size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000223\nalias: water_feat_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"water_feat_type/","title":"Slot: water feature type (water_feat_type)","text":"

The type of water feature present within the building being sampled

URI: MIXS:0000847

"},{"location":"water_feat_type/#inheritance","title":"Inheritance","text":""},{"location":"water_feat_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_feat_type/#properties","title":"Properties","text":""},{"location":"water_feat_type/#aliases","title":"Aliases","text":""},{"location":"water_feat_type/#examples","title":"Examples","text":"Value stream"},{"location":"water_feat_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_feat_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"water_feat_type/#schema-source","title":"Schema Source","text":""},{"location":"water_feat_type/#linkml-source","title":"LinkML Source","text":"
name: water_feat_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of water feature present within the building being sampled\ntitle: water feature type\nexamples:\n- value: stream\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000847\nalias: water_feat_type\ndomain_of:\n- Biosample\nrange: water_feat_type_enum\nmultivalued: false\n\n
"},{"location":"water_prod_rate/","title":"Slot: water production rate (water_prod_rate)","text":"

Water production rates per well (e.g. 987 m3 / day)

URI: MIXS:0000453

"},{"location":"water_prod_rate/#inheritance","title":"Inheritance","text":""},{"location":"water_prod_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_prod_rate/#properties","title":"Properties","text":""},{"location":"water_prod_rate/#aliases","title":"Aliases","text":""},{"location":"water_prod_rate/#examples","title":"Examples","text":"Value"},{"location":"water_prod_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_prod_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_prod_rate/#schema-source","title":"Schema Source","text":""},{"location":"water_prod_rate/#linkml-source","title":"LinkML Source","text":"
name: water_prod_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic meter per day\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Water production rates per well (e.g. 987 m3 / day)\ntitle: water production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000453\nalias: water_prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"water_temp_regm/","title":"Slot: water temperature regimen (water_temp_regm)","text":"

Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000590

"},{"location":"water_temp_regm/#inheritance","title":"Inheritance","text":""},{"location":"water_temp_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_temp_regm/#properties","title":"Properties","text":""},{"location":"water_temp_regm/#aliases","title":"Aliases","text":""},{"location":"water_temp_regm/#examples","title":"Examples","text":"Value 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"water_temp_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_temp_regm/#annotations","title":"Annotations","text":"property value expected_value measurement value;treatment interval and duration"},{"location":"water_temp_regm/#schema-source","title":"Schema Source","text":""},{"location":"water_temp_regm/#linkml-source","title":"LinkML Source","text":"
name: water_temp_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to water with varying\n  degree of temperature, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include multiple regimens\ntitle: water temperature regimen\nexamples:\n- value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000590\nalias: water_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"watering_regm/","title":"Slot: watering regimen (watering_regm)","text":"

Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000591

"},{"location":"watering_regm/#inheritance","title":"Inheritance","text":""},{"location":"watering_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"watering_regm/#properties","title":"Properties","text":""},{"location":"watering_regm/#aliases","title":"Aliases","text":""},{"location":"watering_regm/#examples","title":"Examples","text":"Value 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"watering_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"watering_regm/#annotations","title":"Annotations","text":"property value expected_value measurement value;treatment interval and duration"},{"location":"watering_regm/#schema-source","title":"Schema Source","text":""},{"location":"watering_regm/#linkml-source","title":"LinkML Source","text":"
name: watering_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milliliter, liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to watering frequencies,\n  treatment regimen including how many times the treatment was repeated, how long\n  each treatment lasted, and the start and end time of the entire treatment; can include\n  multiple regimens\ntitle: watering regimen\nexamples:\n- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- watering regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000591\nalias: watering_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"websites/","title":"Slot: websites","text":"

A list of websites that are associated with the entity.

URI: nmdc:websites

"},{"location":"websites/#inheritance","title":"Inheritance","text":""},{"location":"websites/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes PersonValue An attribute value representing a person no"},{"location":"websites/#properties","title":"Properties","text":""},{"location":"websites/#comments","title":"Comments","text":""},{"location":"websites/#see-also","title":"See Also","text":""},{"location":"websites/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"websites/#schema-source","title":"Schema Source","text":""},{"location":"websites/#linkml-source","title":"LinkML Source","text":"
name: websites\ndescription: A list of websites that are associated with the entity.\ncomments:\n- DOIs should not be included as websites. Instead, use the associated_dois slot.\n- A consortium's homepage website should be included in the homepage_website slot,\n  not in websites.\n- consortium is a convenience term for a Study whose study_category value is consortium\n- the website slot and its subproperties are virtually identical to the url slot,\n  except that they are multivalued and url is single-valued.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:url\nrank: 1000\nalias: websites\ndomain_of:\n- PersonValue\n- Study\nrange: string\nmultivalued: true\npattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n\n
"},{"location":"weekday/","title":"Slot: weekday (weekday)","text":"

The day of the week when sampling occurred

URI: MIXS:0000848

"},{"location":"weekday/#inheritance","title":"Inheritance","text":""},{"location":"weekday/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"weekday/#properties","title":"Properties","text":""},{"location":"weekday/#aliases","title":"Aliases","text":""},{"location":"weekday/#examples","title":"Examples","text":"Value Sunday"},{"location":"weekday/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"weekday/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"weekday/#schema-source","title":"Schema Source","text":""},{"location":"weekday/#linkml-source","title":"LinkML Source","text":"
name: weekday\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The day of the week when sampling occurred\ntitle: weekday\nexamples:\n- value: Sunday\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weekday\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000848\nalias: weekday\ndomain_of:\n- Biosample\nrange: weekday_enum\nmultivalued: false\n\n
"},{"location":"win/","title":"Slot: well identification number (win)","text":"

A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)

URI: MIXS:0000297

"},{"location":"win/#inheritance","title":"Inheritance","text":""},{"location":"win/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"win/#properties","title":"Properties","text":""},{"location":"win/#aliases","title":"Aliases","text":""},{"location":"win/#examples","title":"Examples","text":"Value"},{"location":"win/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"win/#annotations","title":"Annotations","text":"property value expected_value text"},{"location":"win/#schema-source","title":"Schema Source","text":""},{"location":"win/#linkml-source","title":"LinkML Source","text":"
name: win\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'A unique identifier of a well or wellbore. This is part of the Global\n  Framework for Well Identification initiative which is compiled by the Professional\n  Petroleum Data Management Association (PPDM) in an effort to improve well identification\n  systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\ntitle: well identification number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- well identification number\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000297\nalias: win\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"wind_direction/","title":"Slot: wind direction (wind_direction)","text":"

Wind direction is the direction from which a wind originates

URI: MIXS:0000757

"},{"location":"wind_direction/#inheritance","title":"Inheritance","text":""},{"location":"wind_direction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wind_direction/#properties","title":"Properties","text":""},{"location":"wind_direction/#aliases","title":"Aliases","text":""},{"location":"wind_direction/#examples","title":"Examples","text":"Value Northwest"},{"location":"wind_direction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wind_direction/#annotations","title":"Annotations","text":"property value expected_value wind direction name"},{"location":"wind_direction/#schema-source","title":"Schema Source","text":""},{"location":"wind_direction/#linkml-source","title":"LinkML Source","text":"
name: wind_direction\nannotations:\n  expected_value:\n    tag: expected_value\n    value: wind direction name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Wind direction is the direction from which a wind originates\ntitle: wind direction\nexamples:\n- value: Northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind direction\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000757\nalias: wind_direction\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"wind_speed/","title":"Slot: wind speed (wind_speed)","text":"

Speed of wind measured at the time of sampling

URI: MIXS:0000118

"},{"location":"wind_speed/#inheritance","title":"Inheritance","text":""},{"location":"wind_speed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wind_speed/#properties","title":"Properties","text":""},{"location":"wind_speed/#aliases","title":"Aliases","text":""},{"location":"wind_speed/#examples","title":"Examples","text":"Value 21 kilometer per hour"},{"location":"wind_speed/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wind_speed/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"wind_speed/#schema-source","title":"Schema Source","text":""},{"location":"wind_speed/#linkml-source","title":"LinkML Source","text":"
name: wind_speed\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter per second, kilometer per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Speed of wind measured at the time of sampling\ntitle: wind speed\nexamples:\n- value: 21 kilometer per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind speed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000118\nalias: wind_speed\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"window_cond/","title":"Slot: window condition (window_cond)","text":"

The physical condition of the window at the time of sampling

URI: MIXS:0000849

"},{"location":"window_cond/#inheritance","title":"Inheritance","text":""},{"location":"window_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_cond/#properties","title":"Properties","text":""},{"location":"window_cond/#aliases","title":"Aliases","text":""},{"location":"window_cond/#examples","title":"Examples","text":"Value rupture"},{"location":"window_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_cond/#schema-source","title":"Schema Source","text":""},{"location":"window_cond/#linkml-source","title":"LinkML Source","text":"
name: window_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the window at the time of sampling\ntitle: window condition\nexamples:\n- value: rupture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000849\nalias: window_cond\ndomain_of:\n- Biosample\nrange: window_cond_enum\nmultivalued: false\n\n
"},{"location":"window_cover/","title":"Slot: window covering (window_cover)","text":"

The type of window covering

URI: MIXS:0000850

"},{"location":"window_cover/#inheritance","title":"Inheritance","text":""},{"location":"window_cover/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_cover/#properties","title":"Properties","text":""},{"location":"window_cover/#aliases","title":"Aliases","text":""},{"location":"window_cover/#examples","title":"Examples","text":"Value curtains"},{"location":"window_cover/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_cover/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_cover/#schema-source","title":"Schema Source","text":""},{"location":"window_cover/#linkml-source","title":"LinkML Source","text":"
name: window_cover\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of window covering\ntitle: window covering\nexamples:\n- value: curtains\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window covering\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000850\nalias: window_cover\ndomain_of:\n- Biosample\nrange: window_cover_enum\nmultivalued: false\n\n
"},{"location":"window_horiz_pos/","title":"Slot: window horizontal position (window_horiz_pos)","text":"

The horizontal position of the window on the wall

URI: MIXS:0000851

"},{"location":"window_horiz_pos/#inheritance","title":"Inheritance","text":""},{"location":"window_horiz_pos/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_horiz_pos/#properties","title":"Properties","text":""},{"location":"window_horiz_pos/#aliases","title":"Aliases","text":""},{"location":"window_horiz_pos/#examples","title":"Examples","text":"Value middle"},{"location":"window_horiz_pos/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_horiz_pos/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_horiz_pos/#schema-source","title":"Schema Source","text":""},{"location":"window_horiz_pos/#linkml-source","title":"LinkML Source","text":"
name: window_horiz_pos\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The horizontal position of the window on the wall\ntitle: window horizontal position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window horizontal position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000851\nalias: window_horiz_pos\ndomain_of:\n- Biosample\nrange: window_horiz_pos_enum\nmultivalued: false\n\n
"},{"location":"window_loc/","title":"Slot: window location (window_loc)","text":"

The relative location of the window within the room

URI: MIXS:0000852

"},{"location":"window_loc/#inheritance","title":"Inheritance","text":""},{"location":"window_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_loc/#properties","title":"Properties","text":""},{"location":"window_loc/#aliases","title":"Aliases","text":""},{"location":"window_loc/#examples","title":"Examples","text":"Value west"},{"location":"window_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_loc/#schema-source","title":"Schema Source","text":""},{"location":"window_loc/#linkml-source","title":"LinkML Source","text":"
name: window_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The relative location of the window within the room\ntitle: window location\nexamples:\n- value: west\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000852\nalias: window_loc\ndomain_of:\n- Biosample\nrange: window_loc_enum\nmultivalued: false\n\n
"},{"location":"window_mat/","title":"Slot: window material (window_mat)","text":"

The type of material used to finish a window

URI: MIXS:0000853

"},{"location":"window_mat/#inheritance","title":"Inheritance","text":""},{"location":"window_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_mat/#properties","title":"Properties","text":""},{"location":"window_mat/#aliases","title":"Aliases","text":""},{"location":"window_mat/#examples","title":"Examples","text":"Value wood"},{"location":"window_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_mat/#schema-source","title":"Schema Source","text":""},{"location":"window_mat/#linkml-source","title":"LinkML Source","text":"
name: window_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of material used to finish a window\ntitle: window material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000853\nalias: window_mat\ndomain_of:\n- Biosample\nrange: window_mat_enum\nmultivalued: false\n\n
"},{"location":"window_open_freq/","title":"Slot: window open frequency (window_open_freq)","text":"

The number of times windows are opened per week

URI: MIXS:0000246

"},{"location":"window_open_freq/#inheritance","title":"Inheritance","text":""},{"location":"window_open_freq/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_open_freq/#properties","title":"Properties","text":""},{"location":"window_open_freq/#aliases","title":"Aliases","text":""},{"location":"window_open_freq/#examples","title":"Examples","text":"Value"},{"location":"window_open_freq/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_open_freq/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"window_open_freq/#schema-source","title":"Schema Source","text":""},{"location":"window_open_freq/#linkml-source","title":"LinkML Source","text":"
name: window_open_freq\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of times windows are opened per week\ntitle: window open frequency\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window open frequency\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000246\nalias: window_open_freq\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"window_size/","title":"Slot: window area/size (window_size)","text":"

The window's length and width

URI: MIXS:0000224

"},{"location":"window_size/#inheritance","title":"Inheritance","text":""},{"location":"window_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_size/#properties","title":"Properties","text":""},{"location":"window_size/#aliases","title":"Aliases","text":""},{"location":"window_size/#examples","title":"Examples","text":"Value"},{"location":"window_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_size/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"window_size/#schema-source","title":"Schema Source","text":""},{"location":"window_size/#linkml-source","title":"LinkML Source","text":"
name: window_size\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: inch, meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The window's length and width\ntitle: window area/size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window area/size\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit} x {float} {unit}'\nslot_uri: MIXS:0000224\nalias: window_size\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"window_status/","title":"Slot: window status (window_status)","text":"

Defines whether the windows were open or closed during environmental testing

URI: MIXS:0000855

"},{"location":"window_status/#inheritance","title":"Inheritance","text":""},{"location":"window_status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_status/#properties","title":"Properties","text":""},{"location":"window_status/#aliases","title":"Aliases","text":""},{"location":"window_status/#examples","title":"Examples","text":"Value open"},{"location":"window_status/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_status/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_status/#schema-source","title":"Schema Source","text":""},{"location":"window_status/#linkml-source","title":"LinkML Source","text":"
name: window_status\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Defines whether the windows were open or closed during environmental\n  testing\ntitle: window status\nexamples:\n- value: open\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window status\nrank: 1000\nis_a: core field\nstring_serialization: '[closed|open]'\nslot_uri: MIXS:0000855\nalias: window_status\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"window_type/","title":"Slot: window type (window_type)","text":"

The type of windows

URI: MIXS:0000856

"},{"location":"window_type/#inheritance","title":"Inheritance","text":""},{"location":"window_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_type/#properties","title":"Properties","text":""},{"location":"window_type/#aliases","title":"Aliases","text":""},{"location":"window_type/#examples","title":"Examples","text":"Value fixed window"},{"location":"window_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_type/#schema-source","title":"Schema Source","text":""},{"location":"window_type/#linkml-source","title":"LinkML Source","text":"
name: window_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of windows\ntitle: window type\nexamples:\n- value: fixed window\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000856\nalias: window_type\ndomain_of:\n- Biosample\nrange: window_type_enum\nmultivalued: false\n\n
"},{"location":"window_vert_pos/","title":"Slot: window vertical position (window_vert_pos)","text":"

The vertical position of the window on the wall

URI: MIXS:0000857

"},{"location":"window_vert_pos/#inheritance","title":"Inheritance","text":""},{"location":"window_vert_pos/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_vert_pos/#properties","title":"Properties","text":""},{"location":"window_vert_pos/#aliases","title":"Aliases","text":""},{"location":"window_vert_pos/#examples","title":"Examples","text":"Value middle"},{"location":"window_vert_pos/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_vert_pos/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_vert_pos/#schema-source","title":"Schema Source","text":""},{"location":"window_vert_pos/#linkml-source","title":"LinkML Source","text":"
name: window_vert_pos\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The vertical position of the window on the wall\ntitle: window vertical position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window vertical position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000857\nalias: window_vert_pos\ndomain_of:\n- Biosample\nrange: window_vert_pos_enum\nmultivalued: false\n\n
"},{"location":"window_water_mold/","title":"Slot: window signs of water/mold (window_water_mold)","text":"

Signs of the presence of mold or mildew on the window.

URI: MIXS:0000854

"},{"location":"window_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"window_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_water_mold/#properties","title":"Properties","text":""},{"location":"window_water_mold/#aliases","title":"Aliases","text":""},{"location":"window_water_mold/#examples","title":"Examples","text":"Value no presence of mold visible"},{"location":"window_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"window_water_mold/#linkml-source","title":"LinkML Source","text":"
name: window_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on the window.\ntitle: window signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000854\nalias: window_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"workflow_execution_set/","title":"Slot: workflow_execution_set","text":"

This property links a database object to the set of workflow executions.

URI: nmdc:workflow_execution_set

"},{"location":"workflow_execution_set/#inheritance","title":"Inheritance","text":""},{"location":"workflow_execution_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"workflow_execution_set/#properties","title":"Properties","text":""},{"location":"workflow_execution_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"workflow_execution_set/#schema-source","title":"Schema Source","text":""},{"location":"workflow_execution_set/#linkml-source","title":"LinkML Source","text":"
name: workflow_execution_set\ndescription: This property links a database object to the set of workflow executions.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: workflow_execution_set\ndomain_of:\n- Database\nrange: WorkflowExecution\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"xylene/","title":"Slot: xylene (xylene)","text":"

Concentration of xylene in the sample

URI: MIXS:0000156

"},{"location":"xylene/#inheritance","title":"Inheritance","text":""},{"location":"xylene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"xylene/#properties","title":"Properties","text":""},{"location":"xylene/#aliases","title":"Aliases","text":""},{"location":"xylene/#examples","title":"Examples","text":"Value"},{"location":"xylene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"xylene/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"xylene/#schema-source","title":"Schema Source","text":""},{"location":"xylene/#linkml-source","title":"LinkML Source","text":"
name: xylene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of xylene in the sample\ntitle: xylene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- xylene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000156\nalias: xylene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"zinc/","title":"Slot: zinc (zinc)","text":"

Concentration of zinc in the sample

URI: nmdc:zinc

"},{"location":"zinc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"zinc/#properties","title":"Properties","text":""},{"location":"zinc/#aliases","title":"Aliases","text":""},{"location":"zinc/#examples","title":"Examples","text":"Value 2.5 mg/kg"},{"location":"zinc/#see-also","title":"See Also","text":""},{"location":"zinc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"zinc/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"zinc/#schema-source","title":"Schema Source","text":""},{"location":"zinc/#linkml-source","title":"LinkML Source","text":"
name: zinc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg (ppm)\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of zinc in the sample\ntitle: zinc\nexamples:\n- value: 2.5 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- zinc\nrank: 1000\nalias: zinc\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"}]} \ No newline at end of file +{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"NMDC","text":"

Schema for National Microbiome Data Collaborative (NMDC). This schema is organized into multiple modules, such as:

URI: https://w3id.org/nmdc/nmdc

"},{"location":"#classes","title":"Classes","text":"Class Description AttributeValue The value for any value of a attribute for a sample ControlledTermValue A controlled term or class from an ontology ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... GeolocationValue A normalized value for a location on the earth's surface ImageValue An attribute value representing an image PersonValue An attribute value representing a person QuantityValue A simple quantity, e TextValue A basic string value TimestampValue A value that is a timestamp CreditAssociation This class supports binding associated researchers to studies Database An abstract holder for any set of metadata and data Doi A centrally registered identifier symbol used to uniquely identify objects gi... EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... FailureCategorization FunctionalAnnotation An assignment of a function term (e FunctionalAnnotationAggMember GenomeFeature A feature localized to an interval along a genome MagBin MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... NamedThing a databased entity or concept/class GeneProduct A molecule encoded by a gene that has an evolved function InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... CalibrationInformation A calibration object that is associated with a process Configuration A set of parameters that define the actions of a process and is shared among ... ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... DataObject An object that primarily consists of symbols that represent information Manifest MaterialEntity Biosample Biological source material which can be characterized by an experiment Instrument A material entity that is designed to perform a function in a scientific inve... ProcessedSample Site FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected OntologyClass ChemicalEntity An atom or molecule that can be represented with a chemical formula EnvironmentalMaterialTerm FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... OrthologyGroup A set of genes or gene products in which all members are orthologous Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... PlannedProcess CollectingBiosamplesFromSite DataGeneration The methods and processes used to generate omics data from a biosample or org... MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... DissolvingProcess A mixing step where a soluble component is mixed with a liquid component Extraction A material separation in which a desired component of an input material is se... FiltrationProcess The process of segregation of phases; e LibraryPreparation MixingProcess The combining of components, particles or layers into a more homogeneous stat... Pooling physical combination of several instances of like material SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... ProtocolExecution A PlannedProces that has PlannedProcess parts StorageProcess A planned process with the objective to preserve and protect material entitie... WorkflowExecution Represents an instance of an execution of a particular workflow MagsAnalysis A workflow execution activity that uses computational binning tools to group ... MetabolomicsAnalysis MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... MetagenomeSequencing Initial sequencing activity that precedes any analysis MetaproteomicsAnalysis MetatranscriptomeAnnotation MetatranscriptomeAssembly MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... NomAnalysis ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... Study A study summarizes the overall goal of a research initiative and outlines the... PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein Protocol"},{"location":"#slots","title":"Slots","text":"Slot Description abs_air_humidity Actual mass of water vapor - mh20 - present in the air water vapor mixture add_date The date on which the information was added to the database add_recov_method Additional (i additional_info Information that doesn't fit anywhere else address The street name and building number where the sampling occurred adj_room List of rooms (room number, room name) immediately adjacent to the sampling r... aero_struc Aerospace structures typically consist of thin plates with stiffeners for the... agrochem_addition Addition of fertilizers, pesticides, etc air_PM_concen Concentration of substances that remain suspended in the air, and comprise mi... air_temp Temperature of the air at the time of sampling air_temp_regm Information about treatment involving an exposure to varying temperatures; sh... al_sat Aluminum saturation (esp al_sat_meth Reference or method used in determining Al saturation alkalinity Alkalinity, the ability of a solution to neutralize acids to the equivalence ... alkalinity_method Method used for alkalinity measurement alkyl_diethers Concentration of alkyl diethers all_proteins the list of protein identifiers that are associated with the peptide sequence alt Altitude is a term used to identify heights of objects such as airplanes, spa... alternative_descriptions A list of alternative descriptions for the entity alternative_identifiers A list of alternative identifiers for the entity alternative_names A list of alternative names used to refer to the entity alternative_titles A list of alternative titles for the entity aminopept_act Measurement of aminopeptidase activity ammonium Concentration of ammonium in the sample ammonium_nitrogen Concentration of ammonium nitrogen in the sample amount_light The unit of illuminance and luminous emittance, measuring luminous flux per u... analysis_identifiers analysis_type Select all the data types associated or available for this biosample analyte_category The type of analyte(s) that were measured in the data generation process and ... ances_data Information about either pedigree or other ancestral information description ... annual_precpt The average of all annual precipitation values known, or an estimated equival... annual_temp Mean annual temperature antibiotic_regm Information about treatment involving antibiotic administration; should inclu... api API gravity is a measure of how heavy or light a petroleum liquid is compared... applied_roles applies_to_person arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c... aromatics_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... asm_score A score for comparing metagenomic assembly quality from same sample asphaltenes_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... assembly_identifiers associated_dois A list of DOIs associated with a resource, such as a list of DOIS associated ... associated_studies The study associated with a resource atmospheric_data Measurement of atmospheric data; can include multiple data avg_dew_point The average of dew point measures taken at the beginning of every hour over a... avg_occup Daily average occupancy of room avg_temp The average of temperatures taken at the beginning of every hour over a 24 ho... bac_prod Bacterial production in the water column measured by isotope uptake bac_resp Measurement of bacterial respiration in the water column bacteria_carb_prod Measurement of bacterial carbon production barometric_press Force per unit area exerted against a surface by the weight of air above that... basin Name of the basin (e bathroom_count The number of bathrooms in the building bedroom_count The number of bedrooms in the building benzene Concentration of benzene in the sample best_protein the specific protein identifier most correctly associated with the peptide se... bin_name bin_quality binned_contig_num biochem_oxygen_dem Amount of dissolved oxygen needed by aerobic biological organisms in a body o... biocide List of biocides (commercial name of product and supplier) and date of admini... biocide_admin_method Method of biocide administration (dose, frequency, duration, time elapsed bet... biogas_retention_time biogas_temperature biol_stat The level of genome modification biomass Amount of biomass; should include the name for the part of biomass measured, ... biomaterial_purity biosample_categories biosample_identifiers biosample_set This property links a database object to the set of samples within it biotic_regm Information about treatment(s) involving use of biotic factors, such as bacte... biotic_relationship Description of relationship(s) between the subject organism and other organis... bishomohopanol Concentration of bishomohopanol blood_press_diast Resting diastolic blood pressure, measured as mm mercury blood_press_syst Resting systolic blood pressure, measured as mm mercury bromide Concentration of bromide build_docs The building design, construction and operation documents build_occup_type The primary function for which a building or discrete part of a building is i... building_setting A location (geography) where a building is set built_struc_age The age of the built structure since construction built_struc_set The characterization of the location of the built structure as high or low hu... built_struc_type A physical structure that is a body or assemblage of bodies in space to form ... bulk_elect_conductivity Electrical conductivity is a measure of the ability to carry electric current... calcium Concentration of calcium in the sample calibration_object the file containing calibration data object calibration_set This property links a database object to the set of calibrations within it calibration_standard the reference standard(s) used for calibration calibration_target the target measurement of the calibration carb_dioxide Carbon dioxide (gas) amount or concentration at the time of sampling carb_monoxide Carbon monoxide (gas) amount or concentration at the time of sampling carb_nitro_ratio Ratio of amount or concentrations of carbon to nitrogen ceil_area The area of the ceiling space within the room ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide... ceil_finish_mat The type of material used to finish a ceiling ceil_struc The construction format of the ceiling ceil_texture The feel, appearance, or consistency of a ceiling surface ceil_thermal_mass The ability of the ceiling to provide inertia against temperature fluctuation... ceil_type The type of ceiling according to the ceiling's appearance or construction ceil_water_mold Signs of the presence of mold or mildew on the ceiling chem_administration List of chemical compounds administered to the host or site where sampling oc... chem_mutagen Treatment involving use of mutagens; should include the name of mutagen, amou... chem_oxygen_dem A measure of the capacity of water to consume oxygen during the decomposition... chem_treat_method Method of chemical administration(dose, frequency, duration, time elapsed bet... chem_treatment List of chemical compounds administered upstream the sampling location where ... chemical_conversion_category The type of chemical conversion process chemical_entity_set This property links a database object to the set of chemical entities within ... chemical_formula A generic grouping for molecular formulae and empirical formulae chimera_check Tool(s) used for chimera checking, including version number and parameters, t... chloride Concentration of chloride in the sample chlorophyll Concentration of chlorophyll chromatographic_category The type of chromatography used in a process climate_environment Treatment involving an exposure to a particular climate; treatment regimen in... collected_from The Site from which a Biosample was collected collecting_biosamples_from_site_set collection_date The time of sampling, either as an instance (single point in time) or interva... collection_date_inc Date the incubation was harvested/collected/ended collection_time The time of sampling, either as an instance (single point) or interval collection_time_inc Time the incubation was harvested/collected/ended community completeness completion_date compression_type If provided, specifies the compression type concentration The concentration of a substance used in a process conditionings Preliminary treatment of either phase with a suitable solution of the other p... conduc Electrical conductivity of water configuration_set This property links a database object to the set of configurations within it contained_in A type of container container_size The volume of the container an analyte is stored in or an activity takes plac... contamination contig_bp Total size in bp of all contigs contigs The sum of the (length*log(length)) of all contigs, times some constant cool_syst_id The cooling system identifier core_field basic fields count crop_rotation Whether or not crop is rotated, and if yes, rotation schedule ctg_l50 Given a set of contigs, the L50 is defined as the sequence length of the shor... ctg_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... ctg_logsum Maximum contig length ctg_max Maximum contig length ctg_n50 Given a set of contigs, each with its own length, the N50 count is defined as... ctg_n90 Given a set of contigs, each with its own length, the N90 count is defined as... ctg_powsum Powersum of all contigs is the same as logsum except that it uses the sum of ... cult_root_med Name or reference for the hydroponic or in vitro culture rooting medium; can ... cur_land_use Present state of sample site cur_vegetation Vegetation classification from one or more standard classification systems, o... cur_vegetation_meth Reference or method used in vegetation classification data_category The category of the file, such as instrument data from data generation or pro... data_generation_set This property links a database object to the set of data generations within i... data_object_set This property links a database object to the set of data objects within it data_object_type The type of file represented by the data object date_created from database class date_last_rain The date of the last time it rained density Density of the sample, which is its mass per unit volume (aka volumetric mass... depos_env Main depositional environment (https://en depth The vertical distance below local surface, e description a human-readable description of a thing dew_point The temperature to which a given parcel of humid air must be cooled, at const... diether_lipids Concentration of diether lipids; can include multiple types of diether lipids direct_infusion_category used when a processed sample is introduced into a mass spectrometer without c... display_order When rendering information, this attribute to specify the order in which the ... diss_carb_dioxide Concentration of dissolved carbon dioxide in the sample or liquid portion of ... diss_hydrogen Concentration of dissolved hydrogen diss_inorg_carb Dissolved inorganic carbon concentration in the sample, typically measured af... diss_inorg_nitro Concentration of dissolved inorganic nitrogen diss_inorg_phosp Concentration of dissolved inorganic phosphorus in the sample diss_iron Concentration of dissolved iron in the sample diss_org_carb Concentration of dissolved organic carbon in the sample, liquid portion of th... diss_org_nitro Dissolved organic nitrogen concentration measured as; total dissolved nitroge... diss_oxygen Concentration of dissolved oxygen diss_oxygen_fluid Concentration of dissolved oxygen in the oil field produced fluids as it cont... dna_absorb1 260/280 measurement of DNA sample purity dna_absorb2 260/230 measurement of DNA sample purity dna_collect_site Provide information on the site your DNA sample was collected from dna_concentration dna_cont_type Tube or plate (96-well) dna_cont_well dna_container_id dna_dnase dna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA dna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... dna_project_contact dna_samp_id dna_sample_format Solution in which the DNA sample has been suspended dna_sample_name Give the DNA sample a name that is meaningful to you dna_seq_project dna_seq_project_name dna_seq_project_pi dna_volume dnase_rna doi_category The resource type the corresponding doi resolves to doi_provider The authority, or organization, the DOI is associated with doi_value A digital object identifier, which is intended to persistantly identify some ... door_comp_type The composite type of the door door_cond The phsical condition of the door door_direct The direction the door opens door_loc The relative location of the door in the room door_mat The material the door is composed of door_move The type of movement of the door door_size The size of the door door_type The type of door material door_type_metal The type of metal door door_type_wood The type of wood door door_water_mold Signs of the presence of mold or mildew on a door down_par Visible waveband radiance and irradiance measurements in the water column drainage_class Drainage classification from a standard system such as the USDA system drawings The buildings architectural drawings; if design is chosen, indicate phase-con... duration The elapsed time of an activity ecosystem An ecosystem is a combination of a physical environment (abiotic factors) and... ecosystem_category Ecosystem categories represent divisions within the ecosystem based on specif... ecosystem_path_id A unique id representing the GOLD classifiers associated with a sample ecosystem_subtype Ecosystem subtypes represent further subdivision of Ecosystem types into more... ecosystem_type Ecosystem types represent things having common characteristics within the Eco... efficiency_percent Percentage of volatile solids removed from the anaerobic digestor elev Elevation of the sampling site is its height above a fixed reference point, m... elevator The number of elevators within the built structure eluent_introduction_category A high-level categorization for how the processed sample is introduced into a... email An email address for an entity such as a person embargoed If true, the data are embargoed and not available for public access emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database emsl_identifiers emsl_project_identifiers Identifiers that link a NMDC study to the EMSL user facility website hosting ... emsl_store_temp The temperature at which the sample should be stored upon delivery to EMSL emulsions Amount or concentration of substances such as paints, adhesives, mayonnaise, ... encodes The gene product encoded by this feature end The end of the feature in positive 1-based integer coordinates end_date The date on which any process or activity was ended ended_at_time env_broad_scale Report the major environmental system the sample or specimen came from env_local_scale Report the entity or entities which are in the sample or specimen\u2019s local vic... env_medium Report the environmental material(s) immediately surrounding the sample or sp... env_package MIxS extension for reporting of measurements and observations obtained from o... environment_field field describing environmental aspect of a sample escalator The number of escalators within the built structure ethylbenzene Concentration of ethylbenzene in the sample etl_software_version from database class eukaryotic_evaluation Contains results from evaluating if a Metagenome-Assembled Genome is of eukar... execution_resource The computing resource or facility where the workflow was executed exp_duct The amount of exposed ductwork in the room exp_pipe The number of exposed pipes in the room experimental_factor Experimental factors are essentially the variable aspects of an experiment de... experimental_factor_other Other details about your sample that you feel can't be accurately represented... ext_door The number of exterior doors in the built structure ext_wall_orient The orientation of the exterior wall ext_window_orient The compass direction the exterior window of the room is facing external_database_identifiers Link to corresponding identifier in external database extraction_targets Provides the target biomolecule that has been separated from a sample during ... extreme_event Unusual physical events that may have affected microbial populations fao_class Soil classification from the FAO World Reference Database for Soil Resources feature_category A Sequence Ontology term that describes the category of a feature feature_type TODO: Yuri to write fertilizer_regm Information about treatment involving the use of fertilizers; should include ... field Name of the hydrocarbon field (e field_research_site_set file_size_bytes Size of the file in bytes filter_material A porous material on which solid particles present in air or other fluid whic... filter_method Type of filter used or how the sample was filtered filter_pore_size A quantitative or qualitative measurement of the physical dimensions of the p... filter_type A device which removes solid particulates or airborne molecular contaminants filtration_category The type of conditioning applied to a filter, device, etc final_concentration When solutions A (containing substance X) and B are combined together, this s... fire Historical and/or physical evidence of fire fireplace_type A firebox with chimney flooding Historical and/or physical evidence of flooding floor_age The time period since installment of the carpet or flooring floor_area The area of the floor space within the room floor_cond The physical condition of the floor at the time of sampling; photos or video ... floor_count The number of floors in the building, including basements and mechanical pent... floor_finish_mat The floor covering type; the finished surface that is walked on floor_struc Refers to the structural elements and subfloor upon which the finish flooring... floor_thermal_mass The ability of the floor to provide inertia against temperature fluctuations floor_water_mold Signs of the presence of mold or mildew in a room fluor Raw or converted fluorescence of water freq_clean The number of times the sample location is cleaned freq_cook The number of times a meal is cooked per week functional_annotation_agg functional_annotation_set This property links a database object to the set of all functional annotation... funding_sources A list of organizations, along with the award numbers, that underwrite financ... fungicide_regm Information about treatment involving use of fungicides; should include the n... furniture The types of furniture present in the sampled room gap_pct The gap size percentage of all scaffolds gaseous_environment Use of conditions with differing gaseous environments; should include the nam... gaseous_substances Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... gc_avg Average of GC content of all contigs gc_std Standard deviation of GC content of all contigs gender_restroom The gender type of the restroom gene_count gene_function_id The identifier for the gene function genetic_mod Genetic modifications of the genome of an organism, which may occur naturally... genome_feature_set This property links a database object to the set of all features geo_loc_name The geographical origin of the sample as defined by the country or sea name f... gff_coordinate A positive 1-based integer coordinate indicating start or end git_url The url that points to the exact github location of a workflow glucosidase_act Measurement of glucosidase activity gnps_identifiers gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... gold_analysis_project_identifiers identifiers for corresponding analysis projects in GOLD gold_biosample_identifiers identifiers for corresponding sample in GOLD gold_identifiers gold_path_field This is a grouping for any of the gold path fields gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD gold_study_identifiers identifiers for corresponding project(s) in GOLD gravidity Whether or not subject is gravid, and if yes date due or date post-conception... gravity Information about treatment involving use of gravity factor to study various ... growth_facil Type of facility where the sampled plant was grown; controlled vocabulary: gr... growth_habit Characteristic shape, appearance or growth form of a plant species growth_hormone_regm Information about treatment involving use of growth hormones; should include ... gtdbtk_class gtdbtk_domain gtdbtk_family gtdbtk_genus gtdbtk_order gtdbtk_phylum gtdbtk_species habitat hall_count The total count of hallways and cooridors in the built structure handidness The handidness of the individual sampled has_boolean_value Links a quantity value to a boolean has_calibration a calibration instance associated with a process has_chromatography_configuration The identifier of the associated ChromatographyConfiguration, providing infor... has_credit_associations This slot links a study to a credit association has_failure_categorization has_function has_input An input to a process has_mass_spectrometry_configuration The identifier of the associated MassSpectrometryConfiguration has_maximum_numeric_value The maximum value part, expressed as number, of the quantity value when the v... has_metabolite_identifications has_minimum_numeric_value The minimum value part, expressed as number, of the quantity value when the v... has_numeric_value Links a quantity value to a number has_output An output from a process has_peptide_quantifications has_process_parts A list of process parts that make up a protocol has_raw_value The value that was specified for an annotation in raw form, i has_unit Links a QuantityValue to a unit hc_produced Main hydrocarbon type produced from resource (i hcr Main Hydrocarbon Resource type hcr_fw_salinity Original formation water salinity (prior to secondary recovery e hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en hcr_pressure Original pressure of the hydrocarbon resource hcr_temp Original temperature of the hydrocarbon resource heat_cool_type Methods of conditioning or heating a room or building heat_deliv_loc The location of heat delivery within the room heat_sys_deliv_meth The method by which the heat is delivered through the system heat_system_id The heating system identifier heavy_metals Heavy metals present in the sequenced sample and their concentrations heavy_metals_meth Reference or method used in determining heavy metals height_carper_fiber The average carpet fiber height in the indoor environment herbicide_regm Information about treatment involving use of herbicides; information about tr... highest_similarity_score homepage_website The website address (URL) of an entity's homepage horizon_meth Reference or method used in determining the horizon host_age Age of host at the time of sampling; relevant scale depends on species and st... host_body_habitat Original body habitat where the sample was obtained from host_body_product Substance produced by the body, e host_body_site Name of body site where the sample was obtained from, such as a specific orga... host_body_temp Core body temperature of the host when sample was collected host_color The color of host host_common_name Common name of the host host_diet Type of diet depending on the host, for animals omnivore, herbivore etc host_disease_stat List of diseases with which the host has been diagnosed; can include multiple... host_dry_mass Measurement of dry mass host_family_relation Familial relationships to other hosts in the same study; can include multiple... host_genotype Observed genotype host_growth_cond Literature reference giving growth conditions of the host host_height The height of subject host_last_meal Content of last meal and time since feeding; can include multiple values host_length The length of subject host_life_stage Description of life stage of host host_name host_phenotype Phenotype of human or other host host_sex Gender or physical sex of the host host_shape Morphological shape of host host_subject_id A unique identifier by which each subject can be referred to, de-identified host_subspecf_genlin Information about the genetic distinctness of the host organism below the sub... host_substrate The growth substrate of the host host_symbiont The taxonomic name of the organism(s) found living in mutualistic, commensali... host_taxid NCBI taxon id of the host, e host_tot_mass Total mass of the host at collection, the unit depends on host host_wet_mass Measurement of wet mass humidity Amount of water vapour in the air, at the time of sampling humidity_regm Information about treatment involving an exposure to varying degree of humidi... id A unique identifier for a thing igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database igsn_identifiers img_identifiers A list of identifiers that relate the biosample to records in the IMG databas... in_manifest inchi inchi_key indoor_space A distinguishable space within a structure, the purpose for which discrete ar... indoor_surf Type of indoor surface indust_eff_percent Percentage of industrial effluents received by wastewater treatment plant infiltrations The amount of time it takes to complete each infiltration activity inorg_particles Concentration of particles such as sand, grit, metal particles, ceramics, etc input_base_count The nucleotide base count number of input reads for QC analysis input_contig_num input_mass Total mass of sample used in activity input_read_bases TODO input_read_count The sequence count number of input reads for QC analysis input_volume The volume of the input sample insdc_analysis_identifiers insdc_assembly_identifiers insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject insdc_biosample_identifiers identifiers for corresponding sample in INSDC insdc_experiment_identifiers insdc_identifiers Any identifier covered by the International Nucleotide Sequence Database Coll... insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA inside_lux The recorded value at sampling time (power density) instrument_set This property links a database object to the set of instruments within it instrument_used What instrument was used during DataGeneration or MaterialProcessing int_wall_cond The physical condition of the wall at the time of sampling; photos or video p... internal_calibration whether internal calibration was used, if false, external calibration was use... investigation_field field describing aspect of the investigation/study to which the sample belong... ionization_source The ionization source used to introduce processed samples into a mass spectro... is_pressurized Whether or not pressure was applied to a thing or process is_stranded Is the (RNA) library stranded or non-stranded (unstranded) isotope_exposure List isotope exposure or addition applied to your sample iw_bt_date_well Injection water breakthrough date per well following a secondary and/or terti... iwf Proportion of the produced fluids derived from injected water at the time of ... jgi_portal_analysis_project_identifiers identifiers for corresponding analysis projects in JGI Portal jgi_portal_identifiers identifiers for entities according to JGI Portal jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... known_as language Should use ISO 639-1 code e last_clean The last time the floor was cleaned (swept, mopped, vacuumed) lat_lon The geographical origin of the sample as defined by latitude and longitude latitude latitude lbc_thirty lime buffer capacity, determined after 30 minute incubation lbceq lime buffer capacity, determined at equilibrium after 5 day incubation library_preparation_kit library_type light_intensity Measurement of light intensity light_regm Information about treatment(s) involving exposure to light, including both li... light_type Application of light to achieve some practical or aesthetic effect link_addit_analys Link to additional analysis results performed on the sample link_class_info Link to digitized soil maps or other soil classification information link_climate_info Link to climate resource lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki local_class Soil classification based on local soil classification system local_class_meth Reference or method used in determining the local soil classification location longitude longitude low_depth_contig_num magnesium Concentration of magnesium in the sample mags_list manganese Concentration of manganese in the sample manifest_category The type of collection that describes the data in the collection manifest_set This property links a database object to the set of manifests within it mass A physical quality that inheres in a bearer by virtue of the proportion of th... mass_analyzers The kind of mass analyzer(s) used during the spectra collection mass_spectrometry_acquisition_strategy Mode of running a mass spectrometer method by which m/z ranges are selected a... mass_spectrum_collection_modes Indicates whether mass spectra were collected in full profile, reduced profil... material_component_separation A material processing in which components of an input material become segrega... material_processing_set This property links a database object to the set of material processing withi... max_occup The maximum amount of people allowed in the indoor environment md5_checksum MD5 checksum of file (pre-compressed) mean_frict_vel Measurement of mean friction velocity mean_peak_frict_vel Measurement of mean peak friction velocity mech_struc mechanical structure: a moving structure mechanical_damage Information about any mechanical damage exerted on the plant; can include mul... members_id metabolite_identified the specific metabolite identifier metagenome_annotation_id The identifier for the analysis activity that generated the functional annota... metagenome_assembly_parameter methane Methane (gas) amount or concentration at the time of sampling mgnify_analysis_identifiers mgnify_identifiers mgnify_project_identifiers identifiers for corresponding project in MGnify micro_biomass_c_meth Reference or method used in determining microbial biomass carbon micro_biomass_meth Reference or method used in determining microbial biomass micro_biomass_n_meth Reference or method used in determining microbial biomass nitrogen microbial_biomass The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_c The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_n The part of the organic matter in the soil that constitutes living microorgan... min_q_value smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... mineral_nutr_regm Information about treatment involving the use of mineral supplements; should ... misc_param Any other measurement performed or parameter collected, that is not listed he... mod_date The last date on which the database information was modified model modifier_substance The type of modification being done n_alkanes Concentration of n-alkanes; can include multiple n-alkanes name A human readable label for an entity ncbi_lineage Comma delimited ordered list of NCBI taxonomy names ncbi_lineage_tax_ids Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId) ncbi_project_name ncbi_taxonomy_name neon_biosample_identifiers neon_identifiers identifiers for entities according to NEON neon_study_identifiers nitrate Concentration of nitrate in the sample nitrate_nitrogen Concentration of nitrate nitrogen in the sample nitrite Concentration of nitrite in the sample nitrite_nitrogen Concentration of nitrite nitrogen in the sample nitro Concentration of nitrogen (total) non_microb_biomass Amount of biomass; should include the name for the part of biomass measured, ... non_microb_biomass_method Reference or method used in determining biomass non_min_nutr_regm Information about treatment involving the exposure of plant to non-mineral nu... notes nucl_acid_amp A link to a literature reference, electronic resource or a standard operating... nucl_acid_ext A link to a literature reference, electronic resource or a standard operating... nucleic_acid_sequence_source_field num_16s num_23s num_5s num_aligned_reads The sequence count number of input reads aligned to assembled contigs num_input_reads The sequence count number of input reads for assembly num_t_rna number_of_contig number_pets The number of pets residing in the sampled space number_plants The number of plant(s) in the sampling space number_resident The number of individuals currently occupying in the sampling location object_set Applies to a property that links a database object to a set of objects objective The scientific objectives associated with the entity occup_density_samp Average number of occupants at time of sampling per square footage occup_document The type of documentation of occupancy occup_samp Number of occupants present at time of sample within the given space omics_processing_identifiers omics_type The type of omics data orcid The ORCID of a person ordered_mobile_phases The solution(s) that moves through a chromatography column org_carb Concentration of organic carbon org_count_qpcr_info If qpcr was used for the cell count, the target gene name, the primer sequenc... org_matter Concentration of organic matter org_nitro Concentration of organic nitrogen org_nitro_method Method used for obtaining organic nitrogen org_particles Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... organism_count Total cell count of any organism (or group of organisms) per gram, volume or ... other_treatment Other treatments applied to your samples that are not applicable to the provi... output_base_count After QC analysis nucleotide base count number output_read_bases TODO output_read_count After QC analysis sequence count number owc_tvdss Depth of the original oil water contact (OWC) zone (average) (m TVDSS) oxy_stat_samp Oxygenation status of sample oxygen Oxygen (gas) amount or concentration at the time of sampling part_of Links a resource to another resource that either logically or physically incl... part_org_carb Concentration of particulate organic carbon part_org_nitro Concentration of particulate organic nitrogen particle_class Particles are classified, based on their size, into six general categories:cl... pcr_cond Description of reaction conditions and components of PCR in the form of 'init... pcr_cycles pcr_primers PCR primers that were used to amplify the sequence of the targeted gene, locu... peptide_sequence peptide_sequence_count count of peptide sequences grouped to the best_protein peptide_spectral_count sum of filter passing MS2 spectra associated with the peptide sequence within... peptide_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... permeability Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... perturbation Type of perturbation, e pesticide_regm Information about treatment involving use of insecticides; should include the... petroleum_hydrocarb Concentration of petroleum hydrocarbon ph Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... ph_meth Reference or method used in determining ph ph_regm Information about treatment involving exposure of plants to varying levels of... phaeopigments Concentration of phaeopigments; can include multiple phaeopigments phase The phase for a coding sequence entity phosphate Concentration of phosphate phosplipid_fatt_acid Concentration of phospholipid fatty acids; can include multiple values photon_flux Measurement of photon flux plant_growth_med Specification of the media for growing the plants or tissue cultured samples,... plant_product Substance produced by the plant, where the sample was obtained from plant_sex Sex of the reproductive parts on the whole plant, e plant_struc Name of plant structure the sample was obtained from; for Plant Ontology (PO)... polarity_mode the polarity of which ions are generated and detected pollutants Pollutant types and, amount or concentrations measured at the time of samplin... pool_dna_extracts Indicate whether multiple DNA extractions were mixed porosity Porosity of deposited sediment is volume of voids divided by the total volume... potassium Concentration of potassium in the sample pour_point Temperature at which a liquid becomes semi solid and loses its flow character... pre_treatment The process of pre-treatment removes materials that can be easily collected f... pres_animal_insect The type and number of animals or insects present in the sampling space pressure Pressure to which the sample is subject to, in atmospheres prev_land_use_meth Reference or method used in determining previous land use and dates previous_land_use Previous land use and dates primary_prod Measurement of primary production, generally measured as isotope uptake primary_treatment The process to produce both a generally homogeneous liquid capable of being t... principal_investigator Principal Investigator who led the study and/or generated the dataset processed_sample_set This property links a database object to the set of processed samples within ... processing_institution The organization that processed the sample prod_rate Oil and/or gas production rates per well (e prod_start_date Date of field's first production profile_image_url A url that points to an image of a person profile_position Cross-sectional position in the hillslope where sample was collected project_id Proposal IDs or names associated with dataset proport_woa_temperature proposal_dna proposal_rna protein_spectral_count sum of filter passing MS2 spectra associated with the best protein within a g... protein_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... protocol_execution_category protocol_execution_set This property links a database object to the set of protocol executions withi... protocol_link qc_comment Slot to store additional comments about laboratory or workflow output qc_failure_what Provides a summary about what caused a lab or workflow process to fail qc_failure_where Describes the nmdc schema class that corresonds to where the failure occurred qc_status Stores information about the result of a process (ie the process of sequencin... quad_pos The quadrant position of the sampling room within the building radiation_regm Information about treatment involving exposure of plant or a plant part to a ... rainfall_regm Information about treatment involving an exposure to a given amount of rainfa... reactor_type Anaerobic digesters can be designed and engineered to operate using a number ... read_qc_analysis_statistic redox_potential Redox potential, measured relative to a hydrogen cell, indicating oxidation o... rel_air_humidity Partial vapor and air pressure, density of the vapor and air, or by the actua... rel_humidity_out The recorded outside relative humidity value at the time of sampling rel_samp_loc The sampling location within the train car related_identifiers Identifiers assigned to a thing that is similar to that which is represented ... replicate_number If sending biological replicates, indicate the rep number here reservoir Name of the reservoir (e resins_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... resolution_categories The relative resolution at which spectra were collected rna_absorb1 260/280 measurement of RNA sample purity rna_absorb2 260/230 measurement of RNA sample purity rna_collect_site Provide information on the site your RNA sample was collected from rna_concentration rna_cont_type Tube or plate (96-well) rna_cont_well rna_container_id rna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA rna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... rna_project_contact rna_samp_id rna_sample_format Solution in which the RNA sample has been suspended rna_sample_name Give the RNA sample a name that is meaningful to you rna_seq_project rna_seq_project_name rna_seq_project_pi rna_volume room_air_exch_rate The rate at which outside air replaces indoor air in a given space room_architec_elem The unique details and component parts that, together, form the architecture ... room_condt The condition of the room at the time of sampling room_connected List of rooms connected to the sampling room by a doorway room_count The total count of rooms in the built structure including all room types room_dim The length, width and height of sampling room room_door_dist Distance between doors (meters) in the hallway between the sampling room and ... room_door_share List of room(s) (room number, room name) sharing a door with the sampling roo... room_hallway List of room(s) (room number, room name) located in the same hallway as sampl... room_loc The position of the room within the building room_moist_dam_hist The history of moisture damage or mold in the past 12 months room_net_area The net floor area of sampling room room_occup Count of room occupancy at time of sampling room_samp_pos The horizontal sampling position in the room relative to architectural elemen... room_type The main purpose or activity of the sampling room room_vol Volume of sampling room room_wall_share List of room(s) (room number, room name) sharing a wall with the sampling roo... room_window_count Number of windows in the room root_cond Relevant rooting conditions such as field plot size, sowing density, containe... root_med_carbon Source of organic carbon in the culture rooting medium; e root_med_macronutr Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... root_med_micronutr Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... root_med_ph pH measurement of the culture rooting medium; e root_med_regl Growth regulators in the culture rooting medium such as cytokinins, auxins, g... root_med_solid Specification of the solidifying agent in the culture rooting medium; e root_med_suppl Organic supplements of the culture rooting medium, such as vitamins, amino ac... salinity The total concentration of all dissolved salts in a liquid or solid sample salinity_category Categorical description of the sample's salinity salinity_meth Reference or method used in determining salinity salt_regm Information about treatment involving use of salts as supplement to liquid an... samp_capt_status Reason for the sample samp_collec_device The device used to collect an environmental sample samp_collec_method The method employed for collecting the sample samp_collect_point Sampling point on the asset were sample was collected (e samp_dis_stage Stage of the disease at the time of sample collection, e samp_floor The floor of the building, where the sampling room is located samp_loc_corr_rate Metal corrosion rate is the speed of metal deterioration due to environmental... samp_mat_process A brief description of any processing applied to the sample during or after r... samp_md In non deviated well, measured depth is equal to the true vertical depth, TVD... samp_name A local identifier or name that for the material sample used for extracting n... samp_preserv Preservative added to the sample (e samp_room_id Sampling room number samp_size The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... samp_sort_meth Method by which samples are sorted; open face filter collecting total suspend... samp_store_dur Duration for which the sample was stored samp_store_loc Location at which sample was stored, usually name of a specific freezer/room samp_store_temp Temperature at which sample was stored, e samp_subtype Name of sample sub-type samp_taxon_id NCBI taxon id of the sample samp_time_out The recent and long term history of outside sampling samp_transport_cond Sample transport duration (in days or hrs) and temperature the sample was exp... samp_tvdss Depth of the sample i samp_type The type of material from which the sample was obtained samp_vol_we_dna_ext Volume (ml) or mass (g) of total collected sample processed for DNA extractio... samp_weather The weather on the sampling day samp_well_name Name of the well (e sample_collection_day sample_collection_hour sample_collection_minute sample_collection_month sample_collection_site sample_collection_year sample_link A unique identifier to assign parent-child, subsample, or sibling samples sample_shipped The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... sample_state_information The chemical phase of a pure sample, or the state of a mixed sample sample_type Type of sample being submitted sampled_portion The portion of the sample that is taken for downstream activity saturates_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... scaf_bp Total size in bp of all scaffolds scaf_l50 Given a set of scaffolds, the L50 is defined as the sequence length of the sh... scaf_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... scaf_l_gt50k Total size in bp of all scaffolds greater than 50 KB scaf_logsum The sum of the (length*log(length)) of all scaffolds, times some constant scaf_max Maximum scaffold length scaf_n50 Given a set of scaffolds, each with its own length, the N50 count is defined ... scaf_n90 Given a set of scaffolds, each with its own length, the N90 count is defined ... scaf_n_gt50k Total sequence count of scaffolds greater than 50 KB scaf_pct_gt50k Total sequence size percentage of scaffolds greater than 50 KB scaf_powsum Powersum of all scaffolds is the same as logsum except that it uses the sum o... scaffolds Total sequence count of all scaffolds season The season when sampling occurred season_environment Treatment involving an exposure to a particular season (e season_precpt The average of all seasonal precipitation values known, or an estimated equiv... season_temp Mean seasonal temperature season_use The seasons the space is occupied secondary_treatment The process for substantially degrading the biological content of the sewage sediment_type Information about the sediment type based on major constituents separation_method The method that was used to separate a substance from a solution or mixture seq_meth Sequencing machine used seq_quality_check Indicate if the sequence has been called by automatic systems (none) or under... seqid The ID of the landmark used to establish the coordinate system for the curren... sequencing_field sewage_type Type of wastewater treatment plant as municipial or industrial shad_dev_water_mold Signs of the presence of mold or mildew on the shading device shading_device_cond The physical condition of the shading device at the time of sampling shading_device_loc The location of the shading device in relation to the built structure shading_device_mat The material the shading device is composed of shading_device_type The type of shading device sieving Collection design of pooled samples and/or sieve size and amount of sample si... silicate Concentration of silicate size_frac Filtering pore size used in sample preparation size_frac_low Refers to the mesh/pore size used to pre-filter/pre-sort the sample size_frac_up Refers to the mesh/pore size used to retain the sample slope_aspect The direction a slope faces slope_gradient Commonly called 'slope' sludge_retent_time The time activated sludge remains in reactor smiles A string encoding of a molecular graph, no chiral or isotopic information sodium Sodium concentration in the sample soil_annual_season_temp soil_horizon Specific layer in the land area which measures parallel to the soil surface a... soil_text_measure The relative proportion of different grain sizes of mineral particles in a so... soil_texture_meth Reference or method used in determining soil texture soil_type Description of the soil type or classification soil_type_meth Reference or method used in determining soil series name or other lower-level... solar_irradiance The amount of solar energy that arrives at a specific area of a surface durin... soluble_inorg_mat Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... soluble_iron_micromol soluble_org_mat Concentration of substances such as urea, fruit sugars, soluble proteins, dru... soluble_react_phosp Concentration of soluble reactive phosphorus source_concentration When solutions A (containing substance X) and B are combined together, this s... source_mat_id A unique identifier assigned to a material sample (as defined by http://rs space_typ_state Customary or normal state of the space specific The building specifications specific_ecosystem Specific ecosystems represent specific features of the environment like aphot... specific_humidity The mass of water vapour in a unit mass of moist air, usually expressed as gr... sr_dep_env Source rock depositional environment (https://en sr_geol_age Geological age of source rock (Additional info: https://en sr_kerog_type Origin of kerogen sr_lithology Lithology of source rock (https://en standing_water_regm Treatment involving an exposure to standing water during a plant's life span,... start The start of the feature in positive 1-based integer coordinates start_date The date on which any process or activity was started start_date_inc Date the incubation was started start_time_inc Time the incubation was started started_at_time stationary_phase The material the stationary phase is comprised of used in chromatography storage_process_set This property links a database object to the set of storage processes within ... store_cond Explain how and for how long the soil sample was stored before DNA extraction... strand The strand on which a feature is located stranded_orientation Lists the strand orientiation for a stranded RNA library preparation study_category The type of research initiative study_identifiers study_image Links a study to one or more images study_set This property links a database object to the set of studies within it subject substance_role The role of a substance in a process substances_used The substances that are combined to enable a ChemicalConversionProcess substances_volume The volume of the combined substances that was included in a ChemicalConversi... substructure_type The substructure or under building is that largely hidden section of the buil... subsurface_depth sulfate Concentration of sulfate in the sample sulfate_fw Original sulfate concentration in the hydrocarbon resource sulfide Concentration of sulfide in the sample surf_air_cont Contaminant identified on surface surf_humidity Surfaces: water activity as a function of air and material moisture surf_material Surface materials at the point of sampling surf_moisture Water held on a surface surf_moisture_ph ph measurement of surface surf_temp Temperature of the surface at the time of sampling suspend_part_matter Concentration of suspended particulate matter suspend_solids Concentration of substances including a wide variety of material, such as sil... tan Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by th... target_gene Targeted gene or locus name for marker gene studies target_subfragment Name of subfragment of a gene or locus technical_reps If sending technical replicates of the same sample, indicate the replicate co... temp Temperature of the sample at the time of sampling temp_out The recorded temperature value at sampling time outside temperature The value of a temperature measurement or temperature used in a process term pointer to an ontology class tertiary_treatment The process providing a final treatment stage to raise the effluent quality b... tidal_stage Stage of tide tillage Note method(s) used for tilling tiss_cult_growth_med Description of plant tissue culture growth media used title A name given to the entity that differs from the name/label programmatically ... toluene Concentration of toluene in the sample too_short_contig_num tot_carb Total carbon content tot_depth_water_col Measurement of total depth of water column tot_diss_nitro Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... tot_inorg_nitro Total inorganic nitrogen content tot_iron Concentration of total iron in the sample tot_nitro Total nitrogen concentration of water samples, calculated by: total nitrogen ... tot_nitro_cont_meth Reference or method used in determining the total nitrogen tot_nitro_content Total nitrogen content of the sample tot_org_c_meth Reference or method used in determining total organic carbon tot_org_carb Definition for soil: total organic carbon content of the soil, definition oth... tot_part_carb Total particulate carbon content tot_phosp Total phosphorus concentration in the sample, calculated by: total phosphorus... tot_phosphate Total amount or concentration of phosphate tot_sulfur Concentration of total sulfur in the sample total_bases train_line The subway line name train_stat_loc The train station collection location train_stop_loc The train stop collection location turbidity Measure of the amount of cloudiness or haziness in water caused by individual... tvdss_of_hcr_press True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... tvdss_of_hcr_temp True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... typ_occup_density Customary or normal density of occupants type the class_uri of the class that has been instantiated unbinned_contig_num url value vendor ventilation_rate Ventilation rate of the system in the sampled premises ventilation_type Ventilation system used in the sampled premises version vfa Concentration of Volatile Fatty Acids in the sample vfa_fw Original volatile fatty acid concentration in the hydrocarbon resource vis_media The building visual media viscosity A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020t... volatile_org_comp Concentration of carbon-based chemicals that easily evaporate at room tempera... volume The volume of a substance wall_area The total area of the sampled room's walls wall_const_type The building class of the wall defined by the composition of the building ele... wall_finish_mat The material utilized to finish the outer most layer of the wall wall_height The average height of the walls in the sampled room wall_loc The relative location of the wall within the room wall_surf_treatment The surface treatment of interior wall wall_texture The feel, appearance, or consistency of a wall surface wall_thermal_mass The ability of the wall to provide inertia against temperature fluctuations wall_water_mold Signs of the presence of mold or mildew on a wall was_generated_by was_informed_by wastewater_type The origin of wastewater such as human waste, rainfall, storm drains, etc water_cont_soil_meth Reference or method used in determining the water content of soil water_content Water content measurement water_current Measurement of magnitude and direction of flow within a fluid water_cut Current amount of water (%) in a produced fluid stream; or the average of the... water_feat_size The size of the water feature water_feat_type The type of water feature present within the building being sampled water_prod_rate Water production rates per well (e water_temp_regm Information about treatment involving an exposure to water with varying degre... watering_regm Information about treatment involving an exposure to watering frequencies, tr... websites A list of websites that are associated with the entity weekday The day of the week when sampling occurred win A unique identifier of a well or wellbore wind_direction Wind direction is the direction from which a wind originates wind_speed Speed of wind measured at the time of sampling window_cond The physical condition of the window at the time of sampling window_cover The type of window covering window_horiz_pos The horizontal position of the window on the wall window_loc The relative location of the window within the room window_mat The type of material used to finish a window window_open_freq The number of times windows are opened per week window_size The window's length and width window_status Defines whether the windows were open or closed during environmental testing window_type The type of windows window_vert_pos The vertical position of the window on the wall window_water_mold Signs of the presence of mold or mildew on the window workflow_execution_set This property links a database object to the set of workflow executions xylene Concentration of xylene in the sample zinc Concentration of zinc in the sample"},{"location":"#enumerations","title":"Enumerations","text":"Enumeration Description AnalysisTypeEnum AnalyteCategoryEnum ArchStrucEnum BiolStatEnum BiosampleCategoryEnum Funding-based, sample location-based, or experimental method-based defined ca... BioticRelationshipEnum BuildDocsEnum BuildOccupTypeEnum BuildingSettingEnum CalibrationStandardEnum CalibrationTargetEnum CeilCondEnum CeilFinishMatEnum CeilTextureEnum CeilTypeEnum ChemicalConversionCategoryEnum ChromatographicCategoryEnum ContainerCategoryEnum The permitted types of containers used in processing metabolomic samples CreditEnum CurLandUseEnum DataCategoryEnum DeposEnvEnum DirectInfusionEnum DNASampleFormatEnum DoiCategoryEnum DoiProviderEnum DoorCompTypeEnum DoorCondEnum DoorDirectEnum DoorLocEnum DoorMatEnum DoorMoveEnum DoorTypeEnum DoorTypeMetalEnum DoorTypeWoodEnum DrainageClassEnum DrawingsEnum EluentIntroductionCategoryEnum ExecutionResourceEnum ExtWallOrientEnum ExtWindowOrientEnum ExtractionTargetEnum FailureWhatEnum The permitted values for describing where a failure occurred during processin... FailureWhereEnum The permitted values for describing where in the process, either a lab or ana... FaoClassEnum FileTypeEnum FilterTypeEnum FloorCondEnum FloorFinishMatEnum FloorStrucEnum FloorWaterMoldEnum FreqCleanEnum FurnitureEnum GenderRestroomEnum GrowthHabitEnum HandidnessEnum HcProducedEnum HcrEnum HcrGeolAgeEnum HeatCoolTypeEnum HeatDelivLocEnum HostSexEnum IndoorSpaceEnum IndoorSurfEnum InstrumentModelEnum InstrumentVendorEnum IntWallCondEnum IonizationSourceEnum JgiContTypeEnum LibraryTypeEnum LightTypeEnum LithologyEnum ManifestCategoryEnum MassAnalyzerEnum MassSpectrometryAcquisitionStrategyEnum MassSpectrumCollectionModeEnum MechStrucEnum OccupDocumentEnum OrganismCountEnum OxyStatSampEnum PlantGrowthMedEnum PlantSexEnum PolarityModeEnum ProcessingInstitutionEnum ProfilePositionEnum ProtocolCategoryEnum The possible protocols that may be followed for an assay QuadPosEnum RelSampLocEnum ResolutionCategoryEnum RNASampleFormatEnum RoomCondtEnum RoomConnectedEnum RoomLocEnum RoomSampPosEnum RoomTypeEnum SampCaptStatusEnum SampCollectPointEnum SampDisStageEnum SampFloorEnum SampMdEnum SampSubtypeEnum SampWeatherEnum SamplePortionEnum SampleStateEnum SampleTypeEnum SeasonUseEnum SedimentTypeEnum SeparationMethodEnum The tool/substance used to separate or filter a solution or mixture ShadingDeviceCondEnum ShadingDeviceTypeEnum SoilHorizonEnum SpecificEnum SrDepEnvEnum SrGeolAgeEnum SrKerogTypeEnum SrLithologyEnum StationaryPhaseEnum The type of stationary phase used in a chromatography process StatusEnum StrandedOrientationEnum This enumeration specifies information about stranded RNA library preparation... StudyCategoryEnum SubstanceRoleEnum SubstructureTypeEnum SurfAirContEnum SurfMaterialEnum TidalStageEnum TillageEnum TrainLineEnum TrainStatLocEnum TrainStopLocEnum VisMediaEnum WallConstTypeEnum WallFinishMatEnum WallLocEnum WallSurfTreatmentEnum WallTextureEnum WaterFeatTypeEnum WeekdayEnum WindowCondEnum WindowCoverEnum WindowHorizPosEnum WindowLocEnum WindowMatEnum WindowTypeEnum WindowVertPosEnum YesNoEnum replaces DnaDnaseEnum and DnaseRnaEnum"},{"location":"#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Bytes An integer value that corresponds to a size in bytes Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... DecimalDegree A decimal degree expresses latitude or longitude as decimal fractions Double A real number that conforms to the xsd:double specification ExternalIdentifier A CURIE representing an external identifier Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer LanguageCode A language code conforming to ISO_639-1 Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Unit Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"#subsets","title":"Subsets","text":"Subset Description Checklist A MIxS checklist ChecklistPackageCombination A combination of a checklist and a package DataObjectSubset Subset consisting of the data objects that either inputs or outputs of proces... DataPortalSubset Subset consisting of entities that Kitware/nmdc-server use to populate the da... Environment Investigation MixsExtension MixsEnvironmentalTriad NucleicAcidSequenceSource Package A MIxS package Proteases SampleSubset Subset consisting of entities linked to the processing of samples Sequencing WorkflowSubset Subset consisting of just the workflow execution activities"},{"location":"AnalysisTypeEnum/","title":"Enum: AnalysisTypeEnum","text":"

URI: AnalysisTypeEnum

"},{"location":"AnalysisTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metabolomics None metagenomics None Standard short-read metagenomic sequencing metagenomics_long_read None Long-read metagenomic sequencing metaproteomics None metatranscriptomics None natural organic matter None bulk chemistry None"},{"location":"AnalysisTypeEnum/#slots","title":"Slots","text":"Name Description analysis_type Select all the data types associated or available for this biosample"},{"location":"AnalysisTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AnalysisTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"AnalysisTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: AnalysisTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  metabolomics:\n    text: metabolomics\n  metagenomics:\n    text: metagenomics\n    description: Standard short-read metagenomic sequencing\n    title: Metagenomics\n  metagenomics_long_read:\n    text: metagenomics_long_read\n    description: Long-read metagenomic sequencing\n    title: Metagenomics (long read)\n  metaproteomics:\n    text: metaproteomics\n  metatranscriptomics:\n    text: metatranscriptomics\n  natural organic matter:\n    text: natural organic matter\n  bulk chemistry:\n    text: bulk chemistry\n\n
"},{"location":"AnalyteCategoryEnum/","title":"Enum: AnalyteCategoryEnum","text":"

URI: AnalyteCategoryEnum

"},{"location":"AnalyteCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metagenome None metatranscriptome None metaproteome None metabolome None lipidome None nom None"},{"location":"AnalyteCategoryEnum/#slots","title":"Slots","text":"Name Description analyte_category The type of analyte(s) that were measured in the data generation process and ..."},{"location":"AnalyteCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AnalyteCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"AnalyteCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: AnalyteCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  metagenome:\n    text: metagenome\n    aliases:\n    - metaG\n  metatranscriptome:\n    text: metatranscriptome\n    aliases:\n    - metaT\n  metaproteome:\n    text: metaproteome\n    aliases:\n    - metaP\n  metabolome:\n    text: metabolome\n    aliases:\n    - metaB\n  lipidome:\n    text: lipidome\n  nom:\n    text: nom\n    aliases:\n    - natural organic matter\n\n
"},{"location":"ArchStrucEnum/","title":"Enum: ArchStrucEnum","text":"

URI: ArchStrucEnum

"},{"location":"ArchStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building None shed None home None"},{"location":"ArchStrucEnum/#slots","title":"Slots","text":"Name Description arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c..."},{"location":"ArchStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ArchStrucEnum/#schema-source","title":"Schema Source","text":""},{"location":"ArchStrucEnum/#linkml-source","title":"LinkML Source","text":"
name: arch_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  building:\n    text: building\n  shed:\n    text: shed\n  home:\n    text: home\n\n
"},{"location":"AttributeValue/","title":"Class: AttributeValue","text":"

The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:AttributeValue

classDiagram\n  class AttributeValue\n  click AttributeValue href \"../AttributeValue\"\n    AttributeValue <|-- QuantityValue\n      click QuantityValue href \"../QuantityValue\"\n    AttributeValue <|-- ImageValue\n      click ImageValue href \"../ImageValue\"\n    AttributeValue <|-- PersonValue\n      click PersonValue href \"../PersonValue\"\n    AttributeValue <|-- TextValue\n      click TextValue href \"../TextValue\"\n    AttributeValue <|-- TimestampValue\n      click TimestampValue href \"../TimestampValue\"\n    AttributeValue <|-- ControlledTermValue\n      click ControlledTermValue href \"../ControlledTermValue\"\n    AttributeValue <|-- GeolocationValue\n      click GeolocationValue href \"../GeolocationValue\"\n\n\n\n  AttributeValue : has_raw_value\n\n  AttributeValue : type\n\n\n\n
"},{"location":"AttributeValue/#inheritance","title":"Inheritance","text":""},{"location":"AttributeValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_raw_value 0..1 String The value that was specified for an annotation in raw form, i direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"AttributeValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AttributeValue/#schema-source","title":"Schema Source","text":""},{"location":"AttributeValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:AttributeValue native nmdc:AttributeValue"},{"location":"AttributeValue/#linkml-source","title":"LinkML Source","text":""},{"location":"AttributeValue/#direct","title":"Direct","text":"
name: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n  hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- has_raw_value\n- type\nclass_uri: nmdc:AttributeValue\n\n
"},{"location":"AttributeValue/#induced","title":"Induced","text":"
name: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n  hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: AttributeValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: AttributeValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:AttributeValue\n\n
"},{"location":"BiolStatEnum/","title":"Enum: BiolStatEnum","text":"

URI: BiolStatEnum

"},{"location":"BiolStatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description wild None natural None semi-natural None inbred line None breeder's line None hybrid None clonal selection None mutant None"},{"location":"BiolStatEnum/#slots","title":"Slots","text":"Name Description biol_stat The level of genome modification"},{"location":"BiolStatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BiolStatEnum/#schema-source","title":"Schema Source","text":""},{"location":"BiolStatEnum/#linkml-source","title":"LinkML Source","text":"
name: biol_stat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  wild:\n    text: wild\n  natural:\n    text: natural\n  semi-natural:\n    text: semi-natural\n  inbred line:\n    text: inbred line\n  breeder's line:\n    text: breeder's line\n  hybrid:\n    text: hybrid\n  clonal selection:\n    text: clonal selection\n  mutant:\n    text: mutant\n\n
"},{"location":"Biosample/","title":"Class: Biosample","text":"

Biological source material which can be characterized by an experiment.

URI: nmdc:Biosample

Note

Mermaid class diagram too large to render.

"},{"location":"Biosample/#inheritance","title":"Inheritance","text":""},{"location":"Biosample/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance associated_studies 1..* Study The study associated with a resource direct biosample_categories * BiosampleCategoryEnum direct collected_from 0..1 FieldResearchSite The Site from which a Biosample was collected direct embargoed 0..1 recommended Boolean If true, the data are embargoed and not available for public access direct host_disease_stat 0..1 TextValue List of diseases with which the host has been diagnosed; can include multiple... direct host_taxid 0..1 ControlledIdentifiedTermValue NCBI taxon id of the host, e direct img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct neon_biosample_identifiers * ExternalIdentifier direct samp_name 0..1 String A local identifier or name that for the material sample used for extracting n... direct gold_biosample_identifiers * Uriorcurie Unique identifier for a biosample submitted to GOLD that matches the NMDC sub... direct insdc_biosample_identifiers * ExternalIdentifier identifiers for corresponding sample in INSDC direct emsl_biosample_identifiers * ExternalIdentifier A list of identifiers for the biosample from the EMSL database direct igsn_biosample_identifiers * ExternalIdentifier A list of identifiers for the biosample from the IGSN database direct abs_air_humidity 0..1 QuantityValue Actual mass of water vapor - mh20 - present in the air water vapor mixture direct add_recov_method 0..1 TextValue Additional (i direct additional_info 0..1 TextValue Information that doesn't fit anywhere else direct address 0..1 TextValue The street name and building number where the sampling occurred direct adj_room 0..1 TextValue List of rooms (room number, room name) immediately adjacent to the sampling r... direct aero_struc 0..1 TextValue Aerospace structures typically consist of thin plates with stiffeners for the... direct agrochem_addition * TextValue Addition of fertilizers, pesticides, etc direct air_PM_concen * TextValue Concentration of substances that remain suspended in the air, and comprise mi... direct air_temp 0..1 QuantityValue Temperature of the air at the time of sampling direct air_temp_regm * TextValue Information about treatment involving an exposure to varying temperatures; sh... direct al_sat 0..1 QuantityValue The relative abundance of aluminum in the sample direct al_sat_meth 0..1 TextValue Reference or method used in determining Aluminum saturation direct alkalinity 0..1 QuantityValue Alkalinity, the ability of a solution to neutralize acids to the equivalence ... direct alkalinity_method 0..1 TextValue Method used for alkalinity measurement direct alkyl_diethers 0..1 QuantityValue Concentration of alkyl diethers direct alt 0..1 QuantityValue Altitude is a term used to identify heights of objects such as airplanes, spa... direct aminopept_act 0..1 QuantityValue Measurement of aminopeptidase activity direct ammonium 0..1 QuantityValue Concentration of ammonium in the sample direct ammonium_nitrogen 0..1 QuantityValue Concentration of ammonium nitrogen in the sample direct amount_light 0..1 QuantityValue The unit of illuminance and luminous emittance, measuring luminous flux per u... direct ances_data 0..1 TextValue Information about either pedigree or other ancestral information description ... direct annual_precpt 0..1 QuantityValue The average of all annual precipitation values known, or an estimated equival... direct annual_temp 0..1 QuantityValue Mean annual temperature direct antibiotic_regm * TextValue Information about treatment involving antibiotic administration; should inclu... direct api 0..1 QuantityValue API gravity is a measure of how heavy or light a petroleum liquid is compared... direct arch_struc 0..1 ArchStrucEnum An architectural structure is a human-made, free-standing, immobile outdoor c... direct aromatics_pc 0..1 TextValue Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... direct asphaltenes_pc 0..1 TextValue Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... direct atmospheric_data * TextValue Measurement of atmospheric data; can include multiple data direct avg_dew_point 0..1 QuantityValue The average of dew point measures taken at the beginning of every hour over a... direct avg_occup 0..1 TextValue Daily average occupancy of room direct avg_temp 0..1 QuantityValue The average of temperatures taken at the beginning of every hour over a 24 ho... direct bac_prod 0..1 QuantityValue Bacterial production in the water column measured by isotope uptake direct bac_resp 0..1 QuantityValue Measurement of bacterial respiration in the water column direct bacteria_carb_prod 0..1 QuantityValue Measurement of bacterial carbon production direct barometric_press 0..1 QuantityValue Force per unit area exerted against a surface by the weight of air above that... direct basin 0..1 TextValue Name of the basin (e direct bathroom_count 0..1 TextValue The number of bathrooms in the building direct bedroom_count 0..1 TextValue The number of bedrooms in the building direct benzene 0..1 QuantityValue Concentration of benzene in the sample direct biochem_oxygen_dem 0..1 QuantityValue Amount of dissolved oxygen needed by aerobic biological organisms in a body o... direct biocide 0..1 TextValue List of biocides (commercial name of product and supplier) and date of admini... direct biocide_admin_method 0..1 TextValue Method of biocide administration (dose, frequency, duration, time elapsed bet... direct biol_stat 0..1 BiolStatEnum The level of genome modification direct biomass * TextValue Amount of biomass; should include the name for the part of biomass measured, ... direct biotic_regm 0..1 TextValue Information about treatment(s) involving use of biotic factors, such as bacte... direct biotic_relationship 0..1 BioticRelationshipEnum Description of relationship(s) between the subject organism and other organis... direct bishomohopanol 0..1 QuantityValue Concentration of bishomohopanol direct blood_press_diast 0..1 QuantityValue Resting diastolic blood pressure, measured as mm mercury direct blood_press_syst 0..1 QuantityValue Resting systolic blood pressure, measured as mm mercury direct bromide 0..1 QuantityValue Concentration of bromide direct build_docs 0..1 BuildDocsEnum The building design, construction and operation documents direct build_occup_type * BuildOccupTypeEnum The primary function for which a building or discrete part of a building is i... direct building_setting 0..1 BuildingSettingEnum A location (geography) where a building is set direct built_struc_age 0..1 QuantityValue The age of the built structure since construction direct built_struc_set 0..1 TextValue The characterization of the location of the built structure as high or low hu... direct built_struc_type 0..1 TextValue A physical structure that is a body or assemblage of bodies in space to form ... direct calcium 0..1 QuantityValue Concentration of calcium in the sample direct carb_dioxide 0..1 QuantityValue Carbon dioxide (gas) amount or concentration at the time of sampling direct carb_monoxide 0..1 QuantityValue Carbon monoxide (gas) amount or concentration at the time of sampling direct carb_nitro_ratio 0..1 QuantityValue Ratio of amount or concentrations of carbon to nitrogen direct ceil_area 0..1 QuantityValue The area of the ceiling space within the room direct ceil_cond 0..1 CeilCondEnum The physical condition of the ceiling at the time of sampling; photos or vide... direct ceil_finish_mat 0..1 CeilFinishMatEnum The type of material used to finish a ceiling direct ceil_struc 0..1 TextValue The construction format of the ceiling direct ceil_texture 0..1 CeilTextureEnum The feel, appearance, or consistency of a ceiling surface direct ceil_thermal_mass 0..1 QuantityValue The ability of the ceiling to provide inertia against temperature fluctuation... direct ceil_type 0..1 CeilTypeEnum The type of ceiling according to the ceiling's appearance or construction direct ceil_water_mold 0..1 TextValue Signs of the presence of mold or mildew on the ceiling direct chem_administration * ControlledTermValue List of chemical compounds administered to the host or site where sampling oc... direct chem_mutagen * TextValue Treatment involving use of mutagens; should include the name of mutagen, amou... direct chem_oxygen_dem 0..1 QuantityValue A measure of the capacity of water to consume oxygen during the decomposition... direct chem_treat_method 0..1 String Method of chemical administration(dose, frequency, duration, time elapsed bet... direct chem_treatment 0..1 TextValue List of chemical compounds administered upstream the sampling location where ... direct chloride 0..1 QuantityValue Concentration of chloride in the sample direct chlorophyll 0..1 QuantityValue Concentration of chlorophyll direct climate_environment * TextValue Treatment involving an exposure to a particular climate; treatment regimen in... direct collection_date 0..1 TimestampValue The time of sampling, either as an instance (single point in time) or interva... direct conduc 0..1 QuantityValue Electrical conductivity of water direct cool_syst_id 0..1 TextValue The cooling system identifier direct core_field 0..1 String basic fields direct crop_rotation 0..1 TextValue Whether or not crop is rotated, and if yes, rotation schedule direct cult_root_med 0..1 TextValue Name or reference for the hydroponic or in vitro culture rooting medium; can ... direct cur_land_use 0..1 CurLandUseEnum Present state of sample site direct cur_vegetation 0..1 TextValue Vegetation classification from one or more standard classification systems, o... direct cur_vegetation_meth 0..1 TextValue Reference or method used in vegetation classification direct date_last_rain 0..1 TimestampValue The date of the last time it rained direct density 0..1 QuantityValue Density of the sample, which is its mass per unit volume (aka volumetric mass... direct depos_env 0..1 DeposEnvEnum Main depositional environment (https://en direct depth 0..1 QuantityValue The vertical distance below local surface, e direct dew_point 0..1 QuantityValue The temperature to which a given parcel of humid air must be cooled, at const... direct diether_lipids * TextValue Concentration of diether lipids; can include multiple types of diether lipids direct diss_carb_dioxide 0..1 QuantityValue Concentration of dissolved carbon dioxide in the sample or liquid portion of ... direct diss_hydrogen 0..1 QuantityValue Concentration of dissolved hydrogen direct diss_inorg_carb 0..1 QuantityValue Dissolved inorganic carbon concentration in the sample, typically measured af... direct diss_inorg_nitro 0..1 QuantityValue Concentration of dissolved inorganic nitrogen direct diss_inorg_phosp 0..1 QuantityValue Concentration of dissolved inorganic phosphorus in the sample direct diss_iron 0..1 QuantityValue Concentration of dissolved iron in the sample direct diss_org_carb 0..1 QuantityValue Concentration of dissolved organic carbon in the sample, liquid portion of th... direct diss_org_nitro 0..1 QuantityValue Dissolved organic nitrogen concentration measured as; total dissolved nitroge... direct diss_oxygen 0..1 QuantityValue Concentration of dissolved oxygen direct diss_oxygen_fluid 0..1 QuantityValue Concentration of dissolved oxygen in the oil field produced fluids as it cont... direct dna_cont_well 0..1 recommended String direct door_comp_type 0..1 DoorCompTypeEnum The composite type of the door direct door_cond 0..1 DoorCondEnum The phsical condition of the door direct door_direct 0..1 DoorDirectEnum The direction the door opens direct door_loc 0..1 DoorLocEnum The relative location of the door in the room direct door_mat 0..1 DoorMatEnum The material the door is composed of direct door_move 0..1 DoorMoveEnum The type of movement of the door direct door_size 0..1 QuantityValue The size of the door direct door_type 0..1 DoorTypeEnum The type of door material direct door_type_metal 0..1 DoorTypeMetalEnum The type of metal door direct door_type_wood 0..1 DoorTypeWoodEnum The type of wood door direct door_water_mold 0..1 TextValue Signs of the presence of mold or mildew on a door direct down_par 0..1 QuantityValue Visible waveband radiance and irradiance measurements in the water column direct drainage_class 0..1 DrainageClassEnum Drainage classification from a standard system such as the USDA system direct drawings 0..1 DrawingsEnum The buildings architectural drawings; if design is chosen, indicate phase-con... direct ecosystem 0..1 String An ecosystem is a combination of a physical environment (abiotic factors) and... direct ecosystem_category 0..1 String Ecosystem categories represent divisions within the ecosystem based on specif... direct ecosystem_subtype 0..1 String Ecosystem subtypes represent further subdivision of Ecosystem types into more... direct ecosystem_type 0..1 String Ecosystem types represent things having common characteristics within the Eco... direct efficiency_percent 0..1 QuantityValue Percentage of volatile solids removed from the anaerobic digestor direct elev 0..1 Float Elevation of the sampling site is its height above a fixed reference point, m... direct elevator 0..1 TextValue The number of elevators within the built structure direct emulsions * TextValue Amount or concentration of substances such as paints, adhesives, mayonnaise, ... direct env_broad_scale 1 ControlledIdentifiedTermValue Report the major environmental system the sample or specimen came from direct env_local_scale 1 ControlledIdentifiedTermValue Report the entity or entities which are in the sample or specimen\u2019s local vic... direct env_medium 1 ControlledIdentifiedTermValue Report the environmental material(s) immediately surrounding the sample or sp... direct env_package 0..1 TextValue MIxS extension for reporting of measurements and observations obtained from o... direct environment_field 0..1 String field describing environmental aspect of a sample direct escalator 0..1 TextValue The number of escalators within the built structure direct ethylbenzene 0..1 QuantityValue Concentration of ethylbenzene in the sample direct exp_duct 0..1 QuantityValue The amount of exposed ductwork in the room direct exp_pipe 0..1 QuantityValue The number of exposed pipes in the room direct experimental_factor 0..1 ControlledTermValue Experimental factors are essentially the variable aspects of an experiment de... direct ext_door 0..1 TextValue The number of exterior doors in the built structure direct ext_wall_orient 0..1 ExtWallOrientEnum The orientation of the exterior wall direct ext_window_orient 0..1 ExtWindowOrientEnum The compass direction the exterior window of the room is facing direct extreme_event 0..1 String Unusual physical events that may have affected microbial populations direct fao_class 0..1 FaoClassEnum Soil classification from the FAO World Reference Database for Soil Resources direct fertilizer_regm * TextValue Information about treatment involving the use of fertilizers; should include ... direct field 0..1 TextValue Name of the hydrocarbon field (e direct filter_type * FilterTypeEnum A device which removes solid particulates or airborne molecular contaminants direct fire 0..1 String Historical and/or physical evidence of fire direct fireplace_type 0..1 TextValue A firebox with chimney direct flooding 0..1 String Historical and/or physical evidence of flooding direct floor_age 0..1 QuantityValue The time period since installment of the carpet or flooring direct floor_area 0..1 QuantityValue The area of the floor space within the room direct floor_cond 0..1 FloorCondEnum The physical condition of the floor at the time of sampling; photos or video ... direct floor_count 0..1 TextValue The number of floors in the building, including basements and mechanical pent... direct floor_finish_mat 0..1 FloorFinishMatEnum The floor covering type; the finished surface that is walked on direct floor_struc 0..1 FloorStrucEnum Refers to the structural elements and subfloor upon which the finish flooring... direct floor_thermal_mass 0..1 QuantityValue The ability of the floor to provide inertia against temperature fluctuations direct floor_water_mold 0..1 FloorWaterMoldEnum Signs of the presence of mold or mildew in a room direct fluor 0..1 QuantityValue Raw or converted fluorescence of water direct freq_clean 0..1 QuantityValue The number of times the sample location is cleaned direct freq_cook 0..1 QuantityValue The number of times a meal is cooked per week direct fungicide_regm * TextValue Information about treatment involving use of fungicides; should include the n... direct furniture 0..1 FurnitureEnum The types of furniture present in the sampled room direct gaseous_environment * TextValue Use of conditions with differing gaseous environments; should include the nam... direct gaseous_substances * TextValue Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... direct gender_restroom 0..1 GenderRestroomEnum The gender type of the restroom direct genetic_mod 0..1 TextValue Genetic modifications of the genome of an organism, which may occur naturally... direct geo_loc_name 0..1 TextValue The geographical origin of the sample as defined by the country or sea name f... direct glucosidase_act 0..1 QuantityValue Measurement of glucosidase activity direct gravidity 0..1 TextValue Whether or not subject is gravid, and if yes date due or date post-conception... direct gravity * TextValue Information about treatment involving use of gravity factor to study various ... direct growth_facil 0..1 ControlledTermValue Type of facility where the sampled plant was grown; controlled vocabulary: gr... direct growth_habit 0..1 GrowthHabitEnum Characteristic shape, appearance or growth form of a plant species direct growth_hormone_regm * TextValue Information about treatment involving use of growth hormones; should include ... direct hall_count 0..1 TextValue The total count of hallways and cooridors in the built structure direct handidness 0..1 HandidnessEnum The handidness of the individual sampled direct hc_produced 0..1 HcProducedEnum Main hydrocarbon type produced from resource (i direct hcr 0..1 HcrEnum Main Hydrocarbon Resource type direct hcr_fw_salinity 0..1 QuantityValue Original formation water salinity (prior to secondary recovery e direct hcr_geol_age 0..1 HcrGeolAgeEnum Geological age of hydrocarbon resource (Additional info: https://en direct hcr_pressure 0..1 TextValue Original pressure of the hydrocarbon resource direct hcr_temp 0..1 TextValue Original temperature of the hydrocarbon resource direct heat_cool_type * HeatCoolTypeEnum Methods of conditioning or heating a room or building direct heat_deliv_loc 0..1 HeatDelivLocEnum The location of heat delivery within the room direct heat_sys_deliv_meth 0..1 String The method by which the heat is delivered through the system direct heat_system_id 0..1 TextValue The heating system identifier direct heavy_metals * TextValue Heavy metals present in the sample and their concentrations direct heavy_metals_meth * TextValue Reference or method used in determining heavy metals direct height_carper_fiber 0..1 QuantityValue The average carpet fiber height in the indoor environment direct herbicide_regm * TextValue Information about treatment involving use of herbicides; information about tr... direct horizon_meth 0..1 TextValue Reference or method used in determining the horizon direct host_age 0..1 QuantityValue Age of host at the time of sampling; relevant scale depends on species and st... direct host_body_habitat 0..1 TextValue Original body habitat where the sample was obtained from direct host_body_product 0..1 ControlledTermValue Substance produced by the body, e direct host_body_site 0..1 ControlledTermValue Name of body site where the sample was obtained from, such as a specific orga... direct host_body_temp 0..1 QuantityValue Core body temperature of the host when sample was collected direct host_color 0..1 TextValue The color of host direct host_common_name 0..1 TextValue Common name of the host direct host_diet * TextValue Type of diet depending on the host, for animals omnivore, herbivore etc direct host_dry_mass 0..1 QuantityValue Measurement of dry mass direct host_family_relation * String Familial relationships to other hosts in the same study; can include multiple... direct host_genotype 0..1 TextValue Observed genotype direct host_growth_cond 0..1 TextValue Literature reference giving growth conditions of the host direct host_height 0..1 QuantityValue The height of subject direct host_last_meal * TextValue Content of last meal and time since feeding; can include multiple values direct host_length 0..1 QuantityValue The length of subject direct host_life_stage 0..1 TextValue Description of life stage of host direct host_phenotype 0..1 ControlledTermValue Phenotype of human or other host direct host_sex 0..1 HostSexEnum Gender or physical sex of the host direct host_shape 0..1 TextValue Morphological shape of host direct host_subject_id 0..1 TextValue A unique identifier by which each subject can be referred to, de-identified direct host_subspecf_genlin * String Information about the genetic distinctness of the host organism below the sub... direct host_substrate 0..1 TextValue The growth substrate of the host direct host_symbiont * String The taxonomic name of the organism(s) found living in mutualistic, commensali... direct host_taxid 0..1 ControlledIdentifiedTermValue NCBI taxon id of the host, e direct host_tot_mass 0..1 QuantityValue Total mass of the host at collection, the unit depends on host direct host_wet_mass 0..1 QuantityValue Measurement of wet mass direct humidity 0..1 QuantityValue Amount of water vapour in the air, at the time of sampling direct humidity_regm * TextValue Information about treatment involving an exposure to varying degree of humidi... direct indoor_space 0..1 IndoorSpaceEnum A distinguishable space within a structure, the purpose for which discrete ar... direct indoor_surf 0..1 IndoorSurfEnum Type of indoor surface direct indust_eff_percent 0..1 QuantityValue Percentage of industrial effluents received by wastewater treatment plant direct inorg_particles * TextValue Concentration of particles such as sand, grit, metal particles, ceramics, etc direct inside_lux 0..1 QuantityValue The recorded value at sampling time (power density) direct int_wall_cond 0..1 IntWallCondEnum The physical condition of the wall at the time of sampling; photos or video p... direct investigation_field 0..1 String field describing aspect of the investigation/study to which the sample belong... direct iw_bt_date_well 0..1 TimestampValue Injection water breakthrough date per well following a secondary and/or terti... direct iwf 0..1 QuantityValue Proportion of the produced fluids derived from injected water at the time of ... direct last_clean 0..1 TimestampValue The last time the floor was cleaned (swept, mopped, vacuumed) direct lat_lon 0..1 GeolocationValue The geographical origin of the sample as defined by latitude and longitude direct lbc_thirty 0..1 QuantityValue lime buffer capacity, determined after 30 minute incubation direct lbceq 0..1 QuantityValue lime buffer capacity, determined at equilibrium after 5 day incubation direct light_intensity 0..1 QuantityValue Measurement of light intensity direct light_regm 0..1 TextValue Information about treatment(s) involving exposure to light, including both li... direct light_type * LightTypeEnum Application of light to achieve some practical or aesthetic effect direct link_addit_analys 0..1 TextValue Link to additional analysis results performed on the sample direct link_class_info 0..1 TextValue Link to digitized soil maps or other soil classification information direct link_climate_info 0..1 TextValue Link to climate resource direct lithology 0..1 LithologyEnum Hydrocarbon resource main lithology (Additional information: http://petrowiki direct local_class 0..1 TextValue Soil classification based on local soil classification system direct local_class_meth 0..1 TextValue Reference or method used in determining the local soil classification direct magnesium 0..1 QuantityValue Concentration of magnesium in the sample direct manganese 0..1 QuantityValue Concentration of manganese in the sample direct max_occup 0..1 QuantityValue The maximum amount of people allowed in the indoor environment direct mean_frict_vel 0..1 QuantityValue Measurement of mean friction velocity direct mean_peak_frict_vel 0..1 QuantityValue Measurement of mean peak friction velocity direct mech_struc 0..1 MechStrucEnum mechanical structure: a moving structure direct mechanical_damage * TextValue Information about any mechanical damage exerted on the plant; can include mul... direct methane 0..1 QuantityValue Methane (gas) amount or concentration at the time of sampling direct micro_biomass_meth 0..1 String Reference or method used in determining microbial biomass direct microbial_biomass 0..1 QuantityValue The part of the organic matter in the soil that constitutes living microorgan... direct mineral_nutr_regm * TextValue Information about treatment involving the use of mineral supplements; should ... direct misc_param * TextValue Any other measurement performed or parameter collected, that is not listed he... direct n_alkanes * TextValue Concentration of n-alkanes; can include multiple n-alkanes direct nitrate 0..1 QuantityValue Concentration of nitrate in the sample direct nitrate_nitrogen 0..1 QuantityValue Concentration of nitrate nitrogen in the sample direct nitrite 0..1 QuantityValue Concentration of nitrite in the sample direct nitrite_nitrogen 0..1 QuantityValue Concentration of nitrite nitrogen in the sample direct nitro 0..1 QuantityValue Concentration of nitrogen (total) direct non_min_nutr_regm * String Information about treatment involving the exposure of plant to non-mineral nu... direct nucleic_acid_sequence_source_field 0..1 String direct number_pets 0..1 QuantityValue The number of pets residing in the sampled space direct number_plants 0..1 QuantityValue The number of plant(s) in the sampling space direct number_resident 0..1 QuantityValue The number of individuals currently occupying in the sampling location direct occup_density_samp 0..1 QuantityValue Average number of occupants at time of sampling per square footage direct occup_document 0..1 OccupDocumentEnum The type of documentation of occupancy direct occup_samp 0..1 QuantityValue Number of occupants present at time of sample within the given space direct org_carb 0..1 QuantityValue Concentration of organic carbon direct org_count_qpcr_info 0..1 String If qpcr was used for the cell count, the target gene name, the primer sequenc... direct org_matter 0..1 QuantityValue Concentration of organic matter direct org_nitro 0..1 QuantityValue Concentration of organic nitrogen direct org_particles * TextValue Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... direct organism_count * QuantityValue Total cell count of any organism (or group of organisms) per gram, volume or ... direct owc_tvdss 0..1 QuantityValue Depth of the original oil water contact (OWC) zone (average) (m TVDSS) direct oxy_stat_samp 0..1 OxyStatSampEnum Oxygenation status of sample direct oxygen 0..1 QuantityValue Oxygen (gas) amount or concentration at the time of sampling direct part_org_carb 0..1 QuantityValue Concentration of particulate organic carbon direct part_org_nitro 0..1 QuantityValue Concentration of particulate organic nitrogen direct particle_class * TextValue Particles are classified, based on their size, into six general categories:cl... direct permeability 0..1 TextValue Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... direct perturbation * TextValue Type of perturbation, e direct pesticide_regm * TextValue Information about treatment involving use of insecticides; should include the... direct petroleum_hydrocarb 0..1 QuantityValue Concentration of petroleum hydrocarbon direct ph 0..1 Double Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... direct ph_meth 0..1 TextValue Reference or method used in determining ph direct ph_regm * TextValue Information about treatment involving exposure of plants to varying levels of... direct phaeopigments * TextValue Concentration of phaeopigments; can include multiple phaeopigments direct phosphate 0..1 QuantityValue Concentration of phosphate direct phosplipid_fatt_acid * TextValue Concentration of phospholipid fatty acids; can include multiple values direct photon_flux 0..1 QuantityValue Measurement of photon flux direct plant_growth_med 0..1 ControlledTermValue Specification of the media for growing the plants or tissue cultured samples,... direct plant_product 0..1 TextValue Substance produced by the plant, where the sample was obtained from direct plant_sex 0..1 PlantSexEnum Sex of the reproductive parts on the whole plant, e direct plant_struc 0..1 ControlledTermValue Name of plant structure the sample was obtained from; for Plant Ontology (PO)... direct pollutants * TextValue Pollutant types and, amount or concentrations measured at the time of samplin... direct porosity 0..1 TextValue Porosity of deposited sediment is volume of voids divided by the total volume... direct potassium 0..1 QuantityValue Concentration of potassium in the sample direct pour_point 0..1 QuantityValue Temperature at which a liquid becomes semi solid and loses its flow character... direct pre_treatment 0..1 TextValue The process of pre-treatment removes materials that can be easily collected f... direct pres_animal_insect 0..1 String The type and number of animals or insects present in the sampling space direct pressure 0..1 QuantityValue Pressure to which the sample is subject to, in atmospheres direct prev_land_use_meth 0..1 String Reference or method used in determining previous land use and dates direct previous_land_use 0..1 TextValue Previous land use and dates direct primary_prod 0..1 QuantityValue Measurement of primary production, generally measured as isotope uptake direct primary_treatment 0..1 TextValue The process to produce both a generally homogeneous liquid capable of being t... direct prod_rate 0..1 QuantityValue Oil and/or gas production rates per well (e direct prod_start_date 0..1 TimestampValue Date of field's first production direct profile_position 0..1 ProfilePositionEnum Cross-sectional position in the hillslope where sample was collected direct quad_pos 0..1 QuadPosEnum The quadrant position of the sampling room within the building direct radiation_regm * TextValue Information about treatment involving exposure of plant or a plant part to a ... direct rainfall_regm * TextValue Information about treatment involving an exposure to a given amount of rainfa... direct reactor_type 0..1 TextValue Anaerobic digesters can be designed and engineered to operate using a number ... direct redox_potential 0..1 QuantityValue Redox potential, measured relative to a hydrogen cell, indicating oxidation o... direct rel_air_humidity 0..1 QuantityValue Partial vapor and air pressure, density of the vapor and air, or by the actua... direct rel_humidity_out 0..1 QuantityValue The recorded outside relative humidity value at the time of sampling direct rel_samp_loc 0..1 RelSampLocEnum The sampling location within the train car direct reservoir 0..1 TextValue Name of the reservoir (e direct resins_pc 0..1 TextValue Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... direct room_air_exch_rate 0..1 QuantityValue The rate at which outside air replaces indoor air in a given space direct room_architec_elem 0..1 String The unique details and component parts that, together, form the architecture ... direct room_condt 0..1 RoomCondtEnum The condition of the room at the time of sampling direct room_connected 0..1 RoomConnectedEnum List of rooms connected to the sampling room by a doorway direct room_count 0..1 TextValue The total count of rooms in the built structure including all room types direct room_dim 0..1 TextValue The length, width and height of sampling room direct room_door_dist 0..1 TextValue Distance between doors (meters) in the hallway between the sampling room and ... direct room_door_share 0..1 TextValue List of room(s) (room number, room name) sharing a door with the sampling roo... direct room_hallway 0..1 TextValue List of room(s) (room number, room name) located in the same hallway as sampl... direct room_loc 0..1 RoomLocEnum The position of the room within the building direct room_moist_dam_hist 0..1 Integer The history of moisture damage or mold in the past 12 months direct room_net_area 0..1 TextValue The net floor area of sampling room direct room_occup 0..1 QuantityValue Count of room occupancy at time of sampling direct room_samp_pos 0..1 RoomSampPosEnum The horizontal sampling position in the room relative to architectural elemen... direct room_type 0..1 RoomTypeEnum The main purpose or activity of the sampling room direct room_vol 0..1 TextValue Volume of sampling room direct room_wall_share 0..1 TextValue List of room(s) (room number, room name) sharing a wall with the sampling roo... direct room_window_count 0..1 Integer Number of windows in the room direct root_cond 0..1 TextValue Relevant rooting conditions such as field plot size, sowing density, containe... direct root_med_carbon 0..1 TextValue Source of organic carbon in the culture rooting medium; e direct root_med_macronutr 0..1 TextValue Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... direct root_med_micronutr 0..1 TextValue Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... direct root_med_ph 0..1 QuantityValue pH measurement of the culture rooting medium; e direct root_med_regl 0..1 TextValue Growth regulators in the culture rooting medium such as cytokinins, auxins, g... direct root_med_solid 0..1 TextValue Specification of the solidifying agent in the culture rooting medium; e direct root_med_suppl 0..1 TextValue Organic supplements of the culture rooting medium, such as vitamins, amino ac... direct salinity 0..1 QuantityValue The total concentration of all dissolved salts in a liquid or solid sample direct salinity_meth 0..1 TextValue Reference or method used in determining salinity direct salt_regm * TextValue Information about treatment involving use of salts as supplement to liquid an... direct samp_capt_status 0..1 SampCaptStatusEnum Reason for the sample direct samp_collec_device 0..1 String The device used to collect an environmental sample direct samp_collec_method 0..1 String The method employed for collecting the sample direct samp_collect_point 0..1 SampCollectPointEnum Sampling point on the asset were sample was collected (e direct samp_dis_stage 0..1 SampDisStageEnum Stage of the disease at the time of sample collection, e direct samp_floor 0..1 SampFloorEnum The floor of the building, where the sampling room is located direct samp_loc_corr_rate 0..1 TextValue Metal corrosion rate is the speed of metal deterioration due to environmental... direct samp_mat_process 0..1 ControlledTermValue A brief description of any processing applied to the sample during or after r... direct samp_md 0..1 QuantityValue In non deviated well, measured depth is equal to the true vertical depth, TVD... direct samp_name 0..1 String A local identifier or name that for the material sample used for extracting n... direct samp_preserv 0..1 TextValue Preservative added to the sample (e direct samp_room_id 0..1 TextValue Sampling room number direct samp_size 0..1 QuantityValue The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... direct samp_sort_meth * TextValue Method by which samples are sorted; open face filter collecting total suspend... direct samp_store_dur 0..1 TextValue Duration for which the sample was stored direct samp_store_loc 0..1 TextValue Location at which sample was stored, usually name of a specific freezer/room direct samp_store_temp 0..1 QuantityValue Temperature at which sample was stored, e direct samp_subtype 0..1 SampSubtypeEnum Name of sample sub-type direct samp_taxon_id 0..1 ControlledIdentifiedTermValue NCBI taxon id of the sample direct samp_time_out 0..1 TextValue The recent and long term history of outside sampling direct samp_transport_cond 0..1 TextValue Sample transport duration (in days or hrs) and temperature the sample was exp... direct samp_tvdss 0..1 TextValue Depth of the sample i direct samp_type 0..1 TextValue The type of material from which the sample was obtained direct samp_weather 0..1 SampWeatherEnum The weather on the sampling day direct samp_well_name 0..1 TextValue Name of the well (e direct saturates_pc 0..1 TextValue Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... direct season 0..1 TextValue The season when sampling occurred direct season_environment * TextValue Treatment involving an exposure to a particular season (e direct season_precpt 0..1 QuantityValue The average of all seasonal precipitation values known, or an estimated equiv... direct season_temp 0..1 QuantityValue Mean seasonal temperature direct season_use 0..1 SeasonUseEnum The seasons the space is occupied direct secondary_treatment 0..1 TextValue The process for substantially degrading the biological content of the sewage direct sediment_type 0..1 SedimentTypeEnum Information about the sediment type based on major constituents direct sequencing_field 0..1 String direct sewage_type 0..1 TextValue Type of wastewater treatment plant as municipial or industrial direct shad_dev_water_mold 0..1 String Signs of the presence of mold or mildew on the shading device direct shading_device_cond 0..1 ShadingDeviceCondEnum The physical condition of the shading device at the time of sampling direct shading_device_loc 0..1 TextValue The location of the shading device in relation to the built structure direct shading_device_mat 0..1 TextValue The material the shading device is composed of direct shading_device_type 0..1 ShadingDeviceTypeEnum The type of shading device direct sieving 0..1 TextValue Collection design of pooled samples and/or sieve size and amount of sample si... direct silicate 0..1 QuantityValue Concentration of silicate direct size_frac 0..1 TextValue Filtering pore size used in sample preparation direct size_frac_low 0..1 QuantityValue Refers to the mesh/pore size used to pre-filter/pre-sort the sample direct size_frac_up 0..1 QuantityValue Refers to the mesh/pore size used to retain the sample direct slope_aspect 0..1 QuantityValue The direction a slope faces direct slope_gradient 0..1 QuantityValue Commonly called 'slope' direct sludge_retent_time 0..1 QuantityValue The time activated sludge remains in reactor direct sodium 0..1 QuantityValue Sodium concentration in the sample direct soil_horizon 0..1 SoilHorizonEnum Specific layer in the land area which measures parallel to the soil surface a... direct soil_text_measure 0..1 QuantityValue The relative proportion of different grain sizes of mineral particles in a so... direct soil_texture_meth 0..1 String Reference or method used in determining soil texture direct soil_type 0..1 TextValue Description of the soil type or classification direct soil_type_meth 0..1 TextValue Reference or method used in determining soil series name or other lower-level... direct solar_irradiance 0..1 QuantityValue The amount of solar energy that arrives at a specific area of a surface durin... direct soluble_inorg_mat * TextValue Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... direct soluble_org_mat * TextValue Concentration of substances such as urea, fruit sugars, soluble proteins, dru... direct soluble_react_phosp 0..1 QuantityValue Concentration of soluble reactive phosphorus direct source_mat_id 0..1 TextValue A globally unique identifier assigned to the biological sample direct space_typ_state 0..1 TextValue Customary or normal state of the space direct specific 0..1 SpecificEnum The building specifications direct specific_ecosystem 0..1 String Specific ecosystems represent specific features of the environment like aphot... direct specific_humidity 0..1 QuantityValue The mass of water vapour in a unit mass of moist air, usually expressed as gr... direct sr_dep_env 0..1 SrDepEnvEnum Source rock depositional environment (https://en direct sr_geol_age 0..1 SrGeolAgeEnum Geological age of source rock (Additional info: https://en direct sr_kerog_type 0..1 SrKerogTypeEnum Origin of kerogen direct sr_lithology 0..1 SrLithologyEnum Lithology of source rock (https://en direct standing_water_regm * TextValue Treatment involving an exposure to standing water during a plant's life span,... direct store_cond 0..1 TextValue Explain how and for how long the soil sample was stored before DNA extraction... direct substructure_type * SubstructureTypeEnum The substructure or under building is that largely hidden section of the buil... direct sulfate 0..1 QuantityValue Concentration of sulfate in the sample direct sulfate_fw 0..1 QuantityValue Original sulfate concentration in the hydrocarbon resource direct sulfide 0..1 QuantityValue Concentration of sulfide in the sample direct surf_air_cont * SurfAirContEnum Contaminant identified on surface direct surf_humidity 0..1 QuantityValue Surfaces: water activity as a function of air and material moisture direct surf_material 0..1 SurfMaterialEnum Surface materials at the point of sampling direct surf_moisture 0..1 QuantityValue Water held on a surface direct surf_moisture_ph 0..1 Double ph measurement of surface direct surf_temp 0..1 QuantityValue Temperature of the surface at the time of sampling direct suspend_part_matter 0..1 QuantityValue Concentration of suspended particulate matter direct suspend_solids * TextValue Concentration of substances including a wide variety of material, such as sil... direct tan 0..1 QuantityValue Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by th... direct temp 0..1 QuantityValue Temperature of the sample at the time of sampling direct temp_out 0..1 QuantityValue The recorded temperature value at sampling time outside direct tertiary_treatment 0..1 TextValue The process providing a final treatment stage to raise the effluent quality b... direct tidal_stage 0..1 TidalStageEnum Stage of tide direct tillage * TillageEnum Note method(s) used for tilling direct tiss_cult_growth_med 0..1 TextValue Description of plant tissue culture growth media used direct toluene 0..1 QuantityValue Concentration of toluene in the sample direct tot_carb 0..1 QuantityValue Total carbon content direct tot_depth_water_col 0..1 QuantityValue Measurement of total depth of water column direct tot_diss_nitro 0..1 QuantityValue Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... direct tot_inorg_nitro 0..1 QuantityValue Total inorganic nitrogen content direct tot_iron 0..1 QuantityValue Concentration of total iron in the sample direct tot_nitro 0..1 QuantityValue Total nitrogen concentration of water samples, calculated by: total nitrogen ... direct tot_nitro_cont_meth 0..1 String Reference or method used in determining the total nitrogen direct tot_nitro_content 0..1 QuantityValue Total nitrogen content of the sample direct tot_org_c_meth 0..1 TextValue Reference or method used in determining total organic carbon direct tot_org_carb 0..1 QuantityValue Definition for soil: total organic carbon content of the soil, definition oth... direct tot_part_carb 0..1 QuantityValue Total particulate carbon content direct tot_phosp 0..1 QuantityValue Total phosphorus concentration in the sample, calculated by: total phosphorus... direct tot_phosphate 0..1 QuantityValue Total amount or concentration of phosphate direct tot_sulfur 0..1 QuantityValue Concentration of total sulfur in the sample direct train_line 0..1 TrainLineEnum The subway line name direct train_stat_loc 0..1 TrainStatLocEnum The train station collection location direct train_stop_loc 0..1 TrainStopLocEnum The train stop collection location direct turbidity 0..1 QuantityValue Measure of the amount of cloudiness or haziness in water caused by individual... direct tvdss_of_hcr_press 0..1 QuantityValue True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... direct tvdss_of_hcr_temp 0..1 QuantityValue True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... direct typ_occup_density 0..1 Double Customary or normal density of occupants direct ventilation_rate 0..1 QuantityValue Ventilation rate of the system in the sampled premises direct ventilation_type 0..1 TextValue Ventilation system used in the sampled premises direct vfa 0..1 QuantityValue Concentration of Volatile Fatty Acids in the sample direct vfa_fw 0..1 QuantityValue Original volatile fatty acid concentration in the hydrocarbon resource direct vis_media 0..1 VisMediaEnum The building visual media direct viscosity 0..1 TextValue A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020t... direct volatile_org_comp * TextValue Concentration of carbon-based chemicals that easily evaporate at room tempera... direct wall_area 0..1 QuantityValue The total area of the sampled room's walls direct wall_const_type 0..1 WallConstTypeEnum The building class of the wall defined by the composition of the building ele... direct wall_finish_mat 0..1 WallFinishMatEnum The material utilized to finish the outer most layer of the wall direct wall_height 0..1 QuantityValue The average height of the walls in the sampled room direct wall_loc 0..1 WallLocEnum The relative location of the wall within the room direct wall_surf_treatment 0..1 WallSurfTreatmentEnum The surface treatment of interior wall direct wall_texture 0..1 WallTextureEnum The feel, appearance, or consistency of a wall surface direct wall_thermal_mass 0..1 QuantityValue The ability of the wall to provide inertia against temperature fluctuations direct wall_water_mold 0..1 TextValue Signs of the presence of mold or mildew on a wall direct wastewater_type 0..1 TextValue The origin of wastewater such as human waste, rainfall, storm drains, etc direct water_cont_soil_meth 0..1 String Reference or method used in determining the water content of soil direct water_content * String Water content measurement direct water_current 0..1 QuantityValue Measurement of magnitude and direction of flow within a fluid direct water_cut 0..1 QuantityValue Current amount of water (%) in a produced fluid stream; or the average of the... direct water_feat_size 0..1 QuantityValue The size of the water feature direct water_feat_type 0..1 WaterFeatTypeEnum The type of water feature present within the building being sampled direct water_prod_rate 0..1 QuantityValue Water production rates per well (e direct water_temp_regm * TextValue Information about treatment involving an exposure to water with varying degre... direct watering_regm * TextValue Information about treatment involving an exposure to watering frequencies, tr... direct weekday 0..1 WeekdayEnum The day of the week when sampling occurred direct win 0..1 TextValue A unique identifier of a well or wellbore direct wind_direction 0..1 TextValue Wind direction is the direction from which a wind originates direct wind_speed 0..1 QuantityValue Speed of wind measured at the time of sampling direct window_cond 0..1 WindowCondEnum The physical condition of the window at the time of sampling direct window_cover 0..1 WindowCoverEnum The type of window covering direct window_horiz_pos 0..1 WindowHorizPosEnum The horizontal position of the window on the wall direct window_loc 0..1 WindowLocEnum The relative location of the window within the room direct window_mat 0..1 WindowMatEnum The type of material used to finish a window direct window_open_freq 0..1 TextValue The number of times windows are opened per week direct window_size 0..1 TextValue The window's length and width direct window_status 0..1 TextValue Defines whether the windows were open or closed during environmental testing direct window_type 0..1 WindowTypeEnum The type of windows direct window_vert_pos 0..1 WindowVertPosEnum The vertical position of the window on the wall direct window_water_mold 0..1 TextValue Signs of the presence of mold or mildew on the window direct xylene 0..1 QuantityValue Concentration of xylene in the sample direct zinc 0..1 QuantityValue Concentration of zinc in the sample direct ecosystem 0..1 String An ecosystem is a combination of a physical environment (abiotic factors) and... direct ecosystem_category 0..1 String Ecosystem categories represent divisions within the ecosystem based on specif... direct ecosystem_type 0..1 String Ecosystem types represent things having common characteristics within the Eco... direct ecosystem_subtype 0..1 String Ecosystem subtypes represent further subdivision of Ecosystem types into more... direct specific_ecosystem 0..1 String Specific ecosystems represent specific features of the environment like aphot... direct add_date 0..1 String The date on which the information was added to the database direct community 0..1 String direct habitat 0..1 String direct host_name 0..1 String direct location 0..1 String direct mod_date 0..1 String The last date on which the database information was modified direct ncbi_taxonomy_name 0..1 String direct proport_woa_temperature 0..1 String direct salinity_category 0..1 String Categorical description of the sample's salinity direct sample_collection_site 0..1 String direct soluble_iron_micromol 0..1 String direct subsurface_depth 0..1 QuantityValue direct air_temp_regm * TextValue Information about treatment involving an exposure to varying temperatures; sh... direct biotic_regm 0..1 TextValue Information about treatment(s) involving use of biotic factors, such as bacte... direct biotic_relationship 0..1 BioticRelationshipEnum Description of relationship(s) between the subject organism and other organis... direct climate_environment * TextValue Treatment involving an exposure to a particular climate; treatment regimen in... direct experimental_factor 0..1 ControlledTermValue Experimental factors are essentially the variable aspects of an experiment de... direct gaseous_environment * TextValue Use of conditions with differing gaseous environments; should include the nam... direct growth_facil 0..1 ControlledTermValue Type of facility where the sampled plant was grown; controlled vocabulary: gr... direct humidity_regm * TextValue Information about treatment involving an exposure to varying degree of humidi... direct light_regm 0..1 TextValue Information about treatment(s) involving exposure to light, including both li... direct phosphate 0..1 QuantityValue Concentration of phosphate direct samp_collec_method 0..1 String The method employed for collecting the sample direct samp_size 0..1 QuantityValue The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... direct source_mat_id 0..1 TextValue A globally unique identifier assigned to the biological sample direct watering_regm * TextValue Information about treatment involving an exposure to watering frequencies, tr... direct dna_absorb1 0..1 recommended Float 260/280 measurement of DNA sample purity direct dna_absorb2 0..1 recommended Float 260/230 measurement of DNA sample purity direct dna_collect_site 0..1 recommended String Provide information on the site your DNA sample was collected from direct dna_concentration 0..1 recommended Float direct dna_cont_type 0..1 recommended JgiContTypeEnum Tube or plate (96-well) direct dna_cont_well 0..1 recommended String direct dna_container_id 0..1 recommended String direct dna_dnase 0..1 recommended YesNoEnum direct dna_isolate_meth 0..1 recommended String Describe the method/protocol/kit used to extract DNA/RNA direct dna_organisms 0..1 recommended String List any organisms known or suspected to grow in co-culture, as well as estim... direct dna_project_contact 0..1 recommended String direct dna_samp_id 0..1 recommended String direct dna_sample_format 0..1 recommended DNASampleFormatEnum Solution in which the DNA sample has been suspended direct dna_sample_name 0..1 recommended String Give the DNA sample a name that is meaningful to you direct dna_seq_project 0..1 recommended String direct dna_seq_project_pi 0..1 recommended String direct dna_seq_project_name 0..1 recommended String direct dna_volume 0..1 recommended Float direct proposal_dna 0..1 recommended String direct dnase_rna 0..1 recommended YesNoEnum direct proposal_rna 0..1 recommended String direct rna_absorb1 0..1 recommended Float 260/280 measurement of RNA sample purity direct rna_absorb2 0..1 recommended Float 260/230 measurement of RNA sample purity direct rna_collect_site 0..1 recommended String Provide information on the site your RNA sample was collected from direct rna_concentration 0..1 recommended Float direct rna_cont_type 0..1 recommended JgiContTypeEnum Tube or plate (96-well) direct rna_cont_well 0..1 recommended String direct rna_container_id 0..1 recommended String direct rna_isolate_meth 0..1 recommended String Describe the method/protocol/kit used to extract DNA/RNA direct rna_organisms 0..1 recommended String List any organisms known or suspected to grow in co-culture, as well as estim... direct rna_project_contact 0..1 recommended String direct rna_samp_id 0..1 recommended String direct rna_sample_format 0..1 recommended RNASampleFormatEnum Solution in which the RNA sample has been suspended direct rna_sample_name 0..1 recommended String Give the RNA sample a name that is meaningful to you direct rna_seq_project 0..1 recommended String direct rna_seq_project_pi 0..1 recommended String direct rna_seq_project_name 0..1 recommended String direct rna_volume 0..1 recommended Float direct collection_date_inc 0..1 recommended String Date the incubation was harvested/collected/ended direct collection_time 0..1 recommended String The time of sampling, either as an instance (single point) or interval direct collection_time_inc 0..1 recommended String Time the incubation was harvested/collected/ended direct experimental_factor_other 0..1 recommended String Other details about your sample that you feel can't be accurately represented... direct filter_method 0..1 recommended String Type of filter used or how the sample was filtered direct isotope_exposure 0..1 recommended String List isotope exposure or addition applied to your sample direct micro_biomass_c_meth 0..1 recommended String Reference or method used in determining microbial biomass carbon direct micro_biomass_n_meth 0..1 String Reference or method used in determining microbial biomass nitrogen direct microbial_biomass_c 0..1 String The part of the organic matter in the soil that constitutes living microorgan... direct microbial_biomass_n 0..1 String The part of the organic matter in the soil that constitutes living microorgan... direct non_microb_biomass 0..1 String Amount of biomass; should include the name for the part of biomass measured, ... direct non_microb_biomass_method 0..1 String Reference or method used in determining biomass direct org_nitro_method 0..1 String Method used for obtaining organic nitrogen direct other_treatment 0..1 recommended String Other treatments applied to your samples that are not applicable to the provi... direct start_date_inc 0..1 recommended String Date the incubation was started direct start_time_inc 0..1 recommended String Time the incubation was started direct project_id 0..1 recommended String Proposal IDs or names associated with dataset direct replicate_number 0..1 recommended String If sending biological replicates, indicate the rep number here direct sample_shipped 0..1 recommended String The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... direct sample_type 0..1 recommended SampleTypeEnum Type of sample being submitted direct technical_reps 0..1 recommended String If sending technical replicates of the same sample, indicate the replicate co... direct analysis_type * recommended AnalysisTypeEnum Select all the data types associated or available for this biosample direct sample_link * recommended String A unique identifier to assign parent-child, subsample, or sibling samples direct bulk_elect_conductivity 0..1 QuantityValue Electrical conductivity is a measure of the ability to carry electric current... direct infiltrations * String The amount of time it takes to complete each infiltration activity direct zinc 0..1 QuantityValue Concentration of zinc in the sample direct manganese 0..1 QuantityValue Concentration of manganese in the sample direct ammonium_nitrogen 0..1 QuantityValue Concentration of ammonium nitrogen in the sample direct nitrate_nitrogen 0..1 QuantityValue Concentration of nitrate nitrogen in the sample direct nitrite_nitrogen 0..1 QuantityValue Concentration of nitrite nitrogen in the sample direct lbc_thirty 0..1 QuantityValue lime buffer capacity, determined after 30 minute incubation direct lbceq 0..1 QuantityValue lime buffer capacity, determined at equilibrium after 5 day incubation direct id 1 Uriorcurie An NMDC assigned unique identifier for a biosample submitted to NMDC NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie Unique identifier for a biosample submitted to additional resources NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Biosample/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_input any_of[range] Biosample MassSpectrometry has_input any_of[range] Biosample Database biosample_set range Biosample Pooling has_input any_of[range] Biosample Extraction has_input any_of[range] Biosample LibraryPreparation has_input any_of[range] Biosample CollectingBiosamplesFromSite has_output range Biosample SubSamplingProcess has_input any_of[range] Biosample MixingProcess has_input any_of[range] Biosample FiltrationProcess has_input any_of[range] Biosample ChromatographicSeparationProcess has_input any_of[range] Biosample DissolvingProcess has_input any_of[range] Biosample ChemicalConversionProcess has_input any_of[range] Biosample MaterialProcessing has_input any_of[range] Biosample DataGeneration has_input any_of[range] Biosample"},{"location":"Biosample/#aliases","title":"Aliases","text":""},{"location":"Biosample/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Biosample/#schema-source","title":"Schema Source","text":""},{"location":"Biosample/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Biosample native nmdc:Biosample exact OBI:0000747, NCIT:C43412, http://purl.obolibrary.org/obo/FBcv_0003024"},{"location":"Biosample/#linkml-source","title":"LinkML Source","text":""},{"location":"Biosample/#direct","title":"Direct","text":"
name: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: A sample contains information about the sequenced source material.\n      Samples are associated with checklists, which define the fields used to annotate\n      the samples. Samples are always associated with a taxon.\nnotes:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: MaterialEntity\nslots:\n- associated_studies\n- biosample_categories\n- collected_from\n- embargoed\n- host_disease_stat\n- host_taxid\n- img_identifiers\n- neon_biosample_identifiers\n- samp_name\n- gold_biosample_identifiers\n- insdc_biosample_identifiers\n- emsl_biosample_identifiers\n- igsn_biosample_identifiers\n- abs_air_humidity\n- add_recov_method\n- additional_info\n- address\n- adj_room\n- aero_struc\n- agrochem_addition\n- air_PM_concen\n- air_temp\n- air_temp_regm\n- al_sat\n- al_sat_meth\n- alkalinity\n- alkalinity_method\n- alkyl_diethers\n- alt\n- aminopept_act\n- ammonium\n- ammonium_nitrogen\n- amount_light\n- ances_data\n- annual_precpt\n- annual_temp\n- antibiotic_regm\n- api\n- arch_struc\n- aromatics_pc\n- asphaltenes_pc\n- atmospheric_data\n- avg_dew_point\n- avg_occup\n- avg_temp\n- bac_prod\n- bac_resp\n- bacteria_carb_prod\n- barometric_press\n- basin\n- bathroom_count\n- bedroom_count\n- benzene\n- biochem_oxygen_dem\n- biocide\n- biocide_admin_method\n- biol_stat\n- biomass\n- biotic_regm\n- biotic_relationship\n- bishomohopanol\n- blood_press_diast\n- blood_press_syst\n- bromide\n- build_docs\n- build_occup_type\n- building_setting\n- built_struc_age\n- built_struc_set\n- built_struc_type\n- calcium\n- carb_dioxide\n- carb_monoxide\n- carb_nitro_ratio\n- ceil_area\n- ceil_cond\n- ceil_finish_mat\n- ceil_struc\n- ceil_texture\n- ceil_thermal_mass\n- ceil_type\n- ceil_water_mold\n- chem_administration\n- chem_mutagen\n- chem_oxygen_dem\n- chem_treat_method\n- chem_treatment\n- chloride\n- chlorophyll\n- climate_environment\n- collection_date\n- conduc\n- cool_syst_id\n- core field\n- crop_rotation\n- cult_root_med\n- cur_land_use\n- cur_vegetation\n- cur_vegetation_meth\n- date_last_rain\n- density\n- depos_env\n- depth\n- dew_point\n- diether_lipids\n- diss_carb_dioxide\n- diss_hydrogen\n- diss_inorg_carb\n- diss_inorg_nitro\n- diss_inorg_phosp\n- diss_iron\n- diss_org_carb\n- diss_org_nitro\n- diss_oxygen\n- diss_oxygen_fluid\n- dna_cont_well\n- door_comp_type\n- door_cond\n- door_direct\n- door_loc\n- door_mat\n- door_move\n- door_size\n- door_type\n- door_type_metal\n- door_type_wood\n- door_water_mold\n- down_par\n- drainage_class\n- drawings\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- efficiency_percent\n- elev\n- elevator\n- emulsions\n- env_broad_scale\n- env_local_scale\n- env_medium\n- env_package\n- environment field\n- escalator\n- ethylbenzene\n- exp_duct\n- exp_pipe\n- experimental_factor\n- ext_door\n- ext_wall_orient\n- ext_window_orient\n- extreme_event\n- fao_class\n- fertilizer_regm\n- field\n- filter_type\n- fire\n- fireplace_type\n- flooding\n- floor_age\n- floor_area\n- floor_cond\n- floor_count\n- floor_finish_mat\n- floor_struc\n- floor_thermal_mass\n- floor_water_mold\n- fluor\n- freq_clean\n- freq_cook\n- fungicide_regm\n- furniture\n- gaseous_environment\n- gaseous_substances\n- gender_restroom\n- genetic_mod\n- geo_loc_name\n- glucosidase_act\n- gravidity\n- gravity\n- growth_facil\n- growth_habit\n- growth_hormone_regm\n- hall_count\n- handidness\n- hc_produced\n- hcr\n- hcr_fw_salinity\n- hcr_geol_age\n- hcr_pressure\n- hcr_temp\n- heat_cool_type\n- heat_deliv_loc\n- heat_sys_deliv_meth\n- heat_system_id\n- heavy_metals\n- heavy_metals_meth\n- height_carper_fiber\n- herbicide_regm\n- horizon_meth\n- host_age\n- host_body_habitat\n- host_body_product\n- host_body_site\n- host_body_temp\n- host_color\n- host_common_name\n- host_diet\n- host_dry_mass\n- host_family_relation\n- host_genotype\n- host_growth_cond\n- host_height\n- host_last_meal\n- host_length\n- host_life_stage\n- host_phenotype\n- host_sex\n- host_shape\n- host_subject_id\n- host_subspecf_genlin\n- host_substrate\n- host_symbiont\n- host_taxid\n- host_tot_mass\n- host_wet_mass\n- humidity\n- humidity_regm\n- indoor_space\n- indoor_surf\n- indust_eff_percent\n- inorg_particles\n- inside_lux\n- int_wall_cond\n- investigation field\n- iw_bt_date_well\n- iwf\n- last_clean\n- lat_lon\n- lbc_thirty\n- lbceq\n- light_intensity\n- light_regm\n- light_type\n- link_addit_analys\n- link_class_info\n- link_climate_info\n- lithology\n- local_class\n- local_class_meth\n- magnesium\n- manganese\n- max_occup\n- mean_frict_vel\n- mean_peak_frict_vel\n- mech_struc\n- mechanical_damage\n- methane\n- micro_biomass_meth\n- microbial_biomass\n- mineral_nutr_regm\n- misc_param\n- n_alkanes\n- nitrate\n- nitrate_nitrogen\n- nitrite\n- nitrite_nitrogen\n- nitro\n- non_min_nutr_regm\n- nucleic acid sequence source field\n- number_pets\n- number_plants\n- number_resident\n- occup_density_samp\n- occup_document\n- occup_samp\n- org_carb\n- org_count_qpcr_info\n- org_matter\n- org_nitro\n- org_particles\n- organism_count\n- owc_tvdss\n- oxy_stat_samp\n- oxygen\n- part_org_carb\n- part_org_nitro\n- particle_class\n- permeability\n- perturbation\n- pesticide_regm\n- petroleum_hydrocarb\n- ph\n- ph_meth\n- ph_regm\n- phaeopigments\n- phosphate\n- phosplipid_fatt_acid\n- photon_flux\n- plant_growth_med\n- plant_product\n- plant_sex\n- plant_struc\n- pollutants\n- porosity\n- potassium\n- pour_point\n- pre_treatment\n- pres_animal_insect\n- pressure\n- prev_land_use_meth\n- previous_land_use\n- primary_prod\n- primary_treatment\n- prod_rate\n- prod_start_date\n- profile_position\n- quad_pos\n- radiation_regm\n- rainfall_regm\n- reactor_type\n- redox_potential\n- rel_air_humidity\n- rel_humidity_out\n- rel_samp_loc\n- reservoir\n- resins_pc\n- room_air_exch_rate\n- room_architec_elem\n- room_condt\n- room_connected\n- room_count\n- room_dim\n- room_door_dist\n- room_door_share\n- room_hallway\n- room_loc\n- room_moist_dam_hist\n- room_net_area\n- room_occup\n- room_samp_pos\n- room_type\n- room_vol\n- room_wall_share\n- room_window_count\n- root_cond\n- root_med_carbon\n- root_med_macronutr\n- root_med_micronutr\n- root_med_ph\n- root_med_regl\n- root_med_solid\n- root_med_suppl\n- salinity\n- salinity_meth\n- salt_regm\n- samp_capt_status\n- samp_collec_device\n- samp_collec_method\n- samp_collect_point\n- samp_dis_stage\n- samp_floor\n- samp_loc_corr_rate\n- samp_mat_process\n- samp_md\n- samp_name\n- samp_preserv\n- samp_room_id\n- samp_size\n- samp_sort_meth\n- samp_store_dur\n- samp_store_loc\n- samp_store_temp\n- samp_subtype\n- samp_taxon_id\n- samp_time_out\n- samp_transport_cond\n- samp_tvdss\n- samp_type\n- samp_weather\n- samp_well_name\n- saturates_pc\n- season\n- season_environment\n- season_precpt\n- season_temp\n- season_use\n- secondary_treatment\n- sediment_type\n- sequencing field\n- sewage_type\n- shad_dev_water_mold\n- shading_device_cond\n- shading_device_loc\n- shading_device_mat\n- shading_device_type\n- sieving\n- silicate\n- size_frac\n- size_frac_low\n- size_frac_up\n- slope_aspect\n- slope_gradient\n- sludge_retent_time\n- sodium\n- soil_horizon\n- soil_text_measure\n- soil_texture_meth\n- soil_type\n- soil_type_meth\n- solar_irradiance\n- soluble_inorg_mat\n- soluble_org_mat\n- soluble_react_phosp\n- source_mat_id\n- space_typ_state\n- specific\n- specific_ecosystem\n- specific_humidity\n- sr_dep_env\n- sr_geol_age\n- sr_kerog_type\n- sr_lithology\n- standing_water_regm\n- store_cond\n- substructure_type\n- sulfate\n- sulfate_fw\n- sulfide\n- surf_air_cont\n- surf_humidity\n- surf_material\n- surf_moisture\n- surf_moisture_ph\n- surf_temp\n- suspend_part_matter\n- suspend_solids\n- tan\n- temp\n- temp_out\n- tertiary_treatment\n- tidal_stage\n- tillage\n- tiss_cult_growth_med\n- toluene\n- tot_carb\n- tot_depth_water_col\n- tot_diss_nitro\n- tot_inorg_nitro\n- tot_iron\n- tot_nitro\n- tot_nitro_cont_meth\n- tot_nitro_content\n- tot_org_c_meth\n- tot_org_carb\n- tot_part_carb\n- tot_phosp\n- tot_phosphate\n- tot_sulfur\n- train_line\n- train_stat_loc\n- train_stop_loc\n- turbidity\n- tvdss_of_hcr_press\n- tvdss_of_hcr_temp\n- typ_occup_density\n- ventilation_rate\n- ventilation_type\n- vfa\n- vfa_fw\n- vis_media\n- viscosity\n- volatile_org_comp\n- wall_area\n- wall_const_type\n- wall_finish_mat\n- wall_height\n- wall_loc\n- wall_surf_treatment\n- wall_texture\n- wall_thermal_mass\n- wall_water_mold\n- wastewater_type\n- water_cont_soil_meth\n- water_content\n- water_current\n- water_cut\n- water_feat_size\n- water_feat_type\n- water_prod_rate\n- water_temp_regm\n- watering_regm\n- weekday\n- win\n- wind_direction\n- wind_speed\n- window_cond\n- window_cover\n- window_horiz_pos\n- window_loc\n- window_mat\n- window_open_freq\n- window_size\n- window_status\n- window_type\n- window_vert_pos\n- window_water_mold\n- xylene\n- zinc\n- ecosystem\n- ecosystem_category\n- ecosystem_type\n- ecosystem_subtype\n- specific_ecosystem\n- add_date\n- community\n- habitat\n- host_name\n- location\n- mod_date\n- ncbi_taxonomy_name\n- proport_woa_temperature\n- salinity_category\n- sample_collection_site\n- soluble_iron_micromol\n- subsurface_depth\n- air_temp_regm\n- biotic_regm\n- biotic_relationship\n- climate_environment\n- experimental_factor\n- gaseous_environment\n- growth_facil\n- humidity_regm\n- light_regm\n- phosphate\n- samp_collec_method\n- samp_size\n- source_mat_id\n- watering_regm\n- dna_absorb1\n- dna_absorb2\n- dna_collect_site\n- dna_concentration\n- dna_cont_type\n- dna_cont_well\n- dna_container_id\n- dna_dnase\n- dna_isolate_meth\n- dna_organisms\n- dna_project_contact\n- dna_samp_id\n- dna_sample_format\n- dna_sample_name\n- dna_seq_project\n- dna_seq_project_pi\n- dna_seq_project_name\n- dna_volume\n- proposal_dna\n- dnase_rna\n- proposal_rna\n- rna_absorb1\n- rna_absorb2\n- rna_collect_site\n- rna_concentration\n- rna_cont_type\n- rna_cont_well\n- rna_container_id\n- rna_isolate_meth\n- rna_organisms\n- rna_project_contact\n- rna_samp_id\n- rna_sample_format\n- rna_sample_name\n- rna_seq_project\n- rna_seq_project_pi\n- rna_seq_project_name\n- rna_volume\n- collection_date_inc\n- collection_time\n- collection_time_inc\n- experimental_factor_other\n- filter_method\n- isotope_exposure\n- micro_biomass_c_meth\n- micro_biomass_n_meth\n- microbial_biomass_c\n- microbial_biomass_n\n- non_microb_biomass\n- non_microb_biomass_method\n- org_nitro_method\n- other_treatment\n- start_date_inc\n- start_time_inc\n- project_id\n- replicate_number\n- sample_shipped\n- sample_type\n- technical_reps\n- analysis_type\n- sample_link\n- bulk_elect_conductivity\n- infiltrations\n- zinc\n- manganese\n- ammonium_nitrogen\n- nitrate_nitrogen\n- nitrite_nitrogen\n- lbc_thirty\n- lbceq\nslot_usage:\n  collected_from:\n    name: collected_from\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  elev:\n    name: elev\n    title: elevation, meters\n    comments:\n    - All elevations must be reported in meters. Provide the numerical portion only.\n    - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n      if needed, to help estimate the elevation based on latitude and longitude coordinates.\n    examples:\n    - value: '100'\n    range: float\n  id:\n    name: id\n    description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_biosample_identifiers:\n    name: gold_biosample_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the GOLD biosample IDs associated with this biosample.\n    description: Unique identifier for a biosample submitted to GOLD that matches\n      the NMDC submitted biosample\n    comments:\n    - This is the ID provided by GOLD that starts with 'GB'\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a biosample submitted to additional resources.\n      Matches the entity that has been submitted to NMDC\n  lat_lon:\n    name: lat_lon\n    notes:\n    - This is currently a required field but it's not clear if this should be required\n      for human hosts\n  env_broad_scale:\n    name: env_broad_scale\n    required: true\n  env_local_scale:\n    name: env_local_scale\n    required: true\n  env_medium:\n    name: env_medium\n    required: true\n  associated_studies:\n    name: associated_studies\n    range: Study\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  fire:\n    name: fire\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    comments:\n    - Provide the date the fire occurred. If extended burning occurred provide the\n      date range.\n    examples:\n    - value: '1871-10-10'\n    - value: 1871-10-01 to 1871-10-31\n    range: string\n    pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n  flooding:\n    name: flooding\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    - What about if the \"day\" isn't known? Is this ok?\n    comments:\n    - Provide the date the flood occurred. If extended flooding occurred provide the\n      date range.\n    examples:\n    - value: '1927-04-15'\n    - value: 1927-04 to 1927-05\n    range: string\n  extreme_event:\n    name: extreme_event\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date, string\n    examples:\n    - value: 1980-05-18, volcanic eruption\n    range: string\n  slope_aspect:\n    name: slope_aspect\n    description: The direction a slope faces. While looking down a slope use a compass\n      to record the direction you are facing (direction or degrees). This measure\n      provides an indication of sun and wind exposure that will influence soil temperature\n      and evapotranspiration.\n    comments:\n    - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n      360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n      is west-facing.\n    examples:\n    - value: '35'\n  slope_gradient:\n    name: slope_gradient\n    todos:\n    - Slope is a percent. How does the validation work? Check to correct examples\n    examples:\n    - value: 10%\n    - value: 10 %\n    - value: '0.10'\n  al_sat:\n    name: al_sat\n    description: The relative abundance of aluminum in the sample\n    title: aluminum saturation/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    notes:\n    - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n      all cations, aluminum held by the cation exchange complex is in equilibrium\n      with aluminum in the soil solution.\n    examples:\n    - value: 27%\n  al_sat_meth:\n    name: al_sat_meth\n    description: Reference or method used in determining Aluminum saturation\n    title: aluminum saturation method/ extreme unusual properties\n    todos:\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n    comments:\n    - Required when aluminum saturation is provided.\n    examples:\n    - value: https://doi.org/10.1371/journal.pone.0176357\n  annual_precpt:\n    name: annual_precpt\n    examples:\n    - value: 8.94 inch\n  cur_vegetation:\n    name: cur_vegetation\n    description: Vegetation classification from one or more standard classification\n      systems, or agricultural crop\n    todos:\n    - Recommend changing this from text value to some king of ontology?\n    comments:\n    - Values provided here can be specific species of vegetation or vegetation regions\n    - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n    examples:\n    - value: deciduous forest\n    - value: forest\n    - value: Bauhinia variegata\n  cur_vegetation_meth:\n    name: cur_vegetation_meth\n    todos:\n    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n      out how they accomplish this if provided.\n    comments:\n    - Required when current vegetation is provided.\n    examples:\n    - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n  heavy_metals:\n    name: heavy_metals\n    description: Heavy metals present in the sample and their concentrations.\n    title: heavy metals/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    comments:\n    - For multiple heavy metals and concentrations, separate by ;\n    examples:\n    - value: mercury 0.09 micrograms per gram\n    - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n  heavy_metals_meth:\n    name: heavy_metals_meth\n    title: heavy metals method/ extreme unusual properties\n    comments:\n    - Required when heavy metals are provided\n    - If different methods are used for multiple metals, indicate the metal and method.\n      Separate metals by ;\n    examples:\n    - value: https://doi.org/10.3390/ijms9040434\n    - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n    multivalued: true\n  season_precpt:\n    name: season_precpt\n    title: average seasonal precipitation\n    todos:\n    - check validation & examples. always mm? so value only? Or value + unit\n    notes:\n    - mean and average are the same thing, but it seems like bad practice to not be\n      consistent. Changed mean to average\n    comments:\n    - Seasons are defined as spring (March, April, May), summer (June, July, August),\n      autumn (September, October, November) and winter (December, January, February).\n    examples:\n    - value: 0.4 inch\n    - value: 10.16 mm\n  water_cont_soil_meth:\n    name: water_cont_soil_meth\n    todos:\n    - Why is it soil water content method in the name but not the title? Is this slot\n      used in other samples?\n    - Soil water content can be measure MANY ways and often, multiple ways are used\n      in one experiment (gravimetric water content and water holding capacity and\n      water filled pore space, to name a few).\n    - Should this be multi valued? How to we manage and validate this?\n    comments:\n    - Required if providing water content\n    examples:\n    - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n    - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n  water_content:\n    name: water_content\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: string\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per gram or cubic centimeter per cubic centimeter\n    todos:\n    - value in preferred unit is too limiting. need to change this\n    - check and correct validation so examples are accepted\n    - how to manage multiple water content methods?\n    examples:\n    - value: 0.75 g water/g dry soil\n    - value: 75% water holding capacity\n    - value: 1.1 g fresh weight/ dry weight\n    - value: 10% water filled pore space\n    range: string\n    multivalued: true\n  ph_meth:\n    name: ph_meth\n    comments:\n    - This can include a link to the instrument used or a citation for the method.\n    examples:\n    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n    - value: https://doi.org/10.2136/sssabookser5.3.c16\n  tot_carb:\n    name: tot_carb\n    todos:\n    - is this inorganic and organic? both? could use some clarification.\n    - ug/L doesn't seem like the right units. Should check this slots usage in databases\n      and re-evaluate. I couldn't find any references that provided this data in this\n      format\n    examples:\n    - value: 1 ug/L\n  tot_nitro_cont_meth:\n    name: tot_nitro_cont_meth\n    examples:\n    - value: https://doi.org/10.2134/agronmonogr9.2.c32\n    - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n  tot_nitro_content:\n    name: tot_nitro_content\n    examples:\n    - value: 5 mg N/ L\n  tot_org_c_meth:\n    name: tot_org_c_meth\n    examples:\n    - value: https://doi.org/10.1080/07352680902776556\n  tot_org_carb:\n    name: tot_org_carb\n    todos:\n    - check description. How are they different?\n    examples:\n    - value: 5 mg N/ L\n  salinity_meth:\n    name: salinity_meth\n    examples:\n    - value: https://doi.org/10.1007/978-1-61779-986-0_28\n  sieving:\n    name: sieving\n    todos:\n    - check validation and examples\n    comments:\n    - Describe how samples were composited or sieved.\n    - Use 'sample link' to indicate which samples were combined.\n    examples:\n    - value: combined 2 cores | 4mm sieved\n    - value: 4 mm sieved and homogenized\n    - value: 50 g | 5 cores | 2 mm sieved\n  climate_environment:\n    name: climate_environment\n    todos:\n    - description says \"can include multiple climates\" but multivalued is set to false\n    - add examples, i need to see some examples to add correctly formatted example.\n  gaseous_environment:\n    name: gaseous_environment\n    todos:\n    - would like to see usage examples for this slot. Requiring micromole/L seems\n      too limiting and doesn't match expected_value value\n    - did I do this right? keep the example that's provided and add another? so as\n      to not override\n    examples:\n    - value: CO2; 500ppm above ambient; constant\n    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n  watering_regm:\n    name: watering_regm\n    examples:\n    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    - value: 75% water holding capacity; constant\n  source_mat_id:\n    name: source_mat_id\n    description: A globally unique identifier assigned to the biological sample.\n    title: source material identifier\n    todos:\n    - Currently, the comments say to use UUIDs. However, if we implement assigning\n      NMDC identifiers with the minter we dont need to require a GUID. It can be an\n      optional field to fill out only if they already have a resolvable ID.\n    comments:\n    - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n      NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n      IDs enable linking to derived analytes and subsamples. If you have not assigned\n      FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n    examples:\n    - value: IGSN:AU1243\n    - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\nclass_uri: nmdc:Biosample\nunique_keys:\n  samp_name_unique_key:\n    unique_key_name: samp_name_unique_key\n    unique_key_slots:\n    - samp_name\nrules:\n- preconditions:\n    slot_conditions:\n      dna_cont_well:\n        name: dna_cont_well\n        pattern: .+\n  postconditions:\n    slot_conditions:\n      dna_cont_type:\n        name: dna_cont_type\n        equals_string: plate\n  description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n    have any value for their plate position.\n  title: dna_well_requires_plate\n- preconditions:\n    slot_conditions:\n      dna_cont_type:\n        name: dna_cont_type\n        equals_string: plate\n  postconditions:\n    slot_conditions:\n      dna_cont_well:\n        name: dna_cont_well\n        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  description: DNA samples in plates must have a plate position that matches the regex.\n    Note the requirement for an empty string in the tube case. Waiting for value_present\n    validation to be added to runtime\n  title: dna_plate_requires_well\n- preconditions:\n    slot_conditions:\n      rna_cont_well:\n        name: rna_cont_well\n        pattern: .+\n  postconditions:\n    slot_conditions:\n      rna_cont_type:\n        name: rna_cont_type\n        equals_string: plate\n  description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n    have any value for their plate position.\n  title: rna_well_requires_plate\n- preconditions:\n    slot_conditions:\n      rna_cont_type:\n        name: rna_cont_type\n        equals_string: plate\n  postconditions:\n    slot_conditions:\n      rna_cont_well:\n        name: rna_cont_well\n        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  description: RNA samples in plates must have a plate position that matches the regex.\n    Note the requirement for an empty string in the tube case. Waiting for value_present\n    validation to be added to runtime\n  title: rna_plate_requires_well\n\n
"},{"location":"Biosample/#induced","title":"Induced","text":"
name: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: A sample contains information about the sequenced source material.\n      Samples are associated with checklists, which define the fields used to annotate\n      the samples. Samples are always associated with a taxon.\nnotes:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: MaterialEntity\nslot_usage:\n  collected_from:\n    name: collected_from\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  elev:\n    name: elev\n    title: elevation, meters\n    comments:\n    - All elevations must be reported in meters. Provide the numerical portion only.\n    - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n      if needed, to help estimate the elevation based on latitude and longitude coordinates.\n    examples:\n    - value: '100'\n    range: float\n  id:\n    name: id\n    description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_biosample_identifiers:\n    name: gold_biosample_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the GOLD biosample IDs associated with this biosample.\n    description: Unique identifier for a biosample submitted to GOLD that matches\n      the NMDC submitted biosample\n    comments:\n    - This is the ID provided by GOLD that starts with 'GB'\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a biosample submitted to additional resources.\n      Matches the entity that has been submitted to NMDC\n  lat_lon:\n    name: lat_lon\n    notes:\n    - This is currently a required field but it's not clear if this should be required\n      for human hosts\n  env_broad_scale:\n    name: env_broad_scale\n    required: true\n  env_local_scale:\n    name: env_local_scale\n    required: true\n  env_medium:\n    name: env_medium\n    required: true\n  associated_studies:\n    name: associated_studies\n    range: Study\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  fire:\n    name: fire\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    comments:\n    - Provide the date the fire occurred. If extended burning occurred provide the\n      date range.\n    examples:\n    - value: '1871-10-10'\n    - value: 1871-10-01 to 1871-10-31\n    range: string\n    pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n  flooding:\n    name: flooding\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    - What about if the \"day\" isn't known? Is this ok?\n    comments:\n    - Provide the date the flood occurred. If extended flooding occurred provide the\n      date range.\n    examples:\n    - value: '1927-04-15'\n    - value: 1927-04 to 1927-05\n    range: string\n  extreme_event:\n    name: extreme_event\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date, string\n    examples:\n    - value: 1980-05-18, volcanic eruption\n    range: string\n  slope_aspect:\n    name: slope_aspect\n    description: The direction a slope faces. While looking down a slope use a compass\n      to record the direction you are facing (direction or degrees). This measure\n      provides an indication of sun and wind exposure that will influence soil temperature\n      and evapotranspiration.\n    comments:\n    - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n      360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n      is west-facing.\n    examples:\n    - value: '35'\n  slope_gradient:\n    name: slope_gradient\n    todos:\n    - Slope is a percent. How does the validation work? Check to correct examples\n    examples:\n    - value: 10%\n    - value: 10 %\n    - value: '0.10'\n  al_sat:\n    name: al_sat\n    description: The relative abundance of aluminum in the sample\n    title: aluminum saturation/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    notes:\n    - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n      all cations, aluminum held by the cation exchange complex is in equilibrium\n      with aluminum in the soil solution.\n    examples:\n    - value: 27%\n  al_sat_meth:\n    name: al_sat_meth\n    description: Reference or method used in determining Aluminum saturation\n    title: aluminum saturation method/ extreme unusual properties\n    todos:\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n    comments:\n    - Required when aluminum saturation is provided.\n    examples:\n    - value: https://doi.org/10.1371/journal.pone.0176357\n  annual_precpt:\n    name: annual_precpt\n    examples:\n    - value: 8.94 inch\n  cur_vegetation:\n    name: cur_vegetation\n    description: Vegetation classification from one or more standard classification\n      systems, or agricultural crop\n    todos:\n    - Recommend changing this from text value to some king of ontology?\n    comments:\n    - Values provided here can be specific species of vegetation or vegetation regions\n    - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n    examples:\n    - value: deciduous forest\n    - value: forest\n    - value: Bauhinia variegata\n  cur_vegetation_meth:\n    name: cur_vegetation_meth\n    todos:\n    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n      out how they accomplish this if provided.\n    comments:\n    - Required when current vegetation is provided.\n    examples:\n    - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n  heavy_metals:\n    name: heavy_metals\n    description: Heavy metals present in the sample and their concentrations.\n    title: heavy metals/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    comments:\n    - For multiple heavy metals and concentrations, separate by ;\n    examples:\n    - value: mercury 0.09 micrograms per gram\n    - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n  heavy_metals_meth:\n    name: heavy_metals_meth\n    title: heavy metals method/ extreme unusual properties\n    comments:\n    - Required when heavy metals are provided\n    - If different methods are used for multiple metals, indicate the metal and method.\n      Separate metals by ;\n    examples:\n    - value: https://doi.org/10.3390/ijms9040434\n    - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n    multivalued: true\n  season_precpt:\n    name: season_precpt\n    title: average seasonal precipitation\n    todos:\n    - check validation & examples. always mm? so value only? Or value + unit\n    notes:\n    - mean and average are the same thing, but it seems like bad practice to not be\n      consistent. Changed mean to average\n    comments:\n    - Seasons are defined as spring (March, April, May), summer (June, July, August),\n      autumn (September, October, November) and winter (December, January, February).\n    examples:\n    - value: 0.4 inch\n    - value: 10.16 mm\n  water_cont_soil_meth:\n    name: water_cont_soil_meth\n    todos:\n    - Why is it soil water content method in the name but not the title? Is this slot\n      used in other samples?\n    - Soil water content can be measure MANY ways and often, multiple ways are used\n      in one experiment (gravimetric water content and water holding capacity and\n      water filled pore space, to name a few).\n    - Should this be multi valued? How to we manage and validate this?\n    comments:\n    - Required if providing water content\n    examples:\n    - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n    - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n  water_content:\n    name: water_content\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: string\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per gram or cubic centimeter per cubic centimeter\n    todos:\n    - value in preferred unit is too limiting. need to change this\n    - check and correct validation so examples are accepted\n    - how to manage multiple water content methods?\n    examples:\n    - value: 0.75 g water/g dry soil\n    - value: 75% water holding capacity\n    - value: 1.1 g fresh weight/ dry weight\n    - value: 10% water filled pore space\n    range: string\n    multivalued: true\n  ph_meth:\n    name: ph_meth\n    comments:\n    - This can include a link to the instrument used or a citation for the method.\n    examples:\n    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n    - value: https://doi.org/10.2136/sssabookser5.3.c16\n  tot_carb:\n    name: tot_carb\n    todos:\n    - is this inorganic and organic? both? could use some clarification.\n    - ug/L doesn't seem like the right units. Should check this slots usage in databases\n      and re-evaluate. I couldn't find any references that provided this data in this\n      format\n    examples:\n    - value: 1 ug/L\n  tot_nitro_cont_meth:\n    name: tot_nitro_cont_meth\n    examples:\n    - value: https://doi.org/10.2134/agronmonogr9.2.c32\n    - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n  tot_nitro_content:\n    name: tot_nitro_content\n    examples:\n    - value: 5 mg N/ L\n  tot_org_c_meth:\n    name: tot_org_c_meth\n    examples:\n    - value: https://doi.org/10.1080/07352680902776556\n  tot_org_carb:\n    name: tot_org_carb\n    todos:\n    - check description. How are they different?\n    examples:\n    - value: 5 mg N/ L\n  salinity_meth:\n    name: salinity_meth\n    examples:\n    - value: https://doi.org/10.1007/978-1-61779-986-0_28\n  sieving:\n    name: sieving\n    todos:\n    - check validation and examples\n    comments:\n    - Describe how samples were composited or sieved.\n    - Use 'sample link' to indicate which samples were combined.\n    examples:\n    - value: combined 2 cores | 4mm sieved\n    - value: 4 mm sieved and homogenized\n    - value: 50 g | 5 cores | 2 mm sieved\n  climate_environment:\n    name: climate_environment\n    todos:\n    - description says \"can include multiple climates\" but multivalued is set to false\n    - add examples, i need to see some examples to add correctly formatted example.\n  gaseous_environment:\n    name: gaseous_environment\n    todos:\n    - would like to see usage examples for this slot. Requiring micromole/L seems\n      too limiting and doesn't match expected_value value\n    - did I do this right? keep the example that's provided and add another? so as\n      to not override\n    examples:\n    - value: CO2; 500ppm above ambient; constant\n    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n  watering_regm:\n    name: watering_regm\n    examples:\n    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    - value: 75% water holding capacity; constant\n  source_mat_id:\n    name: source_mat_id\n    description: A globally unique identifier assigned to the biological sample.\n    title: source material identifier\n    todos:\n    - Currently, the comments say to use UUIDs. However, if we implement assigning\n      NMDC identifiers with the minter we dont need to require a GUID. It can be an\n      optional field to fill out only if they already have a resolvable ID.\n    comments:\n    - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n      NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n      IDs enable linking to derived analytes and subsamples. If you have not assigned\n      FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n    examples:\n    - value: IGSN:AU1243\n    - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\nattributes:\n  associated_studies:\n    name: associated_studies\n    description: The study associated with a resource.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: associated_studies\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: Study\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  biosample_categories:\n    name: biosample_categories\n    title: Categories the biosample belongs to\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: biosample_categories\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: BiosampleCategoryEnum\n    multivalued: true\n  collected_from:\n    name: collected_from\n    description: The Site from which a Biosample was collected\n    todos:\n    - add an OBO slot_uri ?\n    comments:\n    - this illustrates implementing a Biosample relation with a (binary) slot\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: collected_from\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: FieldResearchSite\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  embargoed:\n    name: embargoed\n    description: If true, the data are embargoed and not available for public access.\n    todos:\n    - make this required?\n    - first apply to Biosample\n    - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n    - applying to a Study may not be granular enough\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: embargoed\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: boolean\n    recommended: true\n  host_disease_stat:\n    name: host_disease_stat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: disease name or Disease Ontology term\n    description: List of diseases with which the host has been diagnosed; can include\n      multiple diagnoses. The value of the field depends on host; for humans the terms\n      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,\n      non-human host diseases are free text\n    title: host disease status\n    examples:\n    - value: rabies [DOID:11260]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host disease status\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{termLabel} {[termID]}|{text}'\n    slot_uri: MIXS:0000031\n    alias: host_disease_stat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_taxid:\n    name: host_taxid\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: NCBI taxon identifier\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: NCBI taxon id of the host, e.g. 9606\n    title: host taxid\n    comments:\n    - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host taxid\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000250\n    alias: host_taxid\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    multivalued: false\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: Biosample\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n  neon_biosample_identifiers:\n    name: neon_biosample_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - neon_identifiers\n    alias: neon_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  samp_name:\n    name: samp_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text\n    description: A local identifier or name that for the material sample used for\n      extracting nucleic acids, and subsequent sequencing. It can refer either to\n      the original material collected or to any derived sub-samples. It can have any\n      format, but we suggest that you make it concise, unique and consistent within\n      your lab, and as informative as possible. INSDC requires every sample name from\n      a single Submitter to be unique. Use of a globally unique identifier for the\n      field source_mat_id is recommended in addition to sample_name.\n    title: sample name\n    examples:\n    - value: ISDsoil1\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample name\n    rank: 1000\n    is_a: investigation field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001107\n    alias: samp_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  gold_biosample_identifiers:\n    name: gold_biosample_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the GOLD biosample IDs associated with this biosample.\n    description: Unique identifier for a biosample submitted to GOLD that matches\n      the NMDC submitted biosample\n    comments:\n    - This is the ID provided by GOLD that starts with 'GB'\n    examples:\n    - value: https://bioregistry.io/gold:Gb0312930\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: uriorcurie\n    multivalued: true\n    pattern: ^gold:Gb[0-9]+$\n  insdc_biosample_identifiers:\n    name: insdc_biosample_identifiers\n    description: identifiers for corresponding sample in INSDC\n    examples:\n    - value: https://bioregistry.io/biosample:SAMEA5989477\n    - value: https://bioregistry.io/biosample:SAMD00212331\n      description: I13_N_5-10 sample from Soil fungal diversity along elevational\n        gradients\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/bioregistry/bioregistry/issues/108\n    - https://www.ebi.ac.uk/biosamples/\n    - https://www.ncbi.nlm.nih.gov/biosample\n    - https://www.ddbj.nig.ac.jp/biosample/index-e.html\n    aliases:\n    - EBI biosample identifiers\n    - NCBI biosample identifiers\n    - DDBJ biosample identifiers\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: external_identifier\n    multivalued: true\n    pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n  emsl_biosample_identifiers:\n    name: emsl_biosample_identifiers\n    description: A list of identifiers for the biosample from the EMSL database.  This\n      is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n      EMSL NEXUS database.\n    title: EMSL Biosample Identifiers\n    todos:\n    - removed \"planned\" once NEXUS is online\n    - determine real expansion for emsl prefix\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - emsl_identifiers\n    alias: emsl_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  igsn_biosample_identifiers:\n    name: igsn_biosample_identifiers\n    description: A list of identifiers for the biosample from the IGSN database.\n    title: IGSN Biosample Identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: biosample_identifiers\n    mixins:\n    - igsn_identifiers\n    alias: igsn_biosample_identifiers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  abs_air_humidity:\n    name: abs_air_humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per gram, kilogram per kilogram, kilogram, pound\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Actual mass of water vapor - mh20 - present in the air water vapor\n      mixture\n    title: absolute air humidity\n    examples:\n    - value: 9 gram per gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - absolute air humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000122\n    alias: abs_air_humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  add_recov_method:\n    name: add_recov_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration;timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n      for increase of hydrocarbon recovery from resource and start date for each one\n      of them. If \"other\" is specified, please propose entry in \"additional info\"\n      field\n    title: secondary and tertiary recovery methods and start date\n    examples:\n    - value: Polymer Addition;2018-06-21T14:30Z\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - secondary and tertiary recovery methods and start date\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001009\n    alias: add_recov_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  additional_info:\n    name: additional_info\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information that doesn't fit anywhere else. Can also be used to propose\n      new entries for fields with controlled vocabulary\n    title: additional info\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - additional info\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000300\n    alias: additional_info\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  address:\n    name: address\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The street name and building number where the sampling occurred.\n    title: address\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - address\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer}{text}'\n    slot_uri: MIXS:0000218\n    alias: address\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  adj_room:\n    name: adj_room\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: room name;room number\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of rooms (room number, room name) immediately adjacent to the\n      sampling room\n    title: adjacent rooms\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - adjacent rooms\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{integer}'\n    slot_uri: MIXS:0000219\n    alias: adj_room\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  aero_struc:\n    name: aero_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Aerospace structures typically consist of thin plates with stiffeners\n      for the external surfaces, bulkheads and frames to support the shape and fasteners\n      such as welds, rivets, screws and bolts to hold the components together\n    title: aerospace structure\n    examples:\n    - value: plane\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - aerospace structure\n    rank: 1000\n    is_a: core field\n    string_serialization: '[plane|glider]'\n    slot_uri: MIXS:0000773\n    alias: aero_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  agrochem_addition:\n    name: agrochem_addition\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: agrochemical name;agrochemical amount;timestamp\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Addition of fertilizers, pesticides, etc. - amount and time of applications\n    title: history/agrochemical additions\n    examples:\n    - value: roundup;5 milligram per liter;2018-06-21\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/agrochemical additions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{timestamp}'\n    slot_uri: MIXS:0000639\n    alias: agrochem_addition\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  air_PM_concen:\n    name: air_PM_concen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: particulate matter name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micrograms per cubic meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of substances that remain suspended in the air, and\n      comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can\n      report multiple PM's by entering numeric values preceded by name of PM\n    title: air particulate matter concentration\n    examples:\n    - value: PM2.5;10 microgram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - air particulate matter concentration\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000108\n    alias: air_PM_concen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  air_temp:\n    name: air_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Temperature of the air at the time of sampling\n    title: air temperature\n    examples:\n    - value: 20 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - air temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000124\n    alias: air_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  air_temp_regm:\n    name: air_temp_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: temperature value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to varying temperatures;\n      should include the temperature, treatment regimen including how many times the\n      treatment was repeated, how long each treatment lasted, and the start and end\n      time of the entire treatment; can include different temperature regimens\n    title: air temperature regimen\n    examples:\n    - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - air temperature regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000551\n    alias: air_temp_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  al_sat:\n    name: al_sat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative abundance of aluminum in the sample\n    title: aluminum saturation/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    notes:\n    - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n      all cations, aluminum held by the cation exchange complex is in equilibrium\n      with aluminum in the soil solution.\n    examples:\n    - value: 27%\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - extreme_unusual_properties/Al saturation\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000607\n    alias: al_sat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  al_sat_meth:\n    name: al_sat_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or URL\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining Aluminum saturation\n    title: aluminum saturation method/ extreme unusual properties\n    todos:\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n    comments:\n    - Required when aluminum saturation is provided.\n    examples:\n    - value: https://doi.org/10.1371/journal.pone.0176357\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - extreme_unusual_properties/Al saturation method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000324\n    alias: al_sat_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  alkalinity:\n    name: alkalinity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milliequivalent per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Alkalinity, the ability of a solution to neutralize acids to the\n      equivalence point of carbonate or bicarbonate\n    title: alkalinity\n    examples:\n    - value: 50 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - alkalinity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000421\n    alias: alkalinity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  alkalinity_method:\n    name: alkalinity_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: description of method\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Method used for alkalinity measurement\n    title: alkalinity method\n    examples:\n    - value: titration\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - alkalinity method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000298\n    alias: alkalinity_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  alkyl_diethers:\n    name: alkyl_diethers\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of alkyl diethers\n    title: alkyl diethers\n    examples:\n    - value: 0.005 mole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - alkyl diethers\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000490\n    alias: alkyl_diethers\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  alt:\n    name: alt\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n    description: Altitude is a term used to identify heights of objects such as airplanes,\n      space shuttles, rockets, atmospheric balloons and heights of places such as\n      atmospheric layers and clouds. It is used to measure the height of an object\n      which is above the earth's surface. In this context, the altitude measurement\n      is the vertical distance between the earth's surface above sea level and the\n      sampled position in the air\n    title: altitude\n    examples:\n    - value: 100 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - altitude\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000094\n    alias: alt\n    owner: Biosample\n    domain_of:\n    - agriculture\n    - air\n    - built environment\n    - core\n    - food-animal and animal feed\n    - food-farm environment\n    - food-food production facility\n    - food-human foods\n    - host-associated\n    - human-associated\n    - human-gut\n    - human-oral\n    - human-skin\n    - human-vaginal\n    - hydrocarbon resources-cores\n    - hydrocarbon resources-fluids_swabs\n    - microbial mat_biofilm\n    - miscellaneous natural or artificial environment\n    - plant-associated\n    - sediment\n    - soil\n    - symbiont-associated\n    - wastewater_sludge\n    - water\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  aminopept_act:\n    name: aminopept_act\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per liter per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of aminopeptidase activity\n    title: aminopeptidase activity\n    examples:\n    - value: 0.269 mole per liter per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - aminopeptidase activity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000172\n    alias: aminopept_act\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ammonium:\n    name: ammonium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of ammonium in the sample\n    title: ammonium\n    examples:\n    - value: 1.5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ammonium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000427\n    alias: ammonium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ammonium_nitrogen:\n    name: ammonium_nitrogen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of ammonium nitrogen in the sample\n    title: ammonium nitrogen\n    examples:\n    - value: 2.3 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - ammonium_nitrogen\n    - NH4-N\n    rank: 1000\n    alias: ammonium_nitrogen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  amount_light:\n    name: amount_light\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: lux, lumens per square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The unit of illuminance and luminous emittance, measuring luminous\n      flux per unit area\n    title: amount of light\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - amount of light\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000140\n    alias: amount_light\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ances_data:\n    name: ances_data\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information about either pedigree or other ancestral information\n      description (e.g. parental variety in case of mutant or selection), e.g. A/3*B\n      (meaning [(A x B) x B] x B)\n    title: ancestral data\n    examples:\n    - value: A/3*B\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ancestral data\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000247\n    alias: ances_data\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  annual_precpt:\n    name: annual_precpt\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average of all annual precipitation values known, or an estimated\n      equivalent value derived by such methods as regional indexes or Isohyetal maps.\n    title: mean annual precipitation\n    examples:\n    - value: 8.94 inch\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean annual precipitation\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000644\n    alias: annual_precpt\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  annual_temp:\n    name: annual_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Mean annual temperature\n    title: mean annual temperature\n    examples:\n    - value: 12.5 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean annual temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000642\n    alias: annual_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  antibiotic_regm:\n    name: antibiotic_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: antibiotic name;antibiotic amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving antibiotic administration;\n      should include the name of antibiotic, amount administered, treatment regimen\n      including how many times the treatment was repeated, how long each treatment\n      lasted, and the start and end time of the entire treatment; can include multiple\n      antibiotic regimens\n    title: antibiotic regimen\n    examples:\n    - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - antibiotic regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000553\n    alias: antibiotic_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  api:\n    name: api\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degrees API\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'API gravity is a measure of how heavy or light a petroleum liquid\n      is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.\n      31.1\u00ac\u221e API)'\n    title: API gravity\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - API gravity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000157\n    alias: api\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  arch_struc:\n    name: arch_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: An architectural structure is a human-made, free-standing, immobile\n      outdoor construction\n    title: architectural structure\n    examples:\n    - value: shed\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - architectural structure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000774\n    alias: arch_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: arch_struc_enum\n    multivalued: false\n  aromatics_pc:\n    name: aromatics_pc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n      method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n      and polarity. There are three main methods to obtain SARA results. The most\n      popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n      https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n    title: aromatics wt%\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - aromatics wt%\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000133\n    alias: aromatics_pc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  asphaltenes_pc:\n    name: asphaltenes_pc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n      method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n      and polarity. There are three main methods to obtain SARA results. The most\n      popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n      https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n    title: asphaltenes wt%\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - asphaltenes wt%\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000135\n    alias: asphaltenes_pc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  atmospheric_data:\n    name: atmospheric_data\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: atmospheric data name;measurement value\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Measurement of atmospheric data; can include multiple data\n    title: atmospheric data\n    examples:\n    - value: wind speed;9 knots\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - atmospheric data\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0001097\n    alias: atmospheric_data\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  avg_dew_point:\n    name: avg_dew_point\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average of dew point measures taken at the beginning of every\n      hour over a 24 hour period on the sampling day\n    title: average dew point\n    examples:\n    - value: 25.5 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - average dew point\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000141\n    alias: avg_dew_point\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  avg_occup:\n    name: avg_occup\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Daily average occupancy of room. Indicate the number of person(s)\n      daily occupying the sampling room.\n    title: average daily occupancy\n    examples:\n    - value: '2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - average daily occupancy\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000775\n    alias: avg_occup\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  avg_temp:\n    name: avg_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average of temperatures taken at the beginning of every hour\n      over a 24 hour period on the sampling day\n    title: average temperature\n    examples:\n    - value: 12.5 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - average temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000142\n    alias: avg_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  bac_prod:\n    name: bac_prod\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter per day\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Bacterial production in the water column measured by isotope uptake\n    title: bacterial production\n    examples:\n    - value: 5 milligram per cubic meter per day\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bacterial production\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000683\n    alias: bac_prod\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  bac_resp:\n    name: bac_resp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter per day, micromole oxygen per liter per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of bacterial respiration in the water column\n    title: bacterial respiration\n    examples:\n    - value: 300 micromole oxygen per liter per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bacterial respiration\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000684\n    alias: bac_resp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  bacteria_carb_prod:\n    name: bacteria_carb_prod\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: nanogram per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of bacterial carbon production\n    title: bacterial carbon production\n    examples:\n    - value: 2.53 microgram per liter per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bacterial carbon production\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000173\n    alias: bacteria_carb_prod\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  barometric_press:\n    name: barometric_press\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millibar\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Force per unit area exerted against a surface by the weight of air\n      above that surface\n    title: barometric pressure\n    examples:\n    - value: 5 millibar\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - barometric pressure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000096\n    alias: barometric_press\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  basin:\n    name: basin\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of the basin (e.g. Campos)\n    title: basin name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - basin name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000290\n    alias: basin\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  bathroom_count:\n    name: bathroom_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of bathrooms in the building\n    title: bathroom count\n    examples:\n    - value: '1'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bathroom count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000776\n    alias: bathroom_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  bedroom_count:\n    name: bedroom_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of bedrooms in the building\n    title: bedroom count\n    examples:\n    - value: '2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bedroom count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000777\n    alias: bedroom_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  benzene:\n    name: benzene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of benzene in the sample\n    title: benzene\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - benzene\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000153\n    alias: benzene\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  biochem_oxygen_dem:\n    name: biochem_oxygen_dem\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Amount of dissolved oxygen needed by aerobic biological organisms\n      in a body of water to break down organic material present in a given water sample\n      at certain temperature over a specific time period\n    title: biochemical oxygen demand\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biochemical oxygen demand\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000653\n    alias: biochem_oxygen_dem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  biocide:\n    name: biocide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;name;timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of biocides (commercial name of product and supplier) and date\n      of administration\n    title: biocide administration\n    examples:\n    - value: ALPHA 1427;Baker Hughes;2008-01-23\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biocide administration\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{text};{timestamp}'\n    slot_uri: MIXS:0001011\n    alias: biocide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  biocide_admin_method:\n    name: biocide_admin_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;frequency;duration;duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Method of biocide administration (dose, frequency, duration, time\n      elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3\n      days)\n    title: biocide administration method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biocide administration method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\n    slot_uri: MIXS:0000456\n    alias: biocide_admin_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  biol_stat:\n    name: biol_stat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The level of genome modification.\n    title: biological status\n    examples:\n    - value: natural\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biological status\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000858\n    alias: biol_stat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: biol_stat_enum\n    multivalued: false\n  biomass:\n    name: biomass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: biomass type;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: ton, kilogram, gram\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Amount of biomass; should include the name for the part of biomass\n      measured, e.g. Microbial, total. Can include multiple measurements\n    title: biomass\n    examples:\n    - value: total;20 gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biomass\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000174\n    alias: biomass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  biotic_regm:\n    name: biotic_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information about treatment(s) involving use of biotic factors, such\n      as bacteria, viruses or fungi.\n    title: biotic regimen\n    examples:\n    - value: sample inoculated with Rhizobium spp. Culture\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - biotic regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001038\n    alias: biotic_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  biotic_relationship:\n    name: biotic_relationship\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n    description: Description of relationship(s) between the subject organism and other\n      organism(s) it is associated with. E.g., parasite on species X; mutualist with\n      species Y. The target organism is the subject of the relationship, and the other\n      organism(s) is the object\n    title: observed biotic relationship\n    examples:\n    - value: free living\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - observed biotic relationship\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    slot_uri: MIXS:0000028\n    alias: biotic_relationship\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: biotic_relationship_enum\n    multivalued: false\n  bishomohopanol:\n    name: bishomohopanol\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, microgram per gram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of bishomohopanol\n    title: bishomohopanol\n    examples:\n    - value: 14 microgram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bishomohopanol\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000175\n    alias: bishomohopanol\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  blood_press_diast:\n    name: blood_press_diast\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter mercury\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Resting diastolic blood pressure, measured as mm mercury\n    title: host blood pressure diastolic\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host blood pressure diastolic\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000258\n    alias: blood_press_diast\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  blood_press_syst:\n    name: blood_press_syst\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter mercury\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Resting systolic blood pressure, measured as mm mercury\n    title: host blood pressure systolic\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host blood pressure systolic\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000259\n    alias: blood_press_syst\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  bromide:\n    name: bromide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of bromide\n    title: bromide\n    examples:\n    - value: 0.05 parts per million\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - bromide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000176\n    alias: bromide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  build_docs:\n    name: build_docs\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The building design, construction and operation documents\n    title: design, construction, and operation documents\n    examples:\n    - value: maintenance plans\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - design, construction, and operation documents\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000787\n    alias: build_docs\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: build_docs_enum\n    multivalued: false\n  build_occup_type:\n    name: build_occup_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: The primary function for which a building or discrete part of a building\n      is intended to be used\n    title: building occupancy type\n    examples:\n    - value: market\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - building occupancy type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000761\n    alias: build_occup_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: build_occup_type_enum\n    multivalued: true\n  building_setting:\n    name: building_setting\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A location (geography) where a building is set\n    title: building setting\n    examples:\n    - value: rural\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - building setting\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000768\n    alias: building_setting\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: building_setting_enum\n    multivalued: false\n  built_struc_age:\n    name: built_struc_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: year\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The age of the built structure since construction\n    title: built structure age\n    examples:\n    - value: '15'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - built structure age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000145\n    alias: built_struc_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  built_struc_set:\n    name: built_struc_set\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The characterization of the location of the built structure as high\n      or low human density\n    title: built structure setting\n    examples:\n    - value: rural\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - built structure setting\n    rank: 1000\n    is_a: core field\n    string_serialization: '[urban|rural]'\n    slot_uri: MIXS:0000778\n    alias: built_struc_set\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  built_struc_type:\n    name: built_struc_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A physical structure that is a body or assemblage of bodies in space\n      to form a system capable of supporting loads\n    title: built structure type\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - built structure type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000721\n    alias: built_struc_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  calcium:\n    name: calcium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, micromole per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of calcium in the sample\n    title: calcium\n    examples:\n    - value: 0.2 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - calcium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000432\n    alias: calcium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  carb_dioxide:\n    name: carb_dioxide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Carbon dioxide (gas) amount or concentration at the time of sampling\n    title: carbon dioxide\n    examples:\n    - value: 410 parts per million\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - carbon dioxide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000097\n    alias: carb_dioxide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  carb_monoxide:\n    name: carb_monoxide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Carbon monoxide (gas) amount or concentration at the time of sampling\n    title: carbon monoxide\n    examples:\n    - value: 0.1 parts per million\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - carbon monoxide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000098\n    alias: carb_monoxide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  carb_nitro_ratio:\n    name: carb_nitro_ratio\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Ratio of amount or concentrations of carbon to nitrogen\n    title: carbon/nitrogen ratio\n    examples:\n    - value: '0.417361111'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - carbon/nitrogen ratio\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000310\n    alias: carb_nitro_ratio\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ceil_area:\n    name: ceil_area\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The area of the ceiling space within the room\n    title: ceiling area\n    examples:\n    - value: 25 square meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling area\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000148\n    alias: ceil_area\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ceil_cond:\n    name: ceil_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the ceiling at the time of sampling; photos\n      or video preferred; use drawings to indicate location of damaged areas\n    title: ceiling condition\n    examples:\n    - value: damaged\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000779\n    alias: ceil_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ceil_cond_enum\n    multivalued: false\n  ceil_finish_mat:\n    name: ceil_finish_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of material used to finish a ceiling\n    title: ceiling finish material\n    examples:\n    - value: stucco\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling finish material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000780\n    alias: ceil_finish_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ceil_finish_mat_enum\n    multivalued: false\n  ceil_struc:\n    name: ceil_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The construction format of the ceiling\n    title: ceiling structure\n    examples:\n    - value: concrete\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling structure\n    rank: 1000\n    is_a: core field\n    string_serialization: '[wood frame|concrete]'\n    slot_uri: MIXS:0000782\n    alias: ceil_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  ceil_texture:\n    name: ceil_texture\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The feel, appearance, or consistency of a ceiling surface\n    title: ceiling texture\n    examples:\n    - value: popcorn\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling texture\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000783\n    alias: ceil_texture\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ceil_texture_enum\n    multivalued: false\n  ceil_thermal_mass:\n    name: ceil_thermal_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: joule per degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The ability of the ceiling to provide inertia against temperature\n      fluctuations. Generally this means concrete that is exposed. A metal deck that\n      supports a concrete slab will act thermally as long as it is exposed to room\n      air flow\n    title: ceiling thermal mass\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling thermal mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000143\n    alias: ceil_thermal_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ceil_type:\n    name: ceil_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of ceiling according to the ceiling's appearance or construction\n    title: ceiling type\n    examples:\n    - value: coffered\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000784\n    alias: ceil_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ceil_type_enum\n    multivalued: false\n  ceil_water_mold:\n    name: ceil_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on the ceiling\n    title: ceiling signs of water/mold\n    examples:\n    - value: presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ceiling signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000781\n    alias: ceil_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  chem_administration:\n    name: chem_administration\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: CHEBI;timestamp\n      occurrence:\n        tag: occurrence\n        value: m\n    description: List of chemical compounds administered to the host or site where\n      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can\n      include multiple compounds. For chemical entities of biological interest ontology\n      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi\n    title: chemical administration\n    examples:\n    - value: agar [CHEBI:2509];2018-05-11T20:00Z\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical administration\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]};{timestamp}'\n    slot_uri: MIXS:0000751\n    alias: chem_administration\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  chem_mutagen:\n    name: chem_mutagen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: mutagen name;mutagen amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Treatment involving use of mutagens; should include the name of mutagen,\n      amount administered, treatment regimen including how many times the treatment\n      was repeated, how long each treatment lasted, and the start and end time of\n      the entire treatment; can include multiple mutagen regimens\n    title: chemical mutagen\n    examples:\n    - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical mutagen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000555\n    alias: chem_mutagen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  chem_oxygen_dem:\n    name: chem_oxygen_dem\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A measure of the capacity of water to consume oxygen during the decomposition\n      of organic matter and the oxidation of inorganic chemicals such as ammonia and\n      nitrite\n    title: chemical oxygen demand\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical oxygen demand\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000656\n    alias: chem_oxygen_dem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  chem_treat_method:\n    name: chem_treat_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;frequency;duration;duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Method of chemical administration(dose, frequency, duration, time\n      elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1\n      hr; 0 days)\n    title: chemical treatment method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical treatment method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\n    slot_uri: MIXS:0000457\n    alias: chem_treat_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  chem_treatment:\n    name: chem_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;name;timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of chemical compounds administered upstream the sampling location\n      where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n      demulsifiers, and other production chemicals etc.). The commercial name of the\n      product and name of the supplier should be provided. The date of administration\n      should also be included\n    title: chemical treatment\n    examples:\n    - value: ACCENT 1125;DOW;2010-11-17\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chemical treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{text};{timestamp}'\n    slot_uri: MIXS:0001012\n    alias: chem_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  chloride:\n    name: chloride\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of chloride in the sample\n    title: chloride\n    examples:\n    - value: 5000 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chloride\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000429\n    alias: chloride\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  chlorophyll:\n    name: chlorophyll\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter, microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of chlorophyll\n    title: chlorophyll\n    examples:\n    - value: 5 milligram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - chlorophyll\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000177\n    alias: chlorophyll\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  climate_environment:\n    name: climate_environment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: climate name;treatment interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Treatment involving an exposure to a particular climate; treatment\n      regimen including how many times the treatment was repeated, how long each treatment\n      lasted, and the start and end time of the entire treatment; can include multiple\n      climates\n    title: climate environment\n    todos:\n    - description says \"can include multiple climates\" but multivalued is set to false\n    - add examples, i need to see some examples to add correctly formatted example.\n    examples:\n    - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - climate environment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0001040\n    alias: climate_environment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  collection_date:\n    name: collection_date\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date and time\n    description: 'The time of sampling, either as an instance (single point in time)\n      or interval. In case no exact time is available, the date/time can be right\n      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\n    title: collection date\n    examples:\n    - value: 2018-05-11T10:00:00+01:00; 2018-05-11\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - collection date\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000011\n    alias: collection_date\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  conduc:\n    name: conduc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milliSiemens per centimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Electrical conductivity of water\n    title: conductivity\n    examples:\n    - value: 10 milliSiemens per centimeter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - conductivity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000692\n    alias: conduc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  cool_syst_id:\n    name: cool_syst_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: unique identifier\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The cooling system identifier\n    title: cooling system identifier\n    examples:\n    - value: '12345'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - cooling system identifier\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000785\n    alias: cool_syst_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  core field:\n    name: core field\n    description: basic fields\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: core_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  crop_rotation:\n    name: crop_rotation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: crop rotation status;schedule\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Whether or not crop is rotated, and if yes, rotation schedule\n    title: history/crop rotation\n    examples:\n    - value: yes;R2/2017-01-01/2018-12-31/P6M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/crop rotation\n    rank: 1000\n    is_a: core field\n    string_serialization: '{boolean};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000318\n    alias: crop_rotation\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  cult_root_med:\n    name: cult_root_med\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name, PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name or reference for the hydroponic or in vitro culture rooting\n      medium; can be the name of a commonly used medium or reference to a specific\n      medium, e.g. Murashige and Skoog medium. If the medium has not been formally\n      published, use the rooting medium descriptors.\n    title: culture rooting medium\n    examples:\n    - value: http://himedialabs.com/TD/PT158.pdf\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - culture rooting medium\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}|{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0001041\n    alias: cult_root_med\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  cur_land_use:\n    name: cur_land_use\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Present state of sample site\n    title: current land use\n    examples:\n    - value: conifers\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - current land use\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001080\n    alias: cur_land_use\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: cur_land_use_enum\n    multivalued: false\n  cur_vegetation:\n    name: cur_vegetation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: current vegetation type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Vegetation classification from one or more standard classification\n      systems, or agricultural crop\n    title: current vegetation\n    todos:\n    - Recommend changing this from text value to some king of ontology?\n    comments:\n    - Values provided here can be specific species of vegetation or vegetation regions\n    - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n    examples:\n    - value: deciduous forest\n    - value: forest\n    - value: Bauhinia variegata\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - current vegetation\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000312\n    alias: cur_vegetation\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  cur_vegetation_meth:\n    name: cur_vegetation_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in vegetation classification\n    title: current vegetation method\n    todos:\n    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n      out how they accomplish this if provided.\n    comments:\n    - Required when current vegetation is provided.\n    examples:\n    - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - current vegetation method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000314\n    alias: cur_vegetation_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  date_last_rain:\n    name: date_last_rain\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The date of the last time it rained\n    title: date last rain\n    examples:\n    - value: 2018-05-11:T14:30Z\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - date last rain\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000786\n    alias: date_last_rain\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  density:\n    name: density\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per cubic meter, gram per cubic centimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Density of the sample, which is its mass per unit volume (aka volumetric\n      mass density)\n    title: density\n    examples:\n    - value: 1000 kilogram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - density\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000435\n    alias: density\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  depos_env:\n    name: depos_env\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n      If \"other\" is specified, please propose entry in \"additional info\" field\n    title: depositional environment\n    examples:\n    - value: Continental - Alluvial\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - depositional environment\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000992\n    alias: depos_env\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: depos_env_enum\n    multivalued: false\n  depth:\n    name: depth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n    description: The vertical distance below local surface, e.g. for sediment or soil\n      samples depth is measured from sediment or soil surface, respectively. Depth\n      can be reported as an interval for subsurface samples.\n    title: depth\n    examples:\n    - value: 10 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - depth\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000018\n    alias: depth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  dew_point:\n    name: dew_point\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The temperature to which a given parcel of humid air must be cooled,\n      at constant barometric pressure, for water vapor to condense into water.\n    title: dew point\n    examples:\n    - value: 22 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dew point\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000129\n    alias: dew_point\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diether_lipids:\n    name: diether_lipids\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: diether lipid name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: nanogram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of diether lipids; can include multiple types of diether\n      lipids\n    title: diether lipids\n    examples:\n    - value: 0.2 nanogram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - diether lipids\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000178\n    alias: diether_lipids\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  diss_carb_dioxide:\n    name: diss_carb_dioxide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved carbon dioxide in the sample or liquid\n      portion of the sample\n    title: dissolved carbon dioxide\n    examples:\n    - value: 5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved carbon dioxide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000436\n    alias: diss_carb_dioxide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_hydrogen:\n    name: diss_hydrogen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved hydrogen\n    title: dissolved hydrogen\n    examples:\n    - value: 0.3 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved hydrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000179\n    alias: diss_hydrogen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_inorg_carb:\n    name: diss_inorg_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Dissolved inorganic carbon concentration in the sample, typically\n      measured after filtering the sample using a 0.45 micrometer filter\n    title: dissolved inorganic carbon\n    examples:\n    - value: 2059 micromole per kilogram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved inorganic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000434\n    alias: diss_inorg_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_inorg_nitro:\n    name: diss_inorg_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved inorganic nitrogen\n    title: dissolved inorganic nitrogen\n    examples:\n    - value: 761 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved inorganic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000698\n    alias: diss_inorg_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_inorg_phosp:\n    name: diss_inorg_phosp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved inorganic phosphorus in the sample\n    title: dissolved inorganic phosphorus\n    examples:\n    - value: 56.5 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved inorganic phosphorus\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000106\n    alias: diss_inorg_phosp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_iron:\n    name: diss_iron\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved iron in the sample\n    title: dissolved iron\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved iron\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000139\n    alias: diss_iron\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_org_carb:\n    name: diss_org_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved organic carbon in the sample, liquid portion\n      of the sample, or aqueous phase of the fluid\n    title: dissolved organic carbon\n    examples:\n    - value: 197 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved organic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000433\n    alias: diss_org_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_org_nitro:\n    name: diss_org_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Dissolved organic nitrogen concentration measured as; total dissolved\n      nitrogen - NH4 - NO3 - NO2\n    title: dissolved organic nitrogen\n    examples:\n    - value: 0.05 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved organic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000162\n    alias: diss_org_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_oxygen:\n    name: diss_oxygen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per kilogram, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved oxygen\n    title: dissolved oxygen\n    examples:\n    - value: 175 micromole per kilogram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved oxygen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000119\n    alias: diss_oxygen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  diss_oxygen_fluid:\n    name: diss_oxygen_fluid\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per kilogram, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of dissolved oxygen in the oil field produced fluids\n      as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\n    title: dissolved oxygen in fluids\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - dissolved oxygen in fluids\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000438\n    alias: diss_oxygen_fluid\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  dna_cont_well:\n    name: dna_cont_well\n    title: DNA plate position\n    comments:\n    - Required when 'plate' is selected for container type.\n    - Leave blank if the sample will be shipped in a tube.\n    - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n      pass validation.\n    - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n    examples:\n    - value: B2\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 11\n    string_serialization: '{96 well plate pos}'\n    alias: dna_cont_well\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n    pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  door_comp_type:\n    name: door_comp_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The composite type of the door\n    title: door type, composite\n    examples:\n    - value: revolving\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door type, composite\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000795\n    alias: door_comp_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_comp_type_enum\n    multivalued: false\n  door_cond:\n    name: door_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The phsical condition of the door\n    title: door condition\n    examples:\n    - value: new\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000788\n    alias: door_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_cond_enum\n    multivalued: false\n  door_direct:\n    name: door_direct\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The direction the door opens\n    title: door direction of opening\n    examples:\n    - value: inward\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door direction of opening\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000789\n    alias: door_direct\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_direct_enum\n    multivalued: false\n  door_loc:\n    name: door_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative location of the door in the room\n    title: door location\n    examples:\n    - value: north\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000790\n    alias: door_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_loc_enum\n    multivalued: false\n  door_mat:\n    name: door_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The material the door is composed of\n    title: door material\n    examples:\n    - value: wood\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000791\n    alias: door_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_mat_enum\n    multivalued: false\n  door_move:\n    name: door_move\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of movement of the door\n    title: door movement\n    examples:\n    - value: swinging\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door movement\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000792\n    alias: door_move\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_move_enum\n    multivalued: false\n  door_size:\n    name: door_size\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The size of the door\n    title: door area or size\n    examples:\n    - value: 2.5 square meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door area or size\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000158\n    alias: door_size\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  door_type:\n    name: door_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of door material\n    title: door type\n    examples:\n    - value: wooden\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000794\n    alias: door_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_type_enum\n    multivalued: false\n  door_type_metal:\n    name: door_type_metal\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of metal door\n    title: door type, metal\n    examples:\n    - value: hollow\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door type, metal\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000796\n    alias: door_type_metal\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_type_metal_enum\n    multivalued: false\n  door_type_wood:\n    name: door_type_wood\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of wood door\n    title: door type, wood\n    examples:\n    - value: battened\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door type, wood\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000797\n    alias: door_type_wood\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: door_type_wood_enum\n    multivalued: false\n  door_water_mold:\n    name: door_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on a door\n    title: door signs of water/mold\n    examples:\n    - value: presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - door signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000793\n    alias: door_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  down_par:\n    name: down_par\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microEinstein per square meter per second, microEinstein per square\n          centimeter per second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Visible waveband radiance and irradiance measurements in the water\n      column\n    title: downward PAR\n    examples:\n    - value: 28.71 microEinstein per square meter per second\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - downward PAR\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000703\n    alias: down_par\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  drainage_class:\n    name: drainage_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Drainage classification from a standard system such as the USDA system\n    title: drainage classification\n    examples:\n    - value: well\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - drainage classification\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001085\n    alias: drainage_class\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: drainage_class_enum\n    multivalued: false\n  drawings:\n    name: drawings\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The buildings architectural drawings; if design is chosen, indicate\n      phase-conceptual, schematic, design development, and construction documents\n    title: drawings\n    examples:\n    - value: sketch\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - drawings\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000798\n    alias: drawings\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: drawings_enum\n    multivalued: false\n  ecosystem:\n    name: ecosystem\n    description: An ecosystem is a combination of a physical environment (abiotic\n      factors) and all the organisms (biotic factors) that interact with this environment.\n      Ecosystem is in position 1/5 in a GOLD path.\n    comments:\n    - The abiotic factors play a profound role on the type and composition of organisms\n      in a given environment. The GOLD Ecosystem at the top of the five-level classification\n      system is aimed at capturing the broader environment from which an organism\n      or environmental sample is collected. The three broad groups under Ecosystem\n      are Environmental, Host-associated, and Engineered. They represent samples collected\n      from a natural environment or from another organism or from engineered environments\n      like bioreactors respectively.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_category:\n    name: ecosystem_category\n    description: Ecosystem categories represent divisions within the ecosystem based\n      on specific characteristics of the environment from where an organism or sample\n      is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n    comments:\n    - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n      Ecosystem categories for Host-associated samples can be individual hosts or\n      phyla and for engineered samples it may be manipulated environments like bioreactors,\n      solid waste etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_category\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_subtype:\n    name: ecosystem_subtype\n    description: Ecosystem subtypes represent further subdivision of Ecosystem types\n      into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n      path.\n    comments:\n    - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n      (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n      the Ecosystem subtype category.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_subtype\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_type:\n    name: ecosystem_type\n    description: Ecosystem types represent things having common characteristics within\n      the Ecosystem Category. These common characteristics based grouping is still\n      broad but specific to the characteristics of a given environment. Ecosystem\n      type is in position 3/5 in a GOLD path.\n    comments:\n    - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n      or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n      air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n      type can represent Respiratory system, Digestive system, Roots etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  efficiency_percent:\n    name: efficiency_percent\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Percentage of volatile solids removed from the anaerobic digestor\n    title: efficiency percent\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - efficiency percent\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000657\n    alias: efficiency_percent\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  elev:\n    name: elev\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n    description: Elevation of the sampling site is its height above a fixed reference\n      point, most commonly the mean sea level. Elevation is mainly used when referring\n      to points on the earth's surface, while altitude is used for points above the\n      surface, such as an aircraft in flight or a spacecraft in orbit.\n    title: elevation, meters\n    comments:\n    - All elevations must be reported in meters. Provide the numerical portion only.\n    - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n      if needed, to help estimate the elevation based on latitude and longitude coordinates.\n    examples:\n    - value: '100'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - elevation\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000093\n    alias: elev\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: float\n    multivalued: false\n  elevator:\n    name: elevator\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of elevators within the built structure\n    title: elevator count\n    examples:\n    - value: '2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - elevator count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000799\n    alias: elevator\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  emulsions:\n    name: emulsions\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: emulsion name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Amount or concentration of substances such as paints, adhesives,\n      mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion\n      types\n    title: emulsions\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - emulsions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000660\n    alias: emulsions\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  env_broad_scale:\n    name: env_broad_scale\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: The major environment type(s) where the sample was collected. Recommend\n          subclasses of biome [ENVO:00000428]. Multiple terms can be separated by\n          one or more pipes.\n      tooltip:\n        tag: tooltip\n        value: The biome or major environmental system where the sample or specimen\n          originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]\n          in the Environment Ontology (ENVO). For host-associated or plant-associated\n          samples, use terms from the UBERON or Plant Ontology to describe the broad\n          anatomical or morphological context\n    description: 'Report the major environmental system the sample or specimen came\n      from. The system(s) identified should have a coarse spatial grain, to provide\n      the general environmental context of where the sampling was done (e.g. in the\n      desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.\n      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\n    title: broad-scale environmental context\n    examples:\n    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water\n        sample from the photic zone in middle of the Atlantic Ocean\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - broad-scale environmental context\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000012\n    alias: env_broad_scale\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    required: true\n    multivalued: false\n  env_local_scale:\n    name: env_local_scale\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: Environmental entities having causal influences upon the entity at\n          time of sampling.\n      tooltip:\n        tag: tooltip\n        value: The specific environmental entities or features near the sample or\n          specimen that significantly influence its characteristics or composition.\n          These entities are typically smaller in scale than the broad environmental\n          context. Values for this field should be countable, material nouns and must\n          be chosen from subclasses of BFO:0000040 (material entity) that appear in\n          the Environment Ontology (ENVO). For host-associated or plant-associated\n          samples, use terms from the UBERON or Plant Ontology to describe specific\n          anatomical structures or plant parts.\n    description: 'Report the entity or entities which are in the sample or specimen\u2019s\n      local vicinity and which you believe have significant causal influences on your\n      sample or specimen. We recommend using EnvO terms which are of smaller spatial\n      grain than your entry for env_broad_scale. Terms, such as anatomical sites,\n      from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)\n      are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\n    title: local environmental context\n    examples:\n    - value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from\n        various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb\n        and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub\n        layer [ENVO:01000336].'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - local environmental context\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000013\n    alias: env_local_scale\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    required: true\n    multivalued: false\n  env_medium:\n    name: env_medium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: The material displaced by the entity at time of sampling. Recommend\n          subclasses of environmental material [ENVO:00010483].\n      tooltip:\n        tag: tooltip\n        value: The predominant environmental material or substrate that directly surrounds\n          or hosts the sample or specimen at the time of sampling. Choose values from\n          subclasses of the 'environmental material' class [ENVO:00010483] in the\n          Environment Ontology (ENVO). Values for this field should be measurable\n          or mass material nouns, representing continuous environmental materials.\n          For host-associated or plant-associated samples, use terms from the UBERON\n          or Plant Ontology to indicate a tissue, organ, or plant structure\n    description: 'Report the environmental material(s) immediately surrounding the\n      sample or specimen at the time of sampling. We recommend using subclasses of\n      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO\n      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n      . Terms from other OBO ontologies are permissible as long as they reference\n      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities\n      (e.g. a tree, a leaf, a table top).'\n    title: environmental medium\n    examples:\n    - value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m\n        of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating\n        a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - environmental medium\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000014\n    alias: env_medium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    required: true\n    multivalued: false\n  env_package:\n    name: env_package\n    description: MIxS extension for reporting of measurements and observations obtained\n      from one or more of the environments where the sample was obtained. All environmental\n      packages listed here are further defined in separate subtables. By giving the\n      name of the environmental package, a selection of fields can be made from the\n      subtables and can be reported\n    notes:\n    - no longer in MIxS as of 6.0?\n    in_subset:\n    - mixs extension\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - environmental package\n    rank: 1000\n    alias: env_package\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n  environment field:\n    name: environment field\n    description: field describing environmental aspect of a sample\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: environment_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  escalator:\n    name: escalator\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of escalators within the built structure\n    title: escalator count\n    examples:\n    - value: '4'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - escalator count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000800\n    alias: escalator\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  ethylbenzene:\n    name: ethylbenzene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of ethylbenzene in the sample\n    title: ethylbenzene\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ethylbenzene\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000155\n    alias: ethylbenzene\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  exp_duct:\n    name: exp_duct\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The amount of exposed ductwork in the room\n    title: exposed ductwork\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - exposed ductwork\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000144\n    alias: exp_duct\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  exp_pipe:\n    name: exp_pipe\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of exposed pipes in the room\n    title: exposed pipes\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - exposed pipes\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000220\n    alias: exp_pipe\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  experimental_factor:\n    name: experimental_factor\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text or EFO and/or OBI\n    description: Experimental factors are essentially the variable aspects of an experiment\n      design which can be used to describe an experiment, or set of experiments, in\n      an increasingly detailed manner. This field accepts ontology terms from Experimental\n      Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For\n      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\n    title: experimental factor\n    examples:\n    - value: time series design [EFO:EFO_0001779]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - experimental factor\n    rank: 1000\n    is_a: investigation field\n    string_serialization: '{termLabel} {[termID]}|{text}'\n    slot_uri: MIXS:0000008\n    alias: experimental_factor\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  ext_door:\n    name: ext_door\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of exterior doors in the built structure\n    title: exterior door count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - exterior door count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000170\n    alias: ext_door\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  ext_wall_orient:\n    name: ext_wall_orient\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The orientation of the exterior wall\n    title: orientations of exterior wall\n    examples:\n    - value: northwest\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - orientations of exterior wall\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000817\n    alias: ext_wall_orient\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ext_wall_orient_enum\n    multivalued: false\n  ext_window_orient:\n    name: ext_window_orient\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The compass direction the exterior window of the room is facing\n    title: orientations of exterior window\n    examples:\n    - value: southwest\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - orientations of exterior window\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000818\n    alias: ext_window_orient\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ext_window_orient_enum\n    multivalued: false\n  extreme_event:\n    name: extreme_event\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date, string\n    description: Unusual physical events that may have affected microbial populations\n    title: history/extreme events\n    examples:\n    - value: 1980-05-18, volcanic eruption\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/extreme events\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000320\n    alias: extreme_event\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  fao_class:\n    name: fao_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Soil classification from the FAO World Reference Database for Soil\n      Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\n    title: soil_taxonomic/FAO classification\n    examples:\n    - value: Luvisols\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil_taxonomic/FAO classification\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001083\n    alias: fao_class\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: fao_class_enum\n    multivalued: false\n  fertilizer_regm:\n    name: fertilizer_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: fertilizer name;fertilizer amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving the use of fertilizers; should\n      include the name of fertilizer, amount administered, treatment regimen including\n      how many times the treatment was repeated, how long each treatment lasted, and\n      the start and end time of the entire treatment; can include multiple fertilizer\n      regimens\n    title: fertilizer regimen\n    examples:\n    - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - fertilizer regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000556\n    alias: fertilizer_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  field:\n    name: field\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of the hydrocarbon field (e.g. Albacora)\n    title: field name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - field name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000291\n    alias: field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  filter_type:\n    name: filter_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: A device which removes solid particulates or airborne molecular contaminants\n    title: filter type\n    examples:\n    - value: HEPA\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - filter type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000765\n    alias: filter_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: filter_type_enum\n    multivalued: true\n  fire:\n    name: fire\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    description: Historical and/or physical evidence of fire\n    title: history/fire\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    comments:\n    - Provide the date the fire occurred. If extended burning occurred provide the\n      date range.\n    examples:\n    - value: '1871-10-10'\n    - value: 1871-10-01 to 1871-10-31\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/fire\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001086\n    alias: fire\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n    pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n  fireplace_type:\n    name: fireplace_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A firebox with chimney\n    title: fireplace type\n    examples:\n    - value: wood burning\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - fireplace type\n    rank: 1000\n    is_a: core field\n    string_serialization: '[gas burning|wood burning]'\n    slot_uri: MIXS:0000802\n    alias: fireplace_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  flooding:\n    name: flooding\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: date string\n    description: Historical and/or physical evidence of flooding\n    title: history/flooding\n    todos:\n    - is \"to\" acceptable? Is there a better way to request that be written?\n    - What about if the \"day\" isn't known? Is this ok?\n    comments:\n    - Provide the date the flood occurred. If extended flooding occurred provide the\n      date range.\n    examples:\n    - value: '1927-04-15'\n    - value: 1927-04 to 1927-05\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/flooding\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000319\n    alias: flooding\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  floor_age:\n    name: floor_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: years, weeks, days\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The time period since installment of the carpet or flooring\n    title: floor age\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000164\n    alias: floor_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  floor_area:\n    name: floor_area\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The area of the floor space within the room\n    title: floor area\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor area\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000165\n    alias: floor_area\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  floor_cond:\n    name: floor_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the floor at the time of sampling; photos\n      or video preferred; use drawings to indicate location of damaged areas\n    title: floor condition\n    examples:\n    - value: new\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000803\n    alias: floor_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: floor_cond_enum\n    multivalued: false\n  floor_count:\n    name: floor_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of floors in the building, including basements and mechanical\n      penthouse\n    title: floor count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000225\n    alias: floor_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  floor_finish_mat:\n    name: floor_finish_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The floor covering type; the finished surface that is walked on\n    title: floor finish material\n    examples:\n    - value: carpet\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor finish material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000804\n    alias: floor_finish_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: floor_finish_mat_enum\n    multivalued: false\n  floor_struc:\n    name: floor_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Refers to the structural elements and subfloor upon which the finish\n      flooring is installed\n    title: floor structure\n    examples:\n    - value: concrete\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor structure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000806\n    alias: floor_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: floor_struc_enum\n    multivalued: false\n  floor_thermal_mass:\n    name: floor_thermal_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: joule per degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The ability of the floor to provide inertia against temperature fluctuations\n    title: floor thermal mass\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor thermal mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000166\n    alias: floor_thermal_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  floor_water_mold:\n    name: floor_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew in a room\n    title: floor signs of water/mold\n    examples:\n    - value: ceiling discoloration\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - floor signs of water/mold\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000805\n    alias: floor_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: floor_water_mold_enum\n    multivalued: false\n  fluor:\n    name: fluor\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram chlorophyll a per cubic meter, volts\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Raw or converted fluorescence of water\n    title: fluorescence\n    examples:\n    - value: 2.5 volts\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - fluorescence\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000704\n    alias: fluor\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  freq_clean:\n    name: freq_clean\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration or {text}\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of times the sample location is cleaned. Frequency of\n      cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\n    title: frequency of cleaning\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - frequency of cleaning\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000226\n    alias: freq_clean\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  freq_cook:\n    name: freq_cook\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of times a meal is cooked per week\n    title: frequency of cooking\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - frequency of cooking\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000227\n    alias: freq_cook\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  fungicide_regm:\n    name: fungicide_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: fungicide name;fungicide amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of fungicides; should include\n      the name of fungicide, amount administered, treatment regimen including how\n      many times the treatment was repeated, how long each treatment lasted, and the\n      start and end time of the entire treatment; can include multiple fungicide regimens\n    title: fungicide regimen\n    examples:\n    - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - fungicide regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000557\n    alias: fungicide_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  furniture:\n    name: furniture\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The types of furniture present in the sampled room\n    title: furniture\n    examples:\n    - value: chair\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - furniture\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000807\n    alias: furniture\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: furniture_enum\n    multivalued: false\n  gaseous_environment:\n    name: gaseous_environment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gaseous compound name;gaseous compound amount;treatment interval and\n          duration\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Use of conditions with differing gaseous environments; should include\n      the name of gaseous compound, amount administered, treatment duration, interval\n      and total experimental duration; can include multiple gaseous environment regimens\n    title: gaseous environment\n    todos:\n    - would like to see usage examples for this slot. Requiring micromole/L seems\n      too limiting and doesn't match expected_value value\n    - did I do this right? keep the example that's provided and add another? so as\n      to not override\n    examples:\n    - value: CO2; 500ppm above ambient; constant\n    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gaseous environment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000558\n    alias: gaseous_environment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  gaseous_substances:\n    name: gaseous_substances\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gaseous substance name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Amount or concentration of substances such as hydrogen sulfide, carbon\n      dioxide, methane, etc.; can include multiple substances\n    title: gaseous substances\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gaseous substances\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000661\n    alias: gaseous_substances\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  gender_restroom:\n    name: gender_restroom\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The gender type of the restroom\n    title: gender of restroom\n    examples:\n    - value: male\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gender of restroom\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000808\n    alias: gender_restroom\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: gender_restroom_enum\n    multivalued: false\n  genetic_mod:\n    name: genetic_mod\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url or free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Genetic modifications of the genome of an organism, which may occur\n      naturally by spontaneous mutation, or be introduced by some experimental means,\n      e.g. specification of a transgene or the gene knocked-out or details of transient\n      transfection\n    title: genetic modification\n    examples:\n    - value: aox1A transgenic\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - genetic modification\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0000859\n    alias: genetic_mod\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  geo_loc_name:\n    name: geo_loc_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n          name'\n    description: The geographical origin of the sample as defined by the country or\n      sea name followed by specific region name. Country or sea names should be chosen\n      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n      (http://purl.bioontology.org/ontology/GAZ)\n    title: geographic location (country and/or sea,region)\n    examples:\n    - value: 'USA: Maryland, Bethesda'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - geographic location (country and/or sea,region)\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{term}: {term}, {text}'\n    slot_uri: MIXS:0000010\n    alias: geo_loc_name\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  glucosidase_act:\n    name: glucosidase_act\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mol per liter per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of glucosidase activity\n    title: glucosidase activity\n    examples:\n    - value: 5 mol per liter per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - glucosidase activity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000137\n    alias: glucosidase_act\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  gravidity:\n    name: gravidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gravidity status;timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Whether or not subject is gravid, and if yes date due or date post-conception,\n      specifying which is used\n    title: gravidity\n    examples:\n    - value: yes;due date:2018-05-11\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gravidity\n    rank: 1000\n    is_a: core field\n    string_serialization: '{boolean};{timestamp}'\n    slot_uri: MIXS:0000875\n    alias: gravidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  gravity:\n    name: gravity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gravity factor value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: meter per square second, g\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of gravity factor to study\n      various types of responses in presence, absence or modified levels of gravity;\n      treatment regimen including how many times the treatment was repeated, how long\n      each treatment lasted, and the start and end time of the entire treatment; can\n      include multiple treatments\n    title: gravity\n    examples:\n    - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - gravity\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000559\n    alias: gravity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  growth_facil:\n    name: growth_facil\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text or CO\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n      growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n      use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\n    title: growth facility\n    examples:\n    - value: Growth chamber [CO_715:0000189]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - growth facility\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}|{termLabel} {[termID]}'\n    slot_uri: MIXS:0001043\n    alias: growth_facil\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  growth_habit:\n    name: growth_habit\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Characteristic shape, appearance or growth form of a plant species\n    title: growth habit\n    examples:\n    - value: spreading\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - growth habit\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001044\n    alias: growth_habit\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: growth_habit_enum\n    multivalued: false\n  growth_hormone_regm:\n    name: growth_hormone_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: growth hormone name;growth hormone amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of growth hormones; should\n      include the name of growth hormone, amount administered, treatment regimen including\n      how many times the treatment was repeated, how long each treatment lasted, and\n      the start and end time of the entire treatment; can include multiple growth\n      hormone regimens\n    title: growth hormone regimen\n    examples:\n    - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - growth hormone regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000560\n    alias: growth_hormone_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  hall_count:\n    name: hall_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The total count of hallways and cooridors in the built structure\n    title: hallway/corridor count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hallway/corridor count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000228\n    alias: hall_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  handidness:\n    name: handidness\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The handidness of the individual sampled\n    title: handidness\n    examples:\n    - value: right handedness\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - handidness\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000809\n    alias: handidness\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: handidness_enum\n    multivalued: false\n  hc_produced:\n    name: hc_produced\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n      etc). If \"other\" is specified, please propose entry in \"additional info\" field\n    title: hydrocarbon type produced\n    examples:\n    - value: Gas\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon type produced\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000989\n    alias: hc_produced\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: hc_produced_enum\n    multivalued: false\n  hcr:\n    name: hcr\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR\n      defined as a natural environmental feature containing large amounts of hydrocarbons\n      at high concentrations potentially suitable for commercial exploitation. This\n      term should not be confused with the Hydrocarbon Occurrence term which also\n      includes hydrocarbon-rich environments with currently limited commercial interest\n      such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose\n      entry in \"additional info\" field\n    title: hydrocarbon resource type\n    examples:\n    - value: Oil Sand\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon resource type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000988\n    alias: hcr\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: hcr_enum\n    multivalued: false\n  hcr_fw_salinity:\n    name: hcr_fw_salinity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original formation water salinity (prior to secondary recovery e.g.\n      Waterflooding) expressed as TDS\n    title: formation water salinity\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - formation water salinity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000406\n    alias: hcr_fw_salinity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  hcr_geol_age:\n    name: hcr_geol_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n      If \"other\" is specified, please propose entry in \"additional info\" field'\n    title: hydrocarbon resource geological age\n    examples:\n    - value: Silurian\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon resource geological age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000993\n    alias: hcr_geol_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: hcr_geol_age_enum\n    multivalued: false\n  hcr_pressure:\n    name: hcr_pressure\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: atmosphere, kilopascal\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original pressure of the hydrocarbon resource\n    title: hydrocarbon resource original pressure\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon resource original pressure\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} - {float} {unit}'\n    slot_uri: MIXS:0000395\n    alias: hcr_pressure\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  hcr_temp:\n    name: hcr_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original temperature of the hydrocarbon resource\n    title: hydrocarbon resource original temperature\n    examples:\n    - value: 150-295 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - hydrocarbon resource original temperature\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} - {float} {unit}'\n    slot_uri: MIXS:0000393\n    alias: hcr_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  heat_cool_type:\n    name: heat_cool_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Methods of conditioning or heating a room or building\n    title: heating and cooling system type\n    examples:\n    - value: heat pump\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - heating and cooling system type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000766\n    alias: heat_cool_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: heat_cool_type_enum\n    multivalued: true\n  heat_deliv_loc:\n    name: heat_deliv_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The location of heat delivery within the room\n    title: heating delivery locations\n    examples:\n    - value: north\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - heating delivery locations\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000810\n    alias: heat_deliv_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: heat_deliv_loc_enum\n    multivalued: false\n  heat_sys_deliv_meth:\n    name: heat_sys_deliv_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The method by which the heat is delivered through the system\n    title: heating system delivery method\n    examples:\n    - value: radiant\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - heating system delivery method\n    rank: 1000\n    is_a: core field\n    string_serialization: '[conductive|radiant]'\n    slot_uri: MIXS:0000812\n    alias: heat_sys_deliv_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  heat_system_id:\n    name: heat_system_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: unique identifier\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The heating system identifier\n    title: heating system identifier\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - heating system identifier\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000833\n    alias: heat_system_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  heavy_metals:\n    name: heavy_metals\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: heavy metal name;measurement value unit\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per gram\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Heavy metals present in the sample and their concentrations.\n    title: heavy metals/ extreme unusual properties\n    todos:\n    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n      validate?\n    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n      I would argue this isn't an extreme unusual property. It's just a biogeochemical\n      measurement.\n    comments:\n    - For multiple heavy metals and concentrations, separate by ;\n    examples:\n    - value: mercury 0.09 micrograms per gram\n    - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - extreme_unusual_properties/heavy metals\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000652\n    alias: heavy_metals\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  heavy_metals_meth:\n    name: heavy_metals_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining heavy metals\n    title: heavy metals method/ extreme unusual properties\n    comments:\n    - Required when heavy metals are provided\n    - If different methods are used for multiple metals, indicate the metal and method.\n      Separate metals by ;\n    examples:\n    - value: https://doi.org/10.3390/ijms9040434\n    - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - extreme_unusual_properties/heavy metals method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000343\n    alias: heavy_metals_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  height_carper_fiber:\n    name: height_carper_fiber\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: centimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average carpet fiber height in the indoor environment\n    title: height carpet fiber mat\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - height carpet fiber mat\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000167\n    alias: height_carper_fiber\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  herbicide_regm:\n    name: herbicide_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: herbicide name;herbicide amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of herbicides; information\n      about treatment involving use of growth hormones; should include the name of\n      herbicide, amount administered, treatment regimen including how many times the\n      treatment was repeated, how long each treatment lasted, and the start and end\n      time of the entire treatment; can include multiple regimens\n    title: herbicide regimen\n    examples:\n    - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - herbicide regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000561\n    alias: herbicide_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  horizon_meth:\n    name: horizon_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining the horizon\n    title: soil horizon method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil horizon method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000321\n    alias: horizon_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_age:\n    name: host_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: year, day, hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Age of host at the time of sampling; relevant scale depends on species\n      and study, e.g. Could be seconds for amoebae or centuries for trees\n    title: host age\n    examples:\n    - value: 10 days\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000255\n    alias: host_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_body_habitat:\n    name: host_body_habitat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original body habitat where the sample was obtained from\n    title: host body habitat\n    examples:\n    - value: nasopharynx\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host body habitat\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000866\n    alias: host_body_habitat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_body_product:\n    name: host_body_product\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: FMA or UBERON\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Substance produced by the body, e.g. Stool, mucus, where the sample\n      was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n      ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma\n      or https://www.ebi.ac.uk/ols/ontologies/uberon\n    title: host body product\n    examples:\n    - value: Portion of mucus [fma66938]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host body product\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000888\n    alias: host_body_product\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  host_body_site:\n    name: host_body_site\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: FMA or UBERON\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of body site where the sample was obtained from, such as a specific\n      organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n      (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n      please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\n    title: host body site\n    examples:\n    - value: gill [UBERON:0002535]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host body site\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000867\n    alias: host_body_site\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  host_body_temp:\n    name: host_body_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Core body temperature of the host when sample was collected\n    title: host body temperature\n    examples:\n    - value: 15 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host body temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000274\n    alias: host_body_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_color:\n    name: host_color\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: color\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The color of host\n    title: host color\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host color\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000260\n    alias: host_color\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_common_name:\n    name: host_common_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: common name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Common name of the host.\n    title: host common name\n    examples:\n    - value: human\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host common name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000248\n    alias: host_common_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_diet:\n    name: host_diet\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: diet type\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Type of diet depending on the host, for animals omnivore, herbivore\n      etc., for humans high-fat, meditteranean etc.; can include multiple diet types\n    title: host diet\n    examples:\n    - value: herbivore\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host diet\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000869\n    alias: host_diet\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  host_dry_mass:\n    name: host_dry_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilogram, gram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of dry mass\n    title: host dry mass\n    examples:\n    - value: 500 gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host dry mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000257\n    alias: host_dry_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_family_relation:\n    name: host_family_relation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: relationship type;arbitrary identifier\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Familial relationships to other hosts in the same study; can include\n      multiple relationships\n    title: host family relationship\n    examples:\n    - value: offspring;Mussel25\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host family relationship\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{text}'\n    slot_uri: MIXS:0000872\n    alias: host_family_relation\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  host_genotype:\n    name: host_genotype\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: genotype\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Observed genotype\n    title: host genotype\n    examples:\n    - value: C57BL/6\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host genotype\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000365\n    alias: host_genotype\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_growth_cond:\n    name: host_growth_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url or free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Literature reference giving growth conditions of the host\n    title: host growth conditions\n    examples:\n    - value: https://academic.oup.com/icesjms/article/68/2/349/617247\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host growth conditions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0000871\n    alias: host_growth_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_height:\n    name: host_height\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: centimeter, millimeter, meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The height of subject\n    title: host height\n    examples:\n    - value: 0.1 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host height\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000264\n    alias: host_height\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_last_meal:\n    name: host_last_meal\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: content;duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Content of last meal and time since feeding; can include multiple\n      values\n    title: host last meal\n    examples:\n    - value: corn feed;P2H\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host last meal\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{duration}'\n    slot_uri: MIXS:0000870\n    alias: host_last_meal\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  host_length:\n    name: host_length\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: centimeter, millimeter, meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The length of subject\n    title: host length\n    examples:\n    - value: 1 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host length\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000256\n    alias: host_length\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_life_stage:\n    name: host_life_stage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: stage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Description of life stage of host\n    title: host life stage\n    examples:\n    - value: adult\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host life stage\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000251\n    alias: host_life_stage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_phenotype:\n    name: host_phenotype\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PATO or HP\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Phenotype of human or other host. For phenotypic quality ontology\n      (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.\n      For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\n    title: host phenotype\n    examples:\n    - value: elongated [PATO:0001154]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host phenotype\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000874\n    alias: host_phenotype\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  host_sex:\n    name: host_sex\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Gender or physical sex of the host.\n    title: host sex\n    examples:\n    - value: non-binary\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host sex\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000811\n    alias: host_sex\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: host_sex_enum\n    multivalued: false\n  host_shape:\n    name: host_shape\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: shape\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Morphological shape of host\n    title: host shape\n    examples:\n    - value: round\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host shape\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000261\n    alias: host_shape\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_subject_id:\n    name: host_subject_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: unique identifier\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A unique identifier by which each subject can be referred to, de-identified.\n    title: host subject id\n    examples:\n    - value: MPI123\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host subject id\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000861\n    alias: host_subject_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_subspecf_genlin:\n    name: host_subspecf_genlin\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n          e.g. serovar, biotype, ecotype, variety, cultivar.\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about the genetic distinctness of the host organism below\n      the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n      or any relevant genetic typing schemes like Group I plasmid. Subspecies should\n      not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage\n      name and the lineage rank separated by a colon, e.g., biovar:abc123.\n    title: host subspecific genetic lineage\n    examples:\n    - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host subspecific genetic lineage\n    rank: 1000\n    is_a: core field\n    string_serialization: '{rank name}:{text}'\n    slot_uri: MIXS:0001318\n    alias: host_subspecf_genlin\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  host_substrate:\n    name: host_substrate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: substrate name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The growth substrate of the host.\n    title: host substrate\n    examples:\n    - value: rock\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host substrate\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000252\n    alias: host_substrate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  host_symbiont:\n    name: host_symbiont\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: species name or common name\n      occurrence:\n        tag: occurrence\n        value: m\n    description: The taxonomic name of the organism(s) found living in mutualistic,\n      commensalistic, or parasitic symbiosis with the specific host.\n    title: observed host symbionts\n    examples:\n    - value: flukeworms\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - observed host symbionts\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001298\n    alias: host_symbiont\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  host_tot_mass:\n    name: host_tot_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilogram, gram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total mass of the host at collection, the unit depends on host\n    title: host total mass\n    examples:\n    - value: 2500 gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host total mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000263\n    alias: host_tot_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  host_wet_mass:\n    name: host_wet_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilogram, gram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of wet mass\n    title: host wet mass\n    examples:\n    - value: 1500 gram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - host wet mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000567\n    alias: host_wet_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  humidity:\n    name: humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per cubic meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Amount of water vapour in the air, at the time of sampling\n    title: humidity\n    examples:\n    - value: 25 gram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000100\n    alias: humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  humidity_regm:\n    name: humidity_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: humidity value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per cubic meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to varying degree\n      of humidity; information about treatment involving use of growth hormones; should\n      include amount of humidity administered, treatment regimen including how many\n      times the treatment was repeated, how long each treatment lasted, and the start\n      and end time of the entire treatment; can include multiple regimens\n    title: humidity regimen\n    examples:\n    - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - humidity regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000568\n    alias: humidity_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  indoor_space:\n    name: indoor_space\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A distinguishable space within a structure, the purpose for which\n      discrete areas of a building is used\n    title: indoor space\n    examples:\n    - value: foyer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - indoor space\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000763\n    alias: indoor_space\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: indoor_space_enum\n    multivalued: false\n  indoor_surf:\n    name: indoor_surf\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Type of indoor surface\n    title: indoor surface\n    examples:\n    - value: wall\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - indoor surface\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000764\n    alias: indoor_surf\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: indoor_surf_enum\n    multivalued: false\n  indust_eff_percent:\n    name: indust_eff_percent\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Percentage of industrial effluents received by wastewater treatment\n      plant\n    title: industrial effluent percent\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - industrial effluent percent\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000662\n    alias: indust_eff_percent\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  inorg_particles:\n    name: inorg_particles\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: inorganic particle name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of particles such as sand, grit, metal particles, ceramics,\n      etc.; can include multiple particles\n    title: inorganic particles\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - inorganic particles\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000664\n    alias: inorg_particles\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  inside_lux:\n    name: inside_lux\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilowatt per square metre\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The recorded value at sampling time (power density)\n    title: inside lux light\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - inside lux light\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000168\n    alias: inside_lux\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  int_wall_cond:\n    name: int_wall_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the wall at the time of sampling; photos\n      or video preferred; use drawings to indicate location of damaged areas\n    title: interior wall condition\n    examples:\n    - value: damaged\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - interior wall condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000813\n    alias: int_wall_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: int_wall_cond_enum\n    multivalued: false\n  investigation field:\n    name: investigation field\n    description: field describing aspect of the investigation/study to which the sample\n      belongs\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: investigation_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  iw_bt_date_well:\n    name: iw_bt_date_well\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Injection water breakthrough date per well following a secondary\n      and/or tertiary recovery\n    title: injection water breakthrough date of specific well\n    examples:\n    - value: '2018-05-11'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - injection water breakthrough date of specific well\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001010\n    alias: iw_bt_date_well\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  iwf:\n    name: iwf\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Proportion of the produced fluids derived from injected water at\n      the time of sampling. (e.g. 87%)\n    title: injection water fraction\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - injection water fraction\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000455\n    alias: iwf\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  last_clean:\n    name: last_clean\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The last time the floor was cleaned (swept, mopped, vacuumed)\n    title: last time swept/mopped/vacuumed\n    examples:\n    - value: 2018-05-11:T14:30Z\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - last time swept/mopped/vacuumed\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000814\n    alias: last_clean\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  lat_lon:\n    name: lat_lon\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: decimal degrees,  limit to 8 decimal points\n    description: The geographical origin of the sample as defined by latitude and\n      longitude. The values should be reported in decimal degrees and in WGS84 system\n    title: geographic location (latitude and longitude)\n    notes:\n    - This is currently a required field but it's not clear if this should be required\n      for human hosts\n    examples:\n    - value: 50.586825 6.408977\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - geographic location (latitude and longitude)\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{float} {float}'\n    slot_uri: MIXS:0000009\n    alias: lat_lon\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: GeolocationValue\n    multivalued: false\n  lbc_thirty:\n    name: lbc_thirty\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: ppm CaCO3/pH\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: lime buffer capacity, determined after 30 minute incubation\n    title: lime buffer capacity (at 30 minutes)\n    comments:\n    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n      one pH unit\n    examples:\n    - value: 543 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\n    aliases:\n    - lbc_thirty\n    - lbc30\n    - lime buffer capacity (at 30 minutes)\n    rank: 1000\n    alias: lbc_thirty\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  lbceq:\n    name: lbceq\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: ppm CaCO3/pH\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: lime buffer capacity, determined at equilibrium after 5 day incubation\n    title: lime buffer capacity (after 5 day incubation)\n    comments:\n    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n      one pH unit\n    examples:\n    - value: 1575 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - lbceq\n    - lime buffer capacity (at 5-day equilibrium)\n    rank: 1000\n    alias: lbceq\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  light_intensity:\n    name: light_intensity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: lux\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of light intensity\n    title: light intensity\n    examples:\n    - value: 0.3 lux\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - light intensity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000706\n    alias: light_intensity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  light_regm:\n    name: light_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: exposure type;light intensity;light quality\n      preferred_unit:\n        tag: preferred_unit\n        value: lux; micrometer, nanometer, angstrom\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information about treatment(s) involving exposure to light, including\n      both light intensity and quality.\n    title: light regimen\n    examples:\n    - value: incandescant light;10 lux;450 nanometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - light regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{float} {unit}'\n    slot_uri: MIXS:0000569\n    alias: light_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  light_type:\n    name: light_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Application of light to achieve some practical or aesthetic effect.\n      Lighting includes the use of both artificial light sources such as lamps and\n      light fixtures, as well as natural illumination by capturing daylight. Can also\n      include absence of light\n    title: light type\n    examples:\n    - value: desk lamp\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - light type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000769\n    alias: light_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: light_type_enum\n    multivalued: true\n  link_addit_analys:\n    name: link_addit_analys\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Link to additional analysis results performed on the sample\n    title: links to additional analysis\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - links to additional analysis\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000340\n    alias: link_addit_analys\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  link_class_info:\n    name: link_class_info\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Link to digitized soil maps or other soil classification information\n    title: link to classification information\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - link to classification information\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000329\n    alias: link_class_info\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  link_climate_info:\n    name: link_climate_info\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Link to climate resource\n    title: link to climate information\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - link to climate information\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000328\n    alias: link_climate_info\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  lithology:\n    name: lithology\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n      If \"other\" is specified, please propose entry in \"additional info\" field'\n    title: lithology\n    examples:\n    - value: Volcanic\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - lithology\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000990\n    alias: lithology\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: lithology_enum\n    multivalued: false\n  local_class:\n    name: local_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: local classification name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Soil classification based on local soil classification system\n    title: soil_taxonomic/local classification\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil_taxonomic/local classification\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000330\n    alias: local_class\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  local_class_meth:\n    name: local_class_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining the local soil classification\n    title: soil_taxonomic/local classification method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil_taxonomic/local classification method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000331\n    alias: local_class_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  magnesium:\n    name: magnesium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per liter, milligram per liter, parts per million, micromole per\n          kilogram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of magnesium in the sample\n    title: magnesium\n    examples:\n    - value: 52.8 micromole per kilogram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - magnesium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000431\n    alias: magnesium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  manganese:\n    name: manganese\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg (ppm)\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of manganese in the sample\n    title: manganese\n    examples:\n    - value: 24.7 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - manganese\n    rank: 1000\n    alias: manganese\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  max_occup:\n    name: max_occup\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The maximum amount of people allowed in the indoor environment\n    title: maximum occupancy\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - maximum occupancy\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000229\n    alias: max_occup\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  mean_frict_vel:\n    name: mean_frict_vel\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter per second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of mean friction velocity\n    title: mean friction velocity\n    examples:\n    - value: 0.5 meter per second\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean friction velocity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000498\n    alias: mean_frict_vel\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  mean_peak_frict_vel:\n    name: mean_peak_frict_vel\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter per second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of mean peak friction velocity\n    title: mean peak friction velocity\n    examples:\n    - value: 1 meter per second\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean peak friction velocity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000502\n    alias: mean_peak_frict_vel\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  mech_struc:\n    name: mech_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'mechanical structure: a moving structure'\n    title: mechanical structure\n    examples:\n    - value: elevator\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mechanical structure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000815\n    alias: mech_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: mech_struc_enum\n    multivalued: false\n  mechanical_damage:\n    name: mechanical_damage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: damage type;body site\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about any mechanical damage exerted on the plant; can\n      include multiple damages and sites\n    title: mechanical damage\n    examples:\n    - value: pruning;bark\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mechanical damage\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{text}'\n    slot_uri: MIXS:0001052\n    alias: mechanical_damage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  methane:\n    name: methane\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, parts per billion, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Methane (gas) amount or concentration at the time of sampling\n    title: methane\n    examples:\n    - value: 1800 parts per billion\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - methane\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000101\n    alias: methane\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  micro_biomass_meth:\n    name: micro_biomass_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining microbial biomass\n    title: microbial biomass method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - microbial biomass method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000339\n    alias: micro_biomass_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  microbial_biomass:\n    name: microbial_biomass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: ton, kilogram, gram per kilogram soil\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The part of the organic matter in the soil that constitutes living\n      microorganisms smaller than 5-10 micrometer. If you keep this, you would need\n      to have correction factors used for conversion to the final units\n    title: microbial biomass\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - microbial biomass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000650\n    alias: microbial_biomass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  mineral_nutr_regm:\n    name: mineral_nutr_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: mineral nutrient name;mineral nutrient amount;treatment interval and\n          duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving the use of mineral supplements;\n      should include the name of mineral nutrient, amount administered, treatment\n      regimen including how many times the treatment was repeated, how long each treatment\n      lasted, and the start and end time of the entire treatment; can include multiple\n      mineral nutrient regimens\n    title: mineral nutrient regimen\n    examples:\n    - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mineral nutrient regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000570\n    alias: mineral_nutr_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  misc_param:\n    name: misc_param\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: parameter name;measurement value\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Any other measurement performed or parameter collected, that is not\n      listed here\n    title: miscellaneous parameter\n    examples:\n    - value: Bicarbonate ion concentration;2075 micromole per kilogram\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - miscellaneous parameter\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000752\n    alias: misc_param\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  n_alkanes:\n    name: n_alkanes\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: n-alkane name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of n-alkanes; can include multiple n-alkanes\n    title: n-alkanes\n    examples:\n    - value: n-hexadecane;100 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - n-alkanes\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000503\n    alias: n_alkanes\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  nitrate:\n    name: nitrate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrate in the sample\n    title: nitrate\n    examples:\n    - value: 65 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - nitrate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000425\n    alias: nitrate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  nitrate_nitrogen:\n    name: nitrate_nitrogen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrate nitrogen in the sample\n    title: nitrate_nitrogen\n    comments:\n    - often below some specified limit of detection\n    examples:\n    - value: 0.29 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - nitrate_nitrogen\n    - NO3-N\n    rank: 1000\n    alias: nitrate_nitrogen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  nitrite:\n    name: nitrite\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrite in the sample\n    title: nitrite\n    examples:\n    - value: 0.5 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - nitrite\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000426\n    alias: nitrite\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  nitrite_nitrogen:\n    name: nitrite_nitrogen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrite nitrogen in the sample\n    title: nitrite_nitrogen\n    examples:\n    - value: 1.2 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - nitrite_nitrogen\n    - NO2-N\n    rank: 1000\n    alias: nitrite_nitrogen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  nitro:\n    name: nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of nitrogen (total)\n    title: nitrogen\n    examples:\n    - value: 4.2 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000504\n    alias: nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  non_min_nutr_regm:\n    name: non_min_nutr_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n          and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving the exposure of plant to non-mineral\n      nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n      nutrient, amount administered, treatment regimen including how many times the\n      treatment was repeated, how long each treatment lasted, and the start and end\n      time of the entire treatment; can include multiple non-mineral nutrient regimens\n    title: non-mineral nutrient regimen\n    examples:\n    - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - non-mineral nutrient regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000571\n    alias: non_min_nutr_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  nucleic acid sequence source field:\n    name: nucleic acid sequence source field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: nucleic_acid_sequence_source_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  number_pets:\n    name: number_pets\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of pets residing in the sampled space\n    title: number of pets\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - number of pets\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000231\n    alias: number_pets\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  number_plants:\n    name: number_plants\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of plant(s) in the sampling space\n    title: number of houseplants\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - number of houseplants\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000230\n    alias: number_plants\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  number_resident:\n    name: number_resident\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of individuals currently occupying in the sampling location\n    title: number of residents\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - number of residents\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000232\n    alias: number_resident\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  occup_density_samp:\n    name: occup_density_samp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Average number of occupants at time of sampling per square footage\n    title: occupant density at sampling\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - occupant density at sampling\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000217\n    alias: occup_density_samp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  occup_document:\n    name: occup_document\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of documentation of occupancy\n    title: occupancy documentation\n    examples:\n    - value: estimate\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - occupancy documentation\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000816\n    alias: occup_document\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: occup_document_enum\n    multivalued: false\n  occup_samp:\n    name: occup_samp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Number of occupants present at time of sample within the given space\n    title: occupancy at sampling\n    examples:\n    - value: '10'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - occupancy at sampling\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000772\n    alias: occup_samp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  org_carb:\n    name: org_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of organic carbon\n    title: organic carbon\n    examples:\n    - value: 1.5 microgram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000508\n    alias: org_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  org_count_qpcr_info:\n    name: org_count_qpcr_info\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n          denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n          elongation:degrees_minutes; total cycles\n      preferred_unit:\n        tag: preferred_unit\n        value: number of cells per gram (or ml or cm^2)\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'If qpcr was used for the cell count, the target gene name, the primer\n      sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n      FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n      annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n      30 cycles)'\n    title: organism count qPCR information\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organism count qPCR information\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n      elongation:degrees_minutes; total cycles'\n    slot_uri: MIXS:0000099\n    alias: org_count_qpcr_info\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  org_matter:\n    name: org_matter\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of organic matter\n    title: organic matter\n    examples:\n    - value: 1.75 milligram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organic matter\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000204\n    alias: org_matter\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  org_nitro:\n    name: org_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of organic nitrogen\n    title: organic nitrogen\n    examples:\n    - value: 4 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000205\n    alias: org_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  org_particles:\n    name: org_particles\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: particle name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of particles such as faeces, hairs, food, vomit, paper\n      fibers, plant material, humus, etc.\n    title: organic particles\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organic particles\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000665\n    alias: org_particles\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  organism_count:\n    name: organism_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: organism name;measurement value;enumeration\n      preferred_unit:\n        tag: preferred_unit\n        value: number of cells per cubic meter, number of cells per milliliter, number\n          of cells per cubic centimeter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: 'Total cell count of any organism (or group of organisms) per gram,\n      volume or area of sample, should include name of organism followed by count.\n      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should\n      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\n    title: organism count\n    examples:\n    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - organism count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000103\n    alias: organism_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  owc_tvdss:\n    name: owc_tvdss\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\n    title: oil water contact depth\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - oil water contact depth\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000405\n    alias: owc_tvdss\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  oxy_stat_samp:\n    name: oxy_stat_samp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Oxygenation status of sample\n    title: oxygenation status of sample\n    examples:\n    - value: aerobic\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - oxygenation status of sample\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000753\n    alias: oxy_stat_samp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: oxy_stat_samp_enum\n    multivalued: false\n  oxygen:\n    name: oxygen\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Oxygen (gas) amount or concentration at the time of sampling\n    title: oxygen\n    examples:\n    - value: 600 parts per million\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - oxygen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000104\n    alias: oxygen\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  part_org_carb:\n    name: part_org_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of particulate organic carbon\n    title: particulate organic carbon\n    examples:\n    - value: 1.92 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - particulate organic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000515\n    alias: part_org_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  part_org_nitro:\n    name: part_org_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of particulate organic nitrogen\n    title: particulate organic nitrogen\n    examples:\n    - value: 0.3 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - particulate organic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000719\n    alias: part_org_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  particle_class:\n    name: particle_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: particle name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micrometer\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Particles are classified, based on their size, into six general categories:clay,\n      silt, sand, gravel, cobbles, and boulders; should include amount of particle\n      preceded by the name of the particle type; can include multiple values\n    title: particle classification\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - particle classification\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000206\n    alias: particle_class\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  permeability:\n    name: permeability\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: mD\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Measure of the ability of a hydrocarbon resource to allow fluids\n      to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\n    title: permeability\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - permeability\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} - {integer} {unit}'\n    slot_uri: MIXS:0000404\n    alias: permeability\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  perturbation:\n    name: perturbation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: perturbation type name;perturbation interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Type of perturbation, e.g. chemical administration, physical disturbance,\n      etc., coupled with perturbation regimen including how many times the perturbation\n      was repeated, how long each perturbation lasted, and the start and end time\n      of the entire perturbation period; can include multiple perturbation types\n    title: perturbation\n    examples:\n    - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - perturbation\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000754\n    alias: perturbation\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  pesticide_regm:\n    name: pesticide_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: pesticide name;pesticide amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of insecticides; should\n      include the name of pesticide, amount administered, treatment regimen including\n      how many times the treatment was repeated, how long each treatment lasted, and\n      the start and end time of the entire treatment; can include multiple pesticide\n      regimens\n    title: pesticide regimen\n    examples:\n    - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pesticide regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000573\n    alias: pesticide_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  petroleum_hydrocarb:\n    name: petroleum_hydrocarb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of petroleum hydrocarbon\n    title: petroleum hydrocarbon\n    examples:\n    - value: 0.05 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - petroleum hydrocarbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000516\n    alias: petroleum_hydrocarb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ph:\n    name: ph\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Ph measurement of the sample, or liquid portion of sample, or aqueous\n      phase of the fluid\n    title: pH\n    examples:\n    - value: '7.2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pH\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001001\n    alias: ph\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: double\n    multivalued: false\n  ph_meth:\n    name: ph_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining ph\n    title: pH method\n    comments:\n    - This can include a link to the instrument used or a citation for the method.\n    examples:\n    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n    - value: https://doi.org/10.2136/sssabookser5.3.c16\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pH method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0001106\n    alias: ph_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  ph_regm:\n    name: ph_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;treatment interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving exposure of plants to varying\n      levels of ph of the growth media, treatment regimen including how many times\n      the treatment was repeated, how long each treatment lasted, and the start and\n      end time of the entire treatment; can include multiple regimen\n    title: pH regimen\n    examples:\n    - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pH regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0001056\n    alias: ph_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  phaeopigments:\n    name: phaeopigments\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: phaeopigment name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of phaeopigments; can include multiple phaeopigments\n    title: phaeopigments\n    examples:\n    - value: 2.5 milligram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - phaeopigments\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000180\n    alias: phaeopigments\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  phosphate:\n    name: phosphate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of phosphate\n    title: phosphate\n    examples:\n    - value: 0.7 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - phosphate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000505\n    alias: phosphate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  phosplipid_fatt_acid:\n    name: phosplipid_fatt_acid\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: phospholipid fatty acid name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mole per gram, mole per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of phospholipid fatty acids; can include multiple values\n    title: phospholipid fatty acid\n    examples:\n    - value: 2.98 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - phospholipid fatty acid\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000181\n    alias: phosplipid_fatt_acid\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  photon_flux:\n    name: photon_flux\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: number of photons per second per unit area\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of photon flux\n    title: photon flux\n    examples:\n    - value: 3.926 micromole photons per second per square meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - photon flux\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000725\n    alias: photon_flux\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  plant_growth_med:\n    name: plant_growth_med\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: EO or enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Specification of the media for growing the plants or tissue cultured\n      samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in\n      vitro liquid culture medium. Recommended value is a specific value from EO:plant\n      growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)\n      or other controlled vocabulary\n    title: plant growth medium\n    examples:\n    - value: hydroponic plant culture media [EO:0007067]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - plant growth medium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001057\n    alias: plant_growth_med\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  plant_product:\n    name: plant_product\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: product name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Substance produced by the plant, where the sample was obtained from\n    title: plant product\n    examples:\n    - value: xylem sap [PO:0025539]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - plant product\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001058\n    alias: plant_product\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  plant_sex:\n    name: plant_sex\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sex of the reproductive parts on the whole plant, e.g. pistillate,\n      staminate, monoecieous, hermaphrodite.\n    title: plant sex\n    examples:\n    - value: Hermaphroditic\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - plant sex\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001059\n    alias: plant_sex\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: plant_sex_enum\n    multivalued: false\n  plant_struc:\n    name: plant_struc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PO\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of plant structure the sample was obtained from; for Plant Ontology\n      (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n      e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the\n      sex of it can be recorded here.\n    title: plant structure\n    examples:\n    - value: epidermis [PO:0005679]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - plant structure\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0001060\n    alias: plant_struc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  pollutants:\n    name: pollutants\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: pollutant name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, mole per liter, milligram per liter, microgram per cubic meter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Pollutant types and, amount or concentrations measured at the time\n      of sampling; can report multiple pollutants by entering numeric values preceded\n      by name of pollutant\n    title: pollutants\n    examples:\n    - value: lead;0.15 microgram per cubic meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pollutants\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000107\n    alias: pollutants\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  porosity:\n    name: porosity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value or range\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Porosity of deposited sediment is volume of voids divided by the\n      total volume of sample\n    title: porosity\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - porosity\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} - {float} {unit}'\n    slot_uri: MIXS:0000211\n    alias: porosity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  potassium:\n    name: potassium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of potassium in the sample\n    title: potassium\n    examples:\n    - value: 463 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - potassium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000430\n    alias: potassium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  pour_point:\n    name: pour_point\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Temperature at which a liquid becomes semi solid and loses its flow\n      characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with\n      a high paraffin content, typically found in crude deriving from a larger proportion\n      of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\n    title: pour point\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pour point\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000127\n    alias: pour_point\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  pre_treatment:\n    name: pre_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: pre-treatment type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The process of pre-treatment removes materials that can be easily\n      collected from the raw wastewater\n    title: pre-treatment\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pre-treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000348\n    alias: pre_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  pres_animal_insect:\n    name: pres_animal_insect\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration;count\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type and number of animals or insects present in the sampling\n      space.\n    title: presence of pets, animals, or insects\n    examples:\n    - value: cat;5\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - presence of pets, animals, or insects\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000819\n    alias: pres_animal_insect\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n    pattern: ^(cat|dog|rodent|snake|other);\\d+$\n  pressure:\n    name: pressure\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: atmosphere\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Pressure to which the sample is subject to, in atmospheres\n    title: pressure\n    examples:\n    - value: 50 atmosphere\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pressure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000412\n    alias: pressure\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  prev_land_use_meth:\n    name: prev_land_use_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining previous land use and dates\n    title: history/previous land use method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/previous land use method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000316\n    alias: prev_land_use_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  previous_land_use:\n    name: previous_land_use\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: land use name;date\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Previous land use and dates\n    title: history/previous land use\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/previous land use\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{timestamp}'\n    slot_uri: MIXS:0000315\n    alias: previous_land_use\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  primary_prod:\n    name: primary_prod\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per cubic meter per day, gram per square meter per day\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of primary production, generally measured as isotope\n      uptake\n    title: primary production\n    examples:\n    - value: 100 milligram per cubic meter per day\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - primary production\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000728\n    alias: primary_prod\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  primary_treatment:\n    name: primary_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: primary treatment type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The process to produce both a generally homogeneous liquid capable\n      of being treated biologically and a sludge that can be separately treated or\n      processed\n    title: primary treatment\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - primary treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000349\n    alias: primary_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  prod_rate:\n    name: prod_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic meter per day\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Oil and/or gas production rates per well (e.g. 524 m3 / day)\n    title: production rate\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - production rate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000452\n    alias: prod_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  prod_start_date:\n    name: prod_start_date\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: timestamp\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Date of field's first production\n    title: production start date\n    examples:\n    - value: '2018-05-11'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - production start date\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001008\n    alias: prod_start_date\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TimestampValue\n    multivalued: false\n  profile_position:\n    name: profile_position\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Cross-sectional position in the hillslope where sample was collected.sample\n      area position in relation to surrounding areas\n    title: profile position\n    examples:\n    - value: summit\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - profile position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001084\n    alias: profile_position\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: profile_position_enum\n    multivalued: false\n  quad_pos:\n    name: quad_pos\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The quadrant position of the sampling room within the building\n    title: quadrant position\n    examples:\n    - value: West side\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - quadrant position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000820\n    alias: quad_pos\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: quad_pos_enum\n    multivalued: false\n  radiation_regm:\n    name: radiation_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: radiation type name;radiation amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: rad, gray\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving exposure of plant or a plant\n      part to a particular radiation regimen; should include the radiation type, amount\n      or intensity administered, treatment regimen including how many times the treatment\n      was repeated, how long each treatment lasted, and the start and end time of\n      the entire treatment; can include multiple radiation regimens\n    title: radiation regimen\n    examples:\n    - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - radiation regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000575\n    alias: radiation_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  rainfall_regm:\n    name: rainfall_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to a given amount\n      of rainfall, treatment regimen including how many times the treatment was repeated,\n      how long each treatment lasted, and the start and end time of the entire treatment;\n      can include multiple regimens\n    title: rainfall regimen\n    examples:\n    - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rainfall regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000576\n    alias: rainfall_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  reactor_type:\n    name: reactor_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: reactor type name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Anaerobic digesters can be designed and engineered to operate using\n      a number of different process configurations, as batch or continuous, mesophilic,\n      high solid or low solid, and single stage or multistage\n    title: reactor type\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - reactor type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000350\n    alias: reactor_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  redox_potential:\n    name: redox_potential\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millivolt\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Redox potential, measured relative to a hydrogen cell, indicating\n      oxidation or reduction potential\n    title: redox potential\n    examples:\n    - value: 300 millivolt\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - redox potential\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000182\n    alias: redox_potential\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  rel_air_humidity:\n    name: rel_air_humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Partial vapor and air pressure, density of the vapor and air, or\n      by the actual mass of the vapor and air\n    title: relative air humidity\n    examples:\n    - value: 80%\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - relative air humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000121\n    alias: rel_air_humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  rel_humidity_out:\n    name: rel_humidity_out\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram of air, kilogram of air\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The recorded outside relative humidity value at the time of sampling\n    title: outside relative humidity\n    examples:\n    - value: 12 per kilogram of air\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - outside relative humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000188\n    alias: rel_humidity_out\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  rel_samp_loc:\n    name: rel_samp_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The sampling location within the train car\n    title: relative sampling location\n    examples:\n    - value: center of car\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - relative sampling location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000821\n    alias: rel_samp_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: rel_samp_loc_enum\n    multivalued: false\n  reservoir:\n    name: reservoir\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of the reservoir (e.g. Carapebus)\n    title: reservoir name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - reservoir name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000303\n    alias: reservoir\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  resins_pc:\n    name: resins_pc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n      method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n      and polarity. There are three main methods to obtain SARA results. The most\n      popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n      https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n    title: resins wt%\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - resins wt%\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000134\n    alias: resins_pc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_air_exch_rate:\n    name: room_air_exch_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: liter per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The rate at which outside air replaces indoor air in a given space\n    title: room air exchange rate\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room air exchange rate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000169\n    alias: room_air_exch_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  room_architec_elem:\n    name: room_architec_elem\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The unique details and component parts that, together, form the architecture\n      of a distinguisahable space within a built structure\n    title: room architectural elements\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room architectural elements\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000233\n    alias: room_architec_elem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  room_condt:\n    name: room_condt\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The condition of the room at the time of sampling\n    title: room condition\n    examples:\n    - value: new\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000822\n    alias: room_condt\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_condt_enum\n    multivalued: false\n  room_connected:\n    name: room_connected\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of rooms connected to the sampling room by a doorway\n    title: rooms connected by a doorway\n    examples:\n    - value: office\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooms connected by a doorway\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000826\n    alias: room_connected\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_connected_enum\n    multivalued: false\n  room_count:\n    name: room_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The total count of rooms in the built structure including all room\n      types\n    title: room count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000234\n    alias: room_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_dim:\n    name: room_dim\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The length, width and height of sampling room\n    title: room dimensions\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room dimensions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\n    slot_uri: MIXS:0000192\n    alias: room_dim\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_door_dist:\n    name: room_door_dist\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Distance between doors (meters) in the hallway between the sampling\n      room and adjacent rooms\n    title: room door distance\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room door distance\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} {unit}'\n    slot_uri: MIXS:0000193\n    alias: room_door_dist\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_door_share:\n    name: room_door_share\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: room name;room number\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of room(s) (room number, room name) sharing a door with the\n      sampling room\n    title: rooms that share a door with sampling room\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooms that share a door with sampling room\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{integer}'\n    slot_uri: MIXS:0000242\n    alias: room_door_share\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_hallway:\n    name: room_hallway\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: room name;room number\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of room(s) (room number, room name) located in the same hallway\n      as sampling room\n    title: rooms that are on the same hallway\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooms that are on the same hallway\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{integer}'\n    slot_uri: MIXS:0000238\n    alias: room_hallway\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_loc:\n    name: room_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The position of the room within the building\n    title: room location in building\n    examples:\n    - value: interior room\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room location in building\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000823\n    alias: room_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_loc_enum\n    multivalued: false\n  room_moist_dam_hist:\n    name: room_moist_dam_hist\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The history of moisture damage or mold in the past 12 months. Number\n      of events of moisture damage or mold observed\n    title: room moisture damage or mold history\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room moisture damage or mold history\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000235\n    alias: room_moist_dam_hist\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: integer\n    multivalued: false\n  room_net_area:\n    name: room_net_area\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square feet, square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The net floor area of sampling room. Net area excludes wall thicknesses\n    title: room net area\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room net area\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} {unit}'\n    slot_uri: MIXS:0000194\n    alias: room_net_area\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_occup:\n    name: room_occup\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Count of room occupancy at time of sampling\n    title: room occupancy\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room occupancy\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000236\n    alias: room_occup\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  room_samp_pos:\n    name: room_samp_pos\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The horizontal sampling position in the room relative to architectural\n      elements\n    title: room sampling position\n    examples:\n    - value: south corner\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room sampling position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000824\n    alias: room_samp_pos\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_samp_pos_enum\n    multivalued: false\n  room_type:\n    name: room_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The main purpose or activity of the sampling room. A room is any\n      distinguishable space within a structure\n    title: room type\n    examples:\n    - value: bathroom\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000825\n    alias: room_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: room_type_enum\n    multivalued: false\n  room_vol:\n    name: room_vol\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic feet, cubic meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Volume of sampling room\n    title: room volume\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room volume\n    rank: 1000\n    is_a: core field\n    string_serialization: '{integer} {unit}'\n    slot_uri: MIXS:0000195\n    alias: room_vol\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_wall_share:\n    name: room_wall_share\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: room name;room number\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: List of room(s) (room number, room name) sharing a wall with the\n      sampling room\n    title: rooms that share a wall with sampling room\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooms that share a wall with sampling room\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{integer}'\n    slot_uri: MIXS:0000243\n    alias: room_wall_share\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  room_window_count:\n    name: room_window_count\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Number of windows in the room\n    title: room window count\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - room window count\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000237\n    alias: room_window_count\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: integer\n    multivalued: false\n  root_cond:\n    name: root_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url or free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Relevant rooting conditions such as field plot size, sowing density,\n      container dimensions, number of plants per container.\n    title: rooting conditions\n    examples:\n    - value: http://himedialabs.com/TD/PT158.pdf\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting conditions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0001061\n    alias: root_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_carbon:\n    name: root_med_carbon\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: carbon source name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Source of organic carbon in the culture rooting medium; e.g. sucrose.\n    title: rooting medium carbon\n    examples:\n    - value: sucrose\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium carbon\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000577\n    alias: root_med_carbon\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_macronutr:\n    name: root_med_macronutr\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: macronutrient name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of the culture rooting medium macronutrients (N,P, K,\n      Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\n    title: rooting medium macronutrients\n    examples:\n    - value: KH2PO4;170\u00ac\u2020milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium macronutrients\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000578\n    alias: root_med_macronutr\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_micronutr:\n    name: root_med_micronutr\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: micronutrient name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of the culture rooting medium micronutrients (Fe, Mn,\n      Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\n    title: rooting medium micronutrients\n    examples:\n    - value: H3BO3;6.2\u00ac\u2020milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium micronutrients\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000579\n    alias: root_med_micronutr\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_ph:\n    name: root_med_ph\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: pH measurement of the culture rooting medium; e.g. 5.5.\n    title: rooting medium pH\n    examples:\n    - value: '7.5'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium pH\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001062\n    alias: root_med_ph\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  root_med_regl:\n    name: root_med_regl\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: regulator name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Growth regulators in the culture rooting medium such as cytokinins,\n      auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\n    title: rooting medium regulators\n    examples:\n    - value: abscisic acid;0.75 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium regulators\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000581\n    alias: root_med_regl\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_solid:\n    name: root_med_solid\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Specification of the solidifying agent in the culture rooting medium;\n      e.g. agar.\n    title: rooting medium solidifier\n    examples:\n    - value: agar\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium solidifier\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0001063\n    alias: root_med_solid\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  root_med_suppl:\n    name: root_med_suppl\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: supplement name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Organic supplements of the culture rooting medium, such as vitamins,\n      amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n      (0.5\u00ac\u2020mg/L).\n    title: rooting medium organic supplements\n    examples:\n    - value: nicotinic acid;0.5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - rooting medium organic supplements\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000580\n    alias: root_med_suppl\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  salinity:\n    name: salinity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: practical salinity unit, percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The total concentration of all dissolved salts in a liquid or solid\n      sample. While salinity can be measured by a complete chemical analysis, this\n      method is difficult and time consuming. More often, it is instead derived from\n      the conductivity measurement. This is known as practical salinity. These derivations\n      compare the specific conductance of the sample to a salinity standard such as\n      seawater.\n    title: salinity\n    examples:\n    - value: 25 practical salinity unit\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - salinity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000183\n    alias: salinity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  salinity_meth:\n    name: salinity_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining salinity\n    title: salinity method\n    examples:\n    - value: https://doi.org/10.1007/978-1-61779-986-0_28\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - salinity method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000341\n    alias: salinity_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  salt_regm:\n    name: salt_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: salt name;salt amount;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, microgram, mole per liter, gram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving use of salts as supplement\n      to liquid and soil growth media; should include the name of salt, amount administered,\n      treatment regimen including how many times the treatment was repeated, how long\n      each treatment lasted, and the start and end time of the entire treatment; can\n      include multiple salt regimens\n    title: salt regimen\n    examples:\n    - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - salt regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000582\n    alias: salt_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  samp_capt_status:\n    name: samp_capt_status\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reason for the sample\n    title: sample capture status\n    examples:\n    - value: farm sample\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample capture status\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000860\n    alias: samp_capt_status\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_capt_status_enum\n    multivalued: false\n  samp_collec_device:\n    name: samp_collec_device\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: device name\n    description: The device used to collect an environmental sample. This field accepts\n      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\n    title: sample collection device\n    examples:\n    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample collection device\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{termLabel} {[termID]}|{text}'\n    slot_uri: MIXS:0000002\n    alias: samp_collec_device\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  samp_collec_method:\n    name: samp_collec_method\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url , or text\n    description: The method employed for collecting the sample.\n    title: sample collection method\n    examples:\n    - value: swabbing\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample collection method\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0001225\n    alias: samp_collec_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  samp_collect_point:\n    name: samp_collect_point\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sampling point on the asset were sample was collected (e.g. Wellhead,\n      storage tank, separator, etc). If \"other\" is specified, please propose entry\n      in \"additional info\" field\n    title: sample collection point\n    examples:\n    - value: well\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample collection point\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001015\n    alias: samp_collect_point\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_collect_point_enum\n    multivalued: false\n  samp_dis_stage:\n    name: samp_dis_stage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Stage of the disease at the time of sample collection, e.g. inoculation,\n      penetration, infection, growth and reproduction, dissemination of pathogen.\n    title: sample disease stage\n    examples:\n    - value: infection\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample disease stage\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000249\n    alias: samp_dis_stage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_dis_stage_enum\n    multivalued: false\n  samp_floor:\n    name: samp_floor\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The floor of the building, where the sampling room is located\n    title: sampling floor\n    examples:\n    - value: 4th floor\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sampling floor\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000828\n    alias: samp_floor\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_floor_enum\n    multivalued: false\n  samp_loc_corr_rate:\n    name: samp_loc_corr_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter per year\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Metal corrosion rate is the speed of metal deterioration due to environmental\n      conditions. As environmental conditions change corrosion rates change accordingly.\n      Therefore, long term corrosion rates are generally more informative than short\n      term rates and for that reason they are preferred during reporting. In the case\n      of suspected MIC, corrosion rate measurements at the time of sampling might\n      provide insights into the involvement of certain microbial community members\n      in MIC as well as potential microbial interplays\n    title: corrosion rate at sample location\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - corrosion rate at sample location\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} - {float} {unit}'\n    slot_uri: MIXS:0000136\n    alias: samp_loc_corr_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_mat_process:\n    name: samp_mat_process\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text\n    description: A brief description of any processing applied to the sample during\n      or after retrieving the sample from environment, or a link to the relevant protocol(s)\n      performed.\n    title: sample material processing\n    examples:\n    - value: filtering of seawater, storing samples in ethanol\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample material processing\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000016\n    alias: samp_mat_process\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledTermValue\n    multivalued: false\n  samp_md:\n    name: samp_md\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;enumeration\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: In non deviated well, measured depth is equal to the true vertical\n      depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated\n      wells, the MD is the length of trajectory of the borehole measured from the\n      same reference or datum. Common datums used are ground level (GL), drilling\n      rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL).\n      If \"other\" is specified, please propose entry in \"additional info\" field\n    title: sample measured depth\n    examples:\n    - value: 1534 meter;MSL\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample measured depth\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000413\n    alias: samp_md\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  samp_preserv:\n    name: samp_preserv\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milliliter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n      etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\n    title: preservative added to sample\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - preservative added to sample\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000463\n    alias: samp_preserv\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_room_id:\n    name: samp_room_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sampling room number. This ID should be consistent with the designations\n      on the building floor plans\n    title: sampling room ID or name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sampling room ID or name\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000244\n    alias: samp_room_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_size:\n    name: samp_size\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millliter, gram, milligram, liter\n    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n      sample collected.\n    title: amount or size of sample collected\n    examples:\n    - value: 5 liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - amount or size of sample collected\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    slot_uri: MIXS:0000001\n    alias: samp_size\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  samp_sort_meth:\n    name: samp_sort_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: description of method\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Method by which samples are sorted; open face filter collecting total\n      suspended particles, prefilter to remove particles larger than X micrometers\n      in diameter, where common values of X would be 10 and 2.5 full size sorting\n      in a cascade impactor.\n    title: sample size sorting method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample size sorting method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000216\n    alias: samp_sort_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  samp_store_dur:\n    name: samp_store_dur\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: duration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Duration for which the sample was stored\n    title: sample storage duration\n    examples:\n    - value: P1Y6M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample storage duration\n    rank: 1000\n    is_a: core field\n    string_serialization: '{duration}'\n    slot_uri: MIXS:0000116\n    alias: samp_store_dur\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_store_loc:\n    name: samp_store_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: location name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Location at which sample was stored, usually name of a specific freezer/room\n    title: sample storage location\n    examples:\n    - value: Freezer no:5\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample storage location\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000755\n    alias: samp_store_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_store_temp:\n    name: samp_store_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Temperature at which sample was stored, e.g. -80 degree Celsius\n    title: sample storage temperature\n    examples:\n    - value: -80 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample storage temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000110\n    alias: samp_store_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  samp_subtype:\n    name: samp_subtype\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of sample sub-type. For example if \"sample type\" is \"Produced\n      Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified,\n      please propose entry in \"additional info\" field\n    title: sample subtype\n    examples:\n    - value: biofilm\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample subtype\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000999\n    alias: samp_subtype\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_subtype_enum\n    multivalued: false\n  samp_taxon_id:\n    name: samp_taxon_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: Taxonomy ID\n    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa\n      sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or\n      'blank sample' for negative controls.\n    title: Taxonomy ID of DNA sample\n    comments:\n    - coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Taxonomy ID of DNA sample\n    rank: 1000\n    is_a: investigation field\n    slot_uri: MIXS:0001320\n    alias: samp_taxon_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: ControlledIdentifiedTermValue\n    multivalued: false\n  samp_time_out:\n    name: samp_time_out\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: time\n      preferred_unit:\n        tag: preferred_unit\n        value: hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The recent and long term history of outside sampling\n    title: sampling time outside\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sampling time outside\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000196\n    alias: samp_time_out\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_transport_cond:\n    name: samp_transport_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: days;degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sample transport duration (in days or hrs) and temperature the sample\n      was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\n    title: sample transport conditions\n    examples:\n    - value: 5 days;-20 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample transport conditions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{float} {unit}'\n    slot_uri: MIXS:0000410\n    alias: samp_transport_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_tvdss:\n    name: samp_tvdss\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value or measurement value range\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Depth of the sample i.e. The vertical distance between the sea level\n      and the sampled position in the subsurface. Depth can be reported as an interval\n      for subsurface samples e.g. 1325.75-1362.25 m\n    title: sample true vertical depth subsea\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample true vertical depth subsea\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float}-{float} {unit}'\n    slot_uri: MIXS:0000409\n    alias: samp_tvdss\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_type:\n    name: samp_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: GENEPIO:0001246\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of material from which the sample was obtained. For the\n      Hydrocarbon package, samples include types like core, rock trimmings, drill\n      cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,\n      produced water, injected water, swabs, etc. For the Food Package, samples are\n      usually categorized as food, body products or tissues, or environmental material.\n      This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\n    title: sample type\n    examples:\n    - value: built environment sample [GENEPIO:0001248]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000998\n    alias: samp_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  samp_weather:\n    name: samp_weather\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The weather on the sampling day\n    title: sampling day weather\n    examples:\n    - value: foggy\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sampling day weather\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000827\n    alias: samp_weather\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: samp_weather_enum\n    multivalued: false\n  samp_well_name:\n    name: samp_well_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Name of the well (e.g. BXA1123) where sample was taken\n    title: sample well name\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample well name\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000296\n    alias: samp_well_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  saturates_pc:\n    name: saturates_pc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n      method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n      and polarity. There are three main methods to obtain SARA results. The most\n      popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n      https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n    title: saturates wt%\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - saturates wt%\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000131\n    alias: saturates_pc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  season:\n    name: season\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: NCIT:C94729\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The season when sampling occurred. Any of the four periods into which\n      the year is divided by the equinoxes and solstices. This field accepts terms\n      listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).\n    title: season\n    examples:\n    - value: autumn [NCIT:C94733]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - season\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000829\n    alias: season\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  season_environment:\n    name: season_environment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: seasonal environment name;treatment interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Treatment involving an exposure to a particular season (e.g. Winter,\n      summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n      was repeated, how long each treatment lasted, and the start and end time of\n      the entire treatment\n    title: seasonal environment\n    examples:\n    - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - seasonal environment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0001068\n    alias: season_environment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  season_precpt:\n    name: season_precpt\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: millimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average of all seasonal precipitation values known, or an estimated\n      equivalent value derived by such methods as regional indexes or Isohyetal maps.\n    title: average seasonal precipitation\n    todos:\n    - check validation & examples. always mm? so value only? Or value + unit\n    notes:\n    - mean and average are the same thing, but it seems like bad practice to not be\n      consistent. Changed mean to average\n    comments:\n    - Seasons are defined as spring (March, April, May), summer (June, July, August),\n      autumn (September, October, November) and winter (December, January, February).\n    examples:\n    - value: 0.4 inch\n    - value: 10.16 mm\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean seasonal precipitation\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000645\n    alias: season_precpt\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  season_temp:\n    name: season_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Mean seasonal temperature\n    title: mean seasonal temperature\n    examples:\n    - value: 18 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - mean seasonal temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000643\n    alias: season_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  season_use:\n    name: season_use\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The seasons the space is occupied\n    title: seasonal use\n    examples:\n    - value: Winter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - seasonal use\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000830\n    alias: season_use\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: season_use_enum\n    multivalued: false\n  secondary_treatment:\n    name: secondary_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: secondary treatment type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The process for substantially degrading the biological content of\n      the sewage\n    title: secondary treatment\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - secondary treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000351\n    alias: secondary_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  sediment_type:\n    name: sediment_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Information about the sediment type based on major constituents\n    title: sediment type\n    examples:\n    - value: biogenous\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sediment type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001078\n    alias: sediment_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sediment_type_enum\n    multivalued: false\n  sequencing field:\n    name: sequencing field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    abstract: true\n    alias: sequencing_field\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  sewage_type:\n    name: sewage_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: sewage type name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Type of wastewater treatment plant as municipial or industrial\n    title: sewage type\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sewage type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000215\n    alias: sewage_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  shad_dev_water_mold:\n    name: shad_dev_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on the shading device\n    title: shading device signs of water/mold\n    examples:\n    - value: no presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000834\n    alias: shad_dev_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  shading_device_cond:\n    name: shading_device_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the shading device at the time of sampling\n    title: shading device condition\n    examples:\n    - value: new\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000831\n    alias: shading_device_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: shading_device_cond_enum\n    multivalued: false\n  shading_device_loc:\n    name: shading_device_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The location of the shading device in relation to the built structure\n    title: shading device location\n    examples:\n    - value: exterior\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device location\n    rank: 1000\n    is_a: core field\n    string_serialization: '[exterior|interior]'\n    slot_uri: MIXS:0000832\n    alias: shading_device_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  shading_device_mat:\n    name: shading_device_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: material name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The material the shading device is composed of\n    title: shading device material\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device material\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000245\n    alias: shading_device_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  shading_device_type:\n    name: shading_device_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of shading device\n    title: shading device type\n    examples:\n    - value: slatted aluminum awning\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - shading device type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000835\n    alias: shading_device_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: shading_device_type_enum\n    multivalued: false\n  sieving:\n    name: sieving\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: design name and/or size;amount\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Collection design of pooled samples and/or sieve size and amount\n      of sample sieved\n    title: composite design/sieving\n    todos:\n    - check validation and examples\n    comments:\n    - Describe how samples were composited or sieved.\n    - Use 'sample link' to indicate which samples were combined.\n    examples:\n    - value: combined 2 cores | 4mm sieved\n    - value: 4 mm sieved and homogenized\n    - value: 50 g | 5 cores | 2 mm sieved\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - composite design/sieving\n    rank: 1000\n    is_a: core field\n    string_serialization: '{{text}|{float} {unit}};{float} {unit}'\n    slot_uri: MIXS:0000322\n    alias: sieving\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  silicate:\n    name: silicate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of silicate\n    title: silicate\n    examples:\n    - value: 0.05 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - silicate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000184\n    alias: silicate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  size_frac:\n    name: size_frac\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: filter size value range\n    description: Filtering pore size used in sample preparation\n    title: size fraction selected\n    examples:\n    - value: 0-0.22 micrometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - size fraction selected\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{float}-{float} {unit}'\n    slot_uri: MIXS:0000017\n    alias: size_frac\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  size_frac_low:\n    name: size_frac_low\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: micrometer\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n      Materials larger than the size threshold are excluded from the sample\n    title: size-fraction lower threshold\n    examples:\n    - value: 0.2 micrometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - size-fraction lower threshold\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000735\n    alias: size_frac_low\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  size_frac_up:\n    name: size_frac_up\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: micrometer\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Refers to the mesh/pore size used to retain the sample. Materials\n      smaller than the size threshold are excluded from the sample\n    title: size-fraction upper threshold\n    examples:\n    - value: 20 micrometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - size-fraction upper threshold\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000736\n    alias: size_frac_up\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  slope_aspect:\n    name: slope_aspect\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The direction a slope faces. While looking down a slope use a compass\n      to record the direction you are facing (direction or degrees). This measure\n      provides an indication of sun and wind exposure that will influence soil temperature\n      and evapotranspiration.\n    title: slope aspect\n    comments:\n    - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n      360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n      is west-facing.\n    examples:\n    - value: '35'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - slope aspect\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000647\n    alias: slope_aspect\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  slope_gradient:\n    name: slope_gradient\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Commonly called 'slope'. The angle between ground surface and a horizontal\n      line (in percent). This is the direction that overland water would flow. This\n      measure is usually taken with a hand level meter or clinometer\n    title: slope gradient\n    todos:\n    - Slope is a percent. How does the validation work? Check to correct examples\n    examples:\n    - value: 10%\n    - value: 10 %\n    - value: '0.10'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - slope gradient\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000646\n    alias: slope_gradient\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sludge_retent_time:\n    name: sludge_retent_time\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: hours\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The time activated sludge remains in reactor\n    title: sludge retention time\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sludge retention time\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000669\n    alias: sludge_retent_time\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sodium:\n    name: sodium\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Sodium concentration in the sample\n    title: sodium\n    examples:\n    - value: 10.5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sodium\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000428\n    alias: sodium\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  soil_horizon:\n    name: soil_horizon\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Specific layer in the land area which measures parallel to the soil\n      surface and possesses physical characteristics which differ from the layers\n      above and beneath\n    title: soil horizon\n    examples:\n    - value: A horizon\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil horizon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001082\n    alias: soil_horizon\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: soil_horizon_enum\n    multivalued: false\n  soil_text_measure:\n    name: soil_text_measure\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative proportion of different grain sizes of mineral particles\n      in a soil, as described using a standard system; express as % sand (50 um to\n      2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty\n      clay loam) optional.\n    title: soil texture measurement\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil texture measurement\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000335\n    alias: soil_text_measure\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  soil_texture_meth:\n    name: soil_texture_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining soil texture\n    title: soil texture method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil texture method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000336\n    alias: soil_texture_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  soil_type:\n    name: soil_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: ENVO_00001998\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Description of the soil type or classification. This field accepts\n      terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms\n      can be separated by pipes.\n    title: soil type\n    examples:\n    - value: plinthosol [ENVO:00002250]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000332\n    alias: soil_type\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  soil_type_meth:\n    name: soil_type_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining soil series name or other\n      lower-level classification\n    title: soil type method\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil type method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000334\n    alias: soil_type_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  solar_irradiance:\n    name: solar_irradiance\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: kilowatts per square meter per day, ergs per square centimeter per\n          second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The amount of solar energy that arrives at a specific area of a surface\n      during a specific time interval\n    title: solar irradiance\n    examples:\n    - value: 1.36 kilowatts per square meter per day\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - solar irradiance\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000112\n    alias: solar_irradiance\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  soluble_inorg_mat:\n    name: soluble_inorg_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: soluble inorganic material name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, microgram, mole per liter, gram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of substances such as ammonia, road-salt, sea-salt,\n      cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.\n    title: soluble inorganic material\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soluble inorganic material\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000672\n    alias: soluble_inorg_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  soluble_org_mat:\n    name: soluble_org_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: soluble organic material name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, microgram, mole per liter, gram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of substances such as urea, fruit sugars, soluble proteins,\n      drugs, pharmaceuticals, etc.\n    title: soluble organic material\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soluble organic material\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000673\n    alias: soluble_org_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  soluble_react_phosp:\n    name: soluble_react_phosp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of soluble reactive phosphorus\n    title: soluble reactive phosphorus\n    examples:\n    - value: 0.1 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soluble reactive phosphorus\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000738\n    alias: soluble_react_phosp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  source_mat_id:\n    name: source_mat_id\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: 'for cultures of microorganisms: identifiers for two culture collections;\n          for other material a unique arbitrary identifer'\n    description: A globally unique identifier assigned to the biological sample.\n    title: source material identifier\n    todos:\n    - Currently, the comments say to use UUIDs. However, if we implement assigning\n      NMDC identifiers with the minter we dont need to require a GUID. It can be an\n      optional field to fill out only if they already have a resolvable ID.\n    comments:\n    - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n      NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n      IDs enable linking to derived analytes and subsamples. If you have not assigned\n      FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n    examples:\n    - value: IGSN:AU1243\n    - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source material identifiers\n    rank: 1000\n    is_a: nucleic acid sequence source field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000026\n    alias: source_mat_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  space_typ_state:\n    name: space_typ_state\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Customary or normal state of the space\n    title: space typical state\n    examples:\n    - value: typically occupied\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - space typical state\n    rank: 1000\n    is_a: core field\n    string_serialization: '[typically occupied|typically unoccupied]'\n    slot_uri: MIXS:0000770\n    alias: space_typ_state\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  specific:\n    name: specific\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'The building specifications. If design is chosen, indicate phase:\n      conceptual, schematic, design development, construction documents'\n    title: specifications\n    examples:\n    - value: construction\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - specifications\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000836\n    alias: specific\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: specific_enum\n    multivalued: false\n  specific_ecosystem:\n    name: specific_ecosystem\n    description: Specific ecosystems represent specific features of the environment\n      like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n      Specific ecosystem is in position 5/5 in a GOLD path.\n    comments:\n    - Specific ecosystems help to define samples based on very specific characteristics\n      of an environment under the five-level classification system.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: specific_ecosystem\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  specific_humidity:\n    name: specific_humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram of air, kilogram of air\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The mass of water vapour in a unit mass of moist air, usually expressed\n      as grams of vapour per kilogram of air, or, in air conditioning, as grains per\n      pound.\n    title: specific humidity\n    examples:\n    - value: 15 per kilogram of air\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - specific humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000214\n    alias: specific_humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sr_dep_env:\n    name: sr_dep_env\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n      If \"other\" is specified, please propose entry in \"additional info\" field\n    title: source rock depositional environment\n    examples:\n    - value: Marine\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source rock depositional environment\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000996\n    alias: sr_dep_env\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sr_dep_env_enum\n    multivalued: false\n  sr_geol_age:\n    name: sr_geol_age\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n      If \"other\" is specified, please propose entry in \"additional info\" field'\n    title: source rock geological age\n    examples:\n    - value: Silurian\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source rock geological age\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000997\n    alias: sr_geol_age\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sr_geol_age_enum\n    multivalued: false\n  sr_kerog_type:\n    name: sr_kerog_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic\n      and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/\n      fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris\n      (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen).\n      If \"other\" is specified, please propose entry in \"additional info\" field'\n    title: source rock kerogen type\n    examples:\n    - value: Type IV\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source rock kerogen type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000994\n    alias: sr_kerog_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sr_kerog_type_enum\n    multivalued: false\n  sr_lithology:\n    name: sr_lithology\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n      If \"other\" is specified, please propose entry in \"additional info\" field\n    title: source rock lithology\n    examples:\n    - value: Coal\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - source rock lithology\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000995\n    alias: sr_lithology\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: sr_lithology_enum\n    multivalued: false\n  standing_water_regm:\n    name: standing_water_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: standing water type;treatment interval and duration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Treatment involving an exposure to standing water during a plant's\n      life span, types can be flood water or standing water, treatment regimen including\n      how many times the treatment was repeated, how long each treatment lasted, and\n      the start and end time of the entire treatment; can include multiple regimens\n    title: standing water regimen\n    examples:\n    - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - standing water regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0001069\n    alias: standing_water_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  store_cond:\n    name: store_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: storage condition type;duration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Explain how and for how long the soil sample was stored before DNA\n      extraction (fresh/frozen/other).\n    title: storage conditions\n    examples:\n    - value: -20 degree Celsius freezer;P2Y10D\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - storage conditions\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{duration}'\n    slot_uri: MIXS:0000327\n    alias: store_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  substructure_type:\n    name: substructure_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: The substructure or under building is that largely hidden section\n      of the building which is built off the foundations to the ground floor level\n    title: substructure type\n    examples:\n    - value: basement\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - substructure type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000767\n    alias: substructure_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: substructure_type_enum\n    multivalued: true\n  sulfate:\n    name: sulfate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of sulfate in the sample\n    title: sulfate\n    examples:\n    - value: 5 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sulfate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000423\n    alias: sulfate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sulfate_fw:\n    name: sulfate_fw\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original sulfate concentration in the hydrocarbon resource\n    title: sulfate in formation water\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sulfate in formation water\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000407\n    alias: sulfate_fw\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  sulfide:\n    name: sulfide\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of sulfide in the sample\n    title: sulfide\n    examples:\n    - value: 2 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sulfide\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000424\n    alias: sulfide\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  surf_air_cont:\n    name: surf_air_cont\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Contaminant identified on surface\n    title: surface-air contaminant\n    examples:\n    - value: radon\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface-air contaminant\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000759\n    alias: surf_air_cont\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: surf_air_cont_enum\n    multivalued: true\n  surf_humidity:\n    name: surf_humidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percentage\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Surfaces: water activity as a function of air and material moisture'\n    title: surface humidity\n    examples:\n    - value: 10%\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface humidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000123\n    alias: surf_humidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  surf_material:\n    name: surf_material\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Surface materials at the point of sampling\n    title: surface material\n    examples:\n    - value: wood\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000758\n    alias: surf_material\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: surf_material_enum\n    multivalued: false\n  surf_moisture:\n    name: surf_moisture\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: parts per million, gram per cubic meter, gram per square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Water held on a surface\n    title: surface moisture\n    examples:\n    - value: 0.01 gram per square meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface moisture\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000128\n    alias: surf_moisture\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  surf_moisture_ph:\n    name: surf_moisture_ph\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: ph measurement of surface\n    title: surface moisture pH\n    examples:\n    - value: '7'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface moisture pH\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000760\n    alias: surf_moisture_ph\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: double\n    multivalued: false\n  surf_temp:\n    name: surf_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Temperature of the surface at the time of sampling\n    title: surface temperature\n    examples:\n    - value: 15 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - surface temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000125\n    alias: surf_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  suspend_part_matter:\n    name: suspend_part_matter\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of suspended particulate matter\n    title: suspended particulate matter\n    examples:\n    - value: 0.5 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - suspended particulate matter\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000741\n    alias: suspend_part_matter\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  suspend_solids:\n    name: suspend_solids\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: suspended solid name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram, microgram, milligram per liter, mole per liter, gram per liter,\n          part per million\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of substances including a wide variety of material,\n      such as silt, decaying plant and animal matter; can include multiple substances\n    title: suspended solids\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - suspended solids\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000150\n    alias: suspend_solids\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  tan:\n    name: tan\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n      by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n      the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n      oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\n    title: total acid number\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total acid number\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000120\n    alias: tan\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  temp:\n    name: temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n    description: Temperature of the sample at the time of sampling.\n    title: temperature\n    examples:\n    - value: 25 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - temperature\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000113\n    alias: temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  temp_out:\n    name: temp_out\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The recorded temperature value at sampling time outside\n    title: temperature outside house\n    examples:\n    - value: 5 degree Celsius\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - temperature outside house\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000197\n    alias: temp_out\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tertiary_treatment:\n    name: tertiary_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: tertiary treatment type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The process providing a final treatment stage to raise the effluent\n      quality before it is discharged to the receiving environment\n    title: tertiary treatment\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - tertiary treatment\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000352\n    alias: tertiary_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  tidal_stage:\n    name: tidal_stage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Stage of tide\n    title: tidal stage\n    examples:\n    - value: high tide\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - tidal stage\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000750\n    alias: tidal_stage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: tidal_stage_enum\n    multivalued: false\n  tillage:\n    name: tillage\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Note method(s) used for tilling\n    title: history/tillage\n    examples:\n    - value: chisel\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - history/tillage\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0001081\n    alias: tillage\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: tillage_enum\n    multivalued: true\n  tiss_cult_growth_med:\n    name: tiss_cult_growth_med\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI,url or free text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Description of plant tissue culture growth media used\n    title: tissue culture growth media\n    examples:\n    - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - tissue culture growth media\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n    slot_uri: MIXS:0001070\n    alias: tiss_cult_growth_med\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  toluene:\n    name: toluene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of toluene in the sample\n    title: toluene\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - toluene\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000154\n    alias: toluene\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_carb:\n    name: tot_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total carbon content\n    title: total carbon\n    todos:\n    - is this inorganic and organic? both? could use some clarification.\n    - ug/L doesn't seem like the right units. Should check this slots usage in databases\n      and re-evaluate. I couldn't find any references that provided this data in this\n      format\n    examples:\n    - value: 1 ug/L\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000525\n    alias: tot_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_depth_water_col:\n    name: tot_depth_water_col\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of total depth of water column\n    title: total depth of water column\n    examples:\n    - value: 500 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total depth of water column\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000634\n    alias: tot_depth_water_col\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_diss_nitro:\n    name: tot_diss_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n      by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\n    title: total dissolved nitrogen\n    examples:\n    - value: 40 microgram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total dissolved nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000744\n    alias: tot_diss_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_inorg_nitro:\n    name: tot_inorg_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total inorganic nitrogen content\n    title: total inorganic nitrogen\n    examples:\n    - value: 40 microgram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total inorganic nitrogen\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000745\n    alias: tot_inorg_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_iron:\n    name: tot_iron\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, milligram per kilogram\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of total iron in the sample\n    title: total iron\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total iron\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000105\n    alias: tot_iron\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_nitro:\n    name: tot_nitro\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Total nitrogen concentration of water samples, calculated by: total\n      nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n      without filtering, reported as nitrogen'\n    title: total nitrogen concentration\n    examples:\n    - value: 50 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total nitrogen concentration\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000102\n    alias: tot_nitro\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_nitro_cont_meth:\n    name: tot_nitro_cont_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining the total nitrogen\n    title: total nitrogen content method\n    examples:\n    - value: https://doi.org/10.2134/agronmonogr9.2.c32\n    - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total nitrogen content method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000338\n    alias: tot_nitro_cont_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  tot_nitro_content:\n    name: tot_nitro_content\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter, milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total nitrogen content of the sample\n    title: total nitrogen content\n    examples:\n    - value: 5 mg N/ L\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total nitrogen content\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000530\n    alias: tot_nitro_content\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_org_c_meth:\n    name: tot_org_c_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining total organic carbon\n    title: total organic carbon method\n    examples:\n    - value: https://doi.org/10.1080/07352680902776556\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total organic carbon method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000337\n    alias: tot_org_c_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  tot_org_carb:\n    name: tot_org_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: gram Carbon per kilogram sample material\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Definition for soil: total organic carbon content of the soil, definition\n      otherwise: total organic carbon content'\n    title: total organic carbon\n    todos:\n    - check description. How are they different?\n    examples:\n    - value: 5 mg N/ L\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total organic carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000533\n    alias: tot_org_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_part_carb:\n    name: tot_part_carb\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total particulate carbon content\n    title: total particulate carbon\n    examples:\n    - value: 35 micromole per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total particulate carbon\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000747\n    alias: tot_part_carb\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_phosp:\n    name: tot_phosp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: micromole per liter, milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'Total phosphorus concentration in the sample, calculated by: total\n      phosphorus = total dissolved phosphorus + particulate phosphorus'\n    title: total phosphorus\n    examples:\n    - value: 0.03 milligram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total phosphorus\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000117\n    alias: tot_phosp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_phosphate:\n    name: tot_phosphate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per liter, micromole per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Total amount or concentration of phosphate\n    title: total phosphate\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total phosphate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000689\n    alias: tot_phosphate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tot_sulfur:\n    name: tot_sulfur\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of total sulfur in the sample\n    title: total sulfur\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - total sulfur\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000419\n    alias: tot_sulfur\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  train_line:\n    name: train_line\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The subway line name\n    title: train line\n    examples:\n    - value: red\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - train line\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000837\n    alias: train_line\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: train_line_enum\n    multivalued: false\n  train_stat_loc:\n    name: train_stat_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The train station collection location\n    title: train station collection location\n    examples:\n    - value: forest hills\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - train station collection location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000838\n    alias: train_stat_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: train_stat_loc_enum\n    multivalued: false\n  train_stop_loc:\n    name: train_stop_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The train stop collection location\n    title: train stop collection location\n    examples:\n    - value: end\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - train stop collection location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000839\n    alias: train_stop_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: train_stop_loc_enum\n    multivalued: false\n  turbidity:\n    name: turbidity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: formazin turbidity unit, formazin nephelometric units\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measure of the amount of cloudiness or haziness in water caused by\n      individual particles\n    title: turbidity\n    examples:\n    - value: 0.3 nephelometric turbidity units\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - turbidity\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000191\n    alias: turbidity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tvdss_of_hcr_press:\n    name: tvdss_of_hcr_press\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n      the original pressure was measured (e.g. 1578 m).\n    title: depth (TVDSS) of hydrocarbon resource pressure\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - depth (TVDSS) of hydrocarbon resource pressure\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000397\n    alias: tvdss_of_hcr_press\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  tvdss_of_hcr_temp:\n    name: tvdss_of_hcr_temp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n      the original temperature was measured (e.g. 1345 m).\n    title: depth (TVDSS) of hydrocarbon resource temperature\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - depth (TVDSS) of hydrocarbon resource temperature\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000394\n    alias: tvdss_of_hcr_temp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  typ_occup_density:\n    name: typ_occup_density\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Customary or normal density of occupants\n    title: typical occupant density\n    examples:\n    - value: '25'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - typical occupant density\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000771\n    alias: typ_occup_density\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: double\n    multivalued: false\n  ventilation_rate:\n    name: ventilation_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic meter per minute, liters per second\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Ventilation rate of the system in the sampled premises\n    title: ventilation rate\n    examples:\n    - value: 750 cubic meter per minute\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ventilation rate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000114\n    alias: ventilation_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  ventilation_type:\n    name: ventilation_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: ventilation type name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Ventilation system used in the sampled premises\n    title: ventilation type\n    examples:\n    - value: Operable windows\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - ventilation type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000756\n    alias: ventilation_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  vfa:\n    name: vfa\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of Volatile Fatty Acids in the sample\n    title: volatile fatty acids\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - volatile fatty acids\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000152\n    alias: vfa\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  vfa_fw:\n    name: vfa_fw\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Original volatile fatty acid concentration in the hydrocarbon resource\n    title: vfa in formation water\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - vfa in formation water\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000408\n    alias: vfa_fw\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  vis_media:\n    name: vis_media\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The building visual media\n    title: visual media\n    examples:\n    - value: 3D scans\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - visual media\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000840\n    alias: vis_media\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: vis_media_enum\n    multivalued: false\n  viscosity:\n    name: viscosity\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cP at degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n      stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\n    title: viscosity\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - viscosity\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{float} {unit}'\n    slot_uri: MIXS:0000126\n    alias: viscosity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  volatile_org_comp:\n    name: volatile_org_comp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: volatile organic compound name;measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: microgram per cubic meter, parts per million, nanogram per liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Concentration of carbon-based chemicals that easily evaporate at\n      room temperature; can report multiple volatile organic compounds by entering\n      numeric values preceded by name of compound\n    title: volatile organic compounds\n    examples:\n    - value: formaldehyde;500 nanogram per liter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - volatile organic compounds\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text};{float} {unit}'\n    slot_uri: MIXS:0000115\n    alias: volatile_org_comp\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  wall_area:\n    name: wall_area\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The total area of the sampled room's walls\n    title: wall area\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall area\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000198\n    alias: wall_area\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  wall_const_type:\n    name: wall_const_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The building class of the wall defined by the composition of the\n      building elements and fire-resistance rating.\n    title: wall construction type\n    examples:\n    - value: fire resistive\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall construction type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000841\n    alias: wall_const_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_const_type_enum\n    multivalued: false\n  wall_finish_mat:\n    name: wall_finish_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The material utilized to finish the outer most layer of the wall\n    title: wall finish material\n    examples:\n    - value: wood\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall finish material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000842\n    alias: wall_finish_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_finish_mat_enum\n    multivalued: false\n  wall_height:\n    name: wall_height\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      preferred_unit:\n        tag: preferred_unit\n        value: centimeter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The average height of the walls in the sampled room\n    title: wall height\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall height\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000221\n    alias: wall_height\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  wall_loc:\n    name: wall_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative location of the wall within the room\n    title: wall location\n    examples:\n    - value: north\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000843\n    alias: wall_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_loc_enum\n    multivalued: false\n  wall_surf_treatment:\n    name: wall_surf_treatment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The surface treatment of interior wall\n    title: wall surface treatment\n    examples:\n    - value: paneling\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall surface treatment\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000845\n    alias: wall_surf_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_surf_treatment_enum\n    multivalued: false\n  wall_texture:\n    name: wall_texture\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The feel, appearance, or consistency of a wall surface\n    title: wall texture\n    examples:\n    - value: popcorn\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall texture\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000846\n    alias: wall_texture\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: wall_texture_enum\n    multivalued: false\n  wall_thermal_mass:\n    name: wall_thermal_mass\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: joule per degree Celsius\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The ability of the wall to provide inertia against temperature fluctuations.\n      Generally this means concrete or concrete block that is either exposed or covered\n      only with paint\n    title: wall thermal mass\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall thermal mass\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000222\n    alias: wall_thermal_mass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  wall_water_mold:\n    name: wall_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on a wall\n    title: wall signs of water/mold\n    examples:\n    - value: no presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wall signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000844\n    alias: wall_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  wastewater_type:\n    name: wastewater_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: wastewater type name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The origin of wastewater such as human waste, rainfall, storm drains,\n      etc.\n    title: wastewater type\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wastewater type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000353\n    alias: wastewater_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  water_cont_soil_meth:\n    name: water_cont_soil_meth\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID,DOI or url\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Reference or method used in determining the water content of soil\n    title: water content method\n    todos:\n    - Why is it soil water content method in the name but not the title? Is this slot\n      used in other samples?\n    - Soil water content can be measure MANY ways and often, multiple ways are used\n      in one experiment (gravimetric water content and water holding capacity and\n      water filled pore space, to name a few).\n    - Should this be multi valued? How to we manage and validate this?\n    comments:\n    - Required if providing water content\n    examples:\n    - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n    - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water content method\n    rank: 1000\n    is_a: core field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000323\n    alias: water_cont_soil_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: false\n  water_content:\n    name: water_content\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: string\n      preferred_unit:\n        tag: preferred_unit\n        value: gram per gram or cubic centimeter per cubic centimeter\n    description: Water content measurement\n    title: water content\n    todos:\n    - value in preferred unit is too limiting. need to change this\n    - check and correct validation so examples are accepted\n    - how to manage multiple water content methods?\n    examples:\n    - value: 0.75 g water/g dry soil\n    - value: 75% water holding capacity\n    - value: 1.1 g fresh weight/ dry weight\n    - value: 10% water filled pore space\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water content\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000185\n    alias: water_content\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n  water_current:\n    name: water_current\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic meter per second, knots\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Measurement of magnitude and direction of flow within a fluid\n    title: water current\n    examples:\n    - value: 10 cubic meter per second\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water current\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000203\n    alias: water_current\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  water_cut:\n    name: water_cut\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: percent\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Current amount of water (%) in a produced fluid stream; or the average\n      of the combined streams\n    title: water cut\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water cut\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000454\n    alias: water_cut\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  water_feat_size:\n    name: water_feat_size\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: square meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The size of the water feature\n    title: water feature size\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water feature size\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000223\n    alias: water_feat_size\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  water_feat_type:\n    name: water_feat_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of water feature present within the building being sampled\n    title: water feature type\n    examples:\n    - value: stream\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water feature type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000847\n    alias: water_feat_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: water_feat_type_enum\n    multivalued: false\n  water_prod_rate:\n    name: water_prod_rate\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: cubic meter per day\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Water production rates per well (e.g. 987 m3 / day)\n    title: water production rate\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water production rate\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000453\n    alias: water_prod_rate\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  water_temp_regm:\n    name: water_temp_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: degree Celsius\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to water with varying\n      degree of temperature, treatment regimen including how many times the treatment\n      was repeated, how long each treatment lasted, and the start and end time of\n      the entire treatment; can include multiple regimens\n    title: water temperature regimen\n    examples:\n    - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - water temperature regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000590\n    alias: water_temp_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  watering_regm:\n    name: watering_regm\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value;treatment interval and duration\n      preferred_unit:\n        tag: preferred_unit\n        value: milliliter, liter\n      occurrence:\n        tag: occurrence\n        value: m\n    description: Information about treatment involving an exposure to watering frequencies,\n      treatment regimen including how many times the treatment was repeated, how long\n      each treatment lasted, and the start and end time of the entire treatment; can\n      include multiple regimens\n    title: watering regimen\n    examples:\n    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n    - value: 75% water holding capacity; constant\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - watering regimen\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n    slot_uri: MIXS:0000591\n    alias: watering_regm\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  weekday:\n    name: weekday\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The day of the week when sampling occurred\n    title: weekday\n    examples:\n    - value: Sunday\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - weekday\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000848\n    alias: weekday\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: weekday_enum\n    multivalued: false\n  win:\n    name: win\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: text\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: 'A unique identifier of a well or wellbore. This is part of the Global\n      Framework for Well Identification initiative which is compiled by the Professional\n      Petroleum Data Management Association (PPDM) in an effort to improve well identification\n      systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\n    title: well identification number\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - well identification number\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000297\n    alias: win\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  wind_direction:\n    name: wind_direction\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: wind direction name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Wind direction is the direction from which a wind originates\n    title: wind direction\n    examples:\n    - value: Northwest\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wind direction\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000757\n    alias: wind_direction\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  wind_speed:\n    name: wind_speed\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: meter per second, kilometer per hour\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Speed of wind measured at the time of sampling\n    title: wind speed\n    examples:\n    - value: 21 kilometer per hour\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - wind speed\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000118\n    alias: wind_speed\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  window_cond:\n    name: window_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The physical condition of the window at the time of sampling\n    title: window condition\n    examples:\n    - value: rupture\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window condition\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000849\n    alias: window_cond\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_cond_enum\n    multivalued: false\n  window_cover:\n    name: window_cover\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of window covering\n    title: window covering\n    examples:\n    - value: curtains\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window covering\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000850\n    alias: window_cover\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_cover_enum\n    multivalued: false\n  window_horiz_pos:\n    name: window_horiz_pos\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The horizontal position of the window on the wall\n    title: window horizontal position\n    examples:\n    - value: middle\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window horizontal position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000851\n    alias: window_horiz_pos\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_horiz_pos_enum\n    multivalued: false\n  window_loc:\n    name: window_loc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The relative location of the window within the room\n    title: window location\n    examples:\n    - value: west\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window location\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000852\n    alias: window_loc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_loc_enum\n    multivalued: false\n  window_mat:\n    name: window_mat\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of material used to finish a window\n    title: window material\n    examples:\n    - value: wood\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window material\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000853\n    alias: window_mat\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_mat_enum\n    multivalued: false\n  window_open_freq:\n    name: window_open_freq\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: value\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The number of times windows are opened per week\n    title: window open frequency\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window open frequency\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000246\n    alias: window_open_freq\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  window_size:\n    name: window_size\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: inch, meter\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The window's length and width\n    title: window area/size\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window area/size\n    rank: 1000\n    is_a: core field\n    string_serialization: '{float} {unit} x {float} {unit}'\n    slot_uri: MIXS:0000224\n    alias: window_size\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  window_status:\n    name: window_status\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Defines whether the windows were open or closed during environmental\n      testing\n    title: window status\n    examples:\n    - value: open\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window status\n    rank: 1000\n    is_a: core field\n    string_serialization: '[closed|open]'\n    slot_uri: MIXS:0000855\n    alias: window_status\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  window_type:\n    name: window_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The type of windows\n    title: window type\n    examples:\n    - value: fixed window\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window type\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000856\n    alias: window_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_type_enum\n    multivalued: false\n  window_vert_pos:\n    name: window_vert_pos\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: The vertical position of the window on the wall\n    title: window vertical position\n    examples:\n    - value: middle\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window vertical position\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000857\n    alias: window_vert_pos\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: window_vert_pos_enum\n    multivalued: false\n  window_water_mold:\n    name: window_water_mold\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: enumeration\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Signs of the presence of mold or mildew on the window.\n    title: window signs of water/mold\n    examples:\n    - value: no presence of mold visible\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - window signs of water/mold\n    rank: 1000\n    is_a: core field\n    string_serialization: '[presence of mold visible|no presence of mold visible]'\n    slot_uri: MIXS:0000854\n    alias: window_water_mold\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: TextValue\n    multivalued: false\n  xylene:\n    name: xylene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: milligram per liter, parts per million\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of xylene in the sample\n    title: xylene\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - xylene\n    rank: 1000\n    is_a: core field\n    slot_uri: MIXS:0000156\n    alias: xylene\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n    multivalued: false\n  zinc:\n    name: zinc\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n      preferred_unit:\n        tag: preferred_unit\n        value: mg/kg (ppm)\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Concentration of zinc in the sample\n    title: zinc\n    examples:\n    - value: 2.5 mg/kg\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ornl.gov/content/bio-scales-0\n    aliases:\n    - zinc\n    rank: 1000\n    alias: zinc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  add_date:\n    name: add_date\n    description: The date on which the information was added to the database.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: add_date\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  community:\n    name: community\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: community\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  habitat:\n    name: habitat\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: habitat\n    owner: Biosample\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: string\n  host_name:\n    name: host_name\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: host_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  location:\n    name: location\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: location\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  mod_date:\n    name: mod_date\n    description: The last date on which the database information was modified.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mod_date\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  ncbi_taxonomy_name:\n    name: ncbi_taxonomy_name\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: ncbi_taxonomy_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  proport_woa_temperature:\n    name: proport_woa_temperature\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: proport_woa_temperature\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  salinity_category:\n    name: salinity_category\n    description: 'Categorical description of the sample''s salinity. Examples: halophile,\n      halotolerant, hypersaline, huryhaline'\n    notes:\n    - maps to gold:salinity\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-metadata/pull/297\n    rank: 1000\n    alias: salinity_category\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  sample_collection_site:\n    name: sample_collection_site\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: sample_collection_site\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  soluble_iron_micromol:\n    name: soluble_iron_micromol\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: soluble_iron_micromol\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n  subsurface_depth:\n    name: subsurface_depth\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: subsurface_depth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  dna_absorb1:\n    name: dna_absorb1\n    description: 260/280 measurement of DNA sample purity\n    title: DNA absorbance 260/280\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 7\n    is_a: biomaterial_purity\n    alias: dna_absorb1\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - ProcessedSample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n  dna_absorb2:\n    name: dna_absorb2\n    description: 260/230 measurement of DNA sample purity\n    title: DNA absorbance 260/230\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 8\n    is_a: biomaterial_purity\n    alias: dna_absorb2\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n  dna_collect_site:\n    name: dna_collect_site\n    description: Provide information on the site your DNA sample was collected from\n    title: DNA collection site\n    examples:\n    - value: untreated pond water\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 15\n    string_serialization: '{text}'\n    alias: dna_collect_site\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_concentration:\n    name: dna_concentration\n    title: DNA concentration in ng/ul\n    comments:\n    - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n      a fluorometric method. Acceptable values are 0-2000.\n    examples:\n    - value: '100'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:nucleic_acid_concentration\n    rank: 5\n    alias: dna_concentration\n    owner: Biosample\n    domain_of:\n    - Biosample\n    - ProcessedSample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 2000\n  dna_cont_type:\n    name: dna_cont_type\n    description: Tube or plate (96-well)\n    title: DNA container type\n    examples:\n    - value: plate\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 10\n    alias: dna_cont_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: JgiContTypeEnum\n    recommended: true\n  dna_container_id:\n    name: dna_container_id\n    title: DNA container label\n    comments:\n    - Must be unique across all tubes and plates, and <20 characters. All samples\n      in a plate should have the same plate label.\n    examples:\n    - value: Pond_MT_041618\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 9\n    string_serialization: '{text < 20 characters}'\n    alias: dna_container_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_dnase:\n    name: dna_dnase\n    title: DNase treatment DNA\n    comments:\n    - Note DNase treatment is required for all RNA samples.\n    examples:\n    - value: 'no'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 13\n    alias: dna_dnase\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: YesNoEnum\n    recommended: true\n  dna_isolate_meth:\n    name: dna_isolate_meth\n    description: Describe the method/protocol/kit used to extract DNA/RNA.\n    title: DNA isolation method\n    examples:\n    - value: phenol/chloroform extraction\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Sample Isolation Method\n    rank: 16\n    string_serialization: '{text}'\n    alias: dna_isolate_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_organisms:\n    name: dna_organisms\n    description: List any organisms known or suspected to grow in co-culture, as well\n      as estimated % of the organism in that culture.\n    title: DNA expected organisms\n    examples:\n    - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n        (1%)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 14\n    string_serialization: '{text}'\n    alias: dna_organisms\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_project_contact:\n    name: dna_project_contact\n    title: DNA seq project contact\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: John Jones\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 18\n    string_serialization: '{text}'\n    alias: dna_project_contact\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_samp_id:\n    name: dna_samp_id\n    title: DNA sample ID\n    todos:\n    - Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n      have two identifiers. How to force uniqueness? Moot because that column will\n      be prefilled?\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '187654'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 3\n    string_serialization: '{text}'\n    alias: dna_samp_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_sample_format:\n    name: dna_sample_format\n    description: Solution in which the DNA sample has been suspended\n    title: DNA sample format\n    examples:\n    - value: Water\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 12\n    alias: dna_sample_format\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: DNASampleFormatEnum\n    recommended: true\n  dna_sample_name:\n    name: dna_sample_name\n    description: Give the DNA sample a name that is meaningful to you. Sample names\n      must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n    title: DNA sample name\n    examples:\n    - value: JGI_pond_041618\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 4\n    string_serialization: '{text}'\n    alias: dna_sample_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_seq_project:\n    name: dna_seq_project\n    title: DNA seq project ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '1191234'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Seq Project ID\n    rank: 1\n    string_serialization: '{text}'\n    alias: dna_seq_project\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_seq_project_pi:\n    name: dna_seq_project_pi\n    title: DNA seq project PI\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: Jane Johnson\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 17\n    string_serialization: '{text}'\n    alias: dna_seq_project_pi\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_seq_project_name:\n    name: dna_seq_project_name\n    title: DNA seq project name\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: JGI Pond metagenomics\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 2\n    string_serialization: '{text}'\n    alias: dna_seq_project_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dna_volume:\n    name: dna_volume\n    title: DNA volume in ul\n    comments:\n    - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n      form accepts values < 25, but JGI may refuse to process them unless permission\n      has been granted by a project manager\n    examples:\n    - value: '25'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 6\n    string_serialization: '{float}'\n    alias: dna_volume\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 1000\n  proposal_dna:\n    name: proposal_dna\n    title: DNA proposal ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '504000'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 19\n    string_serialization: '{text}'\n    alias: proposal_dna\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metagenomics\n    range: string\n    recommended: true\n  dnase_rna:\n    name: dnase_rna\n    title: DNase treated\n    comments:\n    - Note DNase treatment is required for all RNA samples.\n    examples:\n    - value: 'no'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Was Sample DNAse treated?\n    rank: 13\n    alias: dnase_rna\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: YesNoEnum\n    recommended: true\n  proposal_rna:\n    name: proposal_rna\n    title: RNA proposal ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '504000'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 19\n    string_serialization: '{text}'\n    alias: proposal_rna\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_absorb1:\n    name: rna_absorb1\n    description: 260/280 measurement of RNA sample purity\n    title: RNA absorbance 260/280\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 7\n    string_serialization: '{float}'\n    alias: rna_absorb1\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: float\n    recommended: true\n  rna_absorb2:\n    name: rna_absorb2\n    description: 260/230 measurement of RNA sample purity\n    title: RNA absorbance 260/230\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 8\n    string_serialization: '{float}'\n    alias: rna_absorb2\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: float\n    recommended: true\n  rna_collect_site:\n    name: rna_collect_site\n    description: Provide information on the site your RNA sample was collected from\n    title: RNA collection site\n    examples:\n    - value: untreated pond water\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 15\n    string_serialization: '{text}'\n    alias: rna_collect_site\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_concentration:\n    name: rna_concentration\n    title: RNA concentration in ng/ul\n    comments:\n    - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n      a fluorometric method. Acceptable values are 0-2000.\n    examples:\n    - value: '100'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:nucleic_acid_concentration\n    rank: 5\n    string_serialization: '{float}'\n    alias: rna_concentration\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 1000\n  rna_cont_type:\n    name: rna_cont_type\n    description: Tube or plate (96-well)\n    title: RNA container type\n    examples:\n    - value: plate\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 10\n    alias: rna_cont_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: JgiContTypeEnum\n    recommended: true\n  rna_cont_well:\n    name: rna_cont_well\n    title: RNA plate position\n    comments:\n    - Required when 'plate' is selected for container type.\n    - Leave blank if the sample will be shipped in a tube.\n    - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n      pass validation.\n    - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n    examples:\n    - value: B2\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 11\n    string_serialization: '{96 well plate pos}'\n    alias: rna_cont_well\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n    pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  rna_container_id:\n    name: rna_container_id\n    title: RNA container label\n    comments:\n    - Must be unique across all tubes and plates, and <20 characters. All samples\n      in a plate should have the same plate label.\n    examples:\n    - value: Pond_MT_041618\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 9\n    string_serialization: '{text < 20 characters}'\n    alias: rna_container_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_isolate_meth:\n    name: rna_isolate_meth\n    description: Describe the method/protocol/kit used to extract DNA/RNA.\n    title: RNA isolation method\n    examples:\n    - value: phenol/chloroform extraction\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Sample Isolation Method\n    rank: 16\n    string_serialization: '{text}'\n    alias: rna_isolate_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_organisms:\n    name: rna_organisms\n    description: List any organisms known or suspected to grow in co-culture, as well\n      as estimated % of the organism in that culture.\n    title: RNA expected organisms\n    examples:\n    - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n        (1%)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 14\n    string_serialization: '{text}'\n    alias: rna_organisms\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_project_contact:\n    name: rna_project_contact\n    title: RNA seq project contact\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: John Jones\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 18\n    string_serialization: '{text}'\n    alias: rna_project_contact\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_samp_id:\n    name: rna_samp_id\n    title: RNA sample ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '187654'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 3\n    string_serialization: '{text}'\n    alias: rna_samp_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_sample_format:\n    name: rna_sample_format\n    description: Solution in which the RNA sample has been suspended\n    title: RNA sample format\n    examples:\n    - value: Water\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 12\n    alias: rna_sample_format\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: RNASampleFormatEnum\n    recommended: true\n  rna_sample_name:\n    name: rna_sample_name\n    description: Give the RNA sample a name that is meaningful to you. Sample names\n      must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n    title: RNA sample name\n    examples:\n    - value: JGI_pond_041618\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 4\n    string_serialization: '{text}'\n    alias: rna_sample_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n    minimum_value: 0\n    maximum_value: 2000\n  rna_seq_project:\n    name: rna_seq_project\n    title: RNA seq project ID\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: '1191234'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Seq Project ID\n    rank: 1\n    string_serialization: '{text}'\n    alias: rna_seq_project\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_seq_project_pi:\n    name: rna_seq_project_pi\n    title: RNA seq project PI\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: Jane Johnson\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 17\n    string_serialization: '{text}'\n    alias: rna_seq_project_pi\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_seq_project_name:\n    name: rna_seq_project_name\n    title: RNA seq project name\n    comments:\n    - Do not edit these values. A template will be provided by NMDC in which these\n      values have been pre-filled.\n    examples:\n    - value: JGI Pond metatranscriptomics\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 2\n    string_serialization: '{text}'\n    alias: rna_seq_project_name\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: string\n    recommended: true\n  rna_volume:\n    name: rna_volume\n    title: RNA volume in ul\n    comments:\n    - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n      form accepts values < 25, but JGI may refuse to process them unless permission\n      has been granted by a project manager\n    examples:\n    - value: '25'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 6\n    string_serialization: '{float}'\n    alias: rna_volume\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: JGI-Metatranscriptomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 1000\n  collection_date_inc:\n    name: collection_date_inc\n    description: Date the incubation was harvested/collected/ended. Only relevant\n      for incubation samples.\n    title: incubation collection date\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n      date only\n    comments:\n    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n      are all acceptable.\n    examples:\n    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 2\n    string_serialization: '{date, arbitrary precision}'\n    alias: collection_date_inc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  collection_time:\n    name: collection_time\n    description: The time of sampling, either as an instance (single point) or interval.\n    title: collection time, GMT\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n      time only\n    comments:\n    - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n    examples:\n    - value: 13:33 or 13:33:55\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 1\n    string_serialization: '{time, seconds optional}'\n    alias: collection_time\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  collection_time_inc:\n    name: collection_time_inc\n    description: Time the incubation was harvested/collected/ended. Only relevant\n      for incubation samples.\n    title: incubation collection time, GMT\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n      time only\n    comments:\n    - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n    examples:\n    - value: 13:33 or 13:33:55\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 3\n    string_serialization: '{time, seconds optional}'\n    alias: collection_time_inc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  experimental_factor_other:\n    name: experimental_factor_other\n    description: Other details about your sample that you feel can't be accurately\n      represented in the available columns.\n    title: experimental factor- other\n    comments:\n    - This slot accepts open-ended text about your sample.\n    - We recommend using key:value pairs.\n    - Provided pairs will be considered for inclusion as future slots/terms in this\n      data collection template.\n    examples:\n    - value: 'experimental treatment: value'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000008\n    - MIXS:0000300\n    rank: 7\n    string_serialization: '{text}'\n    alias: experimental_factor_other\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  filter_method:\n    name: filter_method\n    description: Type of filter used or how the sample was filtered\n    title: filter method\n    comments:\n    - describe the filter or provide a catalog number and manufacturer\n    examples:\n    - value: C18\n    - value: Basix PES, 13-100-106 FisherSci\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000765\n    rank: 6\n    string_serialization: '{text}'\n    alias: filter_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  isotope_exposure:\n    name: isotope_exposure\n    description: List isotope exposure or addition applied to your sample.\n    title: isotope exposure/addition\n    todos:\n    - Can we make the H218O correctly super and subscripted?\n    comments:\n    - This is required when your experimental design includes the use of isotopically\n      labeled compounds\n    examples:\n    - value: 13C glucose\n    - value: H218O\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000751\n    rank: 16\n    string_serialization: '{termLabel} {[termID]}; {timestamp}'\n    alias: isotope_exposure\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  micro_biomass_c_meth:\n    name: micro_biomass_c_meth\n    description: Reference or method used in determining microbial biomass carbon\n    title: microbial biomass carbon method\n    todos:\n    - How should we separate values? | or ;? lets be consistent\n    comments:\n    - required if \"microbial_biomass_c\" is provided\n    examples:\n    - value: https://doi.org/10.1016/0038-0717(87)90052-6\n    - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000339\n    rank: 11\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    alias: micro_biomass_c_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  micro_biomass_n_meth:\n    name: micro_biomass_n_meth\n    description: Reference or method used in determining microbial biomass nitrogen\n    title: microbial biomass nitrogen method\n    comments:\n    - required if \"microbial_biomass_n\" is provided\n    examples:\n    - value: https://doi.org/10.1016/0038-0717(87)90052-6\n    - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000339\n    rank: 13\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    alias: micro_biomass_n_meth\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  microbial_biomass_c:\n    name: microbial_biomass_c\n    description: The part of the organic matter in the soil that constitutes living\n      microorganisms smaller than 5-10 micrometer.\n    title: microbial biomass carbon\n    comments:\n    - If you provide this, correction factors used for conversion to the final units\n      and method are required\n    examples:\n    - value: 0.05 ug C/g dry soil\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000650\n    rank: 10\n    string_serialization: '{float} {unit}'\n    alias: microbial_biomass_c\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  microbial_biomass_n:\n    name: microbial_biomass_n\n    description: The part of the organic matter in the soil that constitutes living\n      microorganisms smaller than 5-10 micrometer.\n    title: microbial biomass nitrogen\n    comments:\n    - If you provide this, correction factors used for conversion to the final units\n      and method are required\n    examples:\n    - value: 0.05 ug N/g dry soil\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000650\n    rank: 12\n    string_serialization: '{float} {unit}'\n    alias: microbial_biomass_n\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  non_microb_biomass:\n    name: non_microb_biomass\n    description: Amount of biomass; should include the name for the part of biomass\n      measured, e.g.insect, plant, total. Can include multiple measurements separated\n      by ;\n    title: non-microbial biomass\n    examples:\n    - value: insect 0.23 ug; plant 1g\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000174\n    - MIXS:0000650\n    rank: 8\n    string_serialization: '{text};{float} {unit}'\n    alias: non_microb_biomass\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  non_microb_biomass_method:\n    name: non_microb_biomass_method\n    description: Reference or method used in determining biomass\n    title: non-microbial biomass method\n    comments:\n    - required if \"non-microbial biomass\" is provided\n    examples:\n    - value: https://doi.org/10.1038/s41467-021-26181-3\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000650\n    rank: 9\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    alias: non_microb_biomass_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  org_nitro_method:\n    name: org_nitro_method\n    description: Method used for obtaining organic nitrogen\n    title: organic nitrogen method\n    comments:\n    - required if \"org_nitro\" is provided\n    examples:\n    - value: https://doi.org/10.1016/0038-0717(85)90144-0\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000338\n    - MIXS:0000205\n    rank: 14\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    alias: org_nitro_method\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n  other_treatment:\n    name: other_treatment\n    description: Other treatments applied to your samples that are not applicable\n      to the provided fields\n    title: other treatments\n    notes:\n    - Values entered here will be used to determine potential new slots.\n    comments:\n    - This is an open text field to provide any treatments that cannot be captured\n      in the provided slots.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000300\n    rank: 15\n    string_serialization: '{text}'\n    alias: other_treatment\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  start_date_inc:\n    name: start_date_inc\n    description: Date the incubation was started. Only relevant for incubation samples.\n    title: incubation start date\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n      date only\n    comments:\n    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n      are all acceptable.\n    examples:\n    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 4\n    string_serialization: '{date, arbitrary precision}'\n    alias: start_date_inc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  start_time_inc:\n    name: start_time_inc\n    description: Time the incubation was started. Only relevant for incubation samples.\n    title: incubation start time, GMT\n    notes:\n    - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n      time only\n    comments:\n    - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n    examples:\n    - value: 13:33 or 13:33:55\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIXS:0000011\n    rank: 5\n    string_serialization: '{time, seconds optional}'\n    alias: start_time_inc\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: MIxS Inspired\n    range: string\n    recommended: true\n  project_id:\n    name: project_id\n    description: Proposal IDs or names associated with dataset\n    title: project ID\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1\n    string_serialization: '{text}'\n    alias: project_id\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: string\n    recommended: true\n  replicate_number:\n    name: replicate_number\n    description: If sending biological replicates, indicate the rep number here.\n    title: replicate number\n    comments:\n    - This will guide staff in ensuring your samples are blocked & randomized correctly\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 6\n    string_serialization: '{integer}'\n    alias: replicate_number\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: string\n    recommended: true\n  sample_shipped:\n    name: sample_shipped\n    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n      sample sent to EMSL.\n    title: sample shipped amount\n    comments:\n    - This field is only required when completing metadata for samples being submitted\n      to EMSL for analyses.\n    examples:\n    - value: 15 g\n    - value: 100 uL\n    - value: 5 mL\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 3\n    string_serialization: '{float} {unit}'\n    alias: sample_shipped\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: string\n    recommended: true\n  sample_type:\n    name: sample_type\n    description: Type of sample being submitted\n    title: sample type\n    comments:\n    - This can vary from 'environmental package' if the sample is an extraction.\n    examples:\n    - value: water extracted soil\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 2\n    alias: sample_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: SampleTypeEnum\n    recommended: true\n  technical_reps:\n    name: technical_reps\n    description: If sending technical replicates of the same sample, indicate the\n      replicate count.\n    title: number technical replicate\n    comments:\n    - This field is only required when completing metadata for samples being submitted\n      to EMSL for analyses.\n    examples:\n    - value: '2'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 5\n    string_serialization: '{integer}'\n    alias: technical_reps\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: EMSL\n    range: string\n    recommended: true\n  analysis_type:\n    name: analysis_type\n    description: Select all the data types associated or available for this biosample\n    title: analysis/data type\n    examples:\n    - value: metagenomics; metabolomics; proteomics\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - MIxS:investigation_type\n    rank: 3\n    alias: analysis_type\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: Sample ID\n    range: AnalysisTypeEnum\n    recommended: true\n    multivalued: true\n  sample_link:\n    name: sample_link\n    description: A unique identifier to assign parent-child, subsample, or sibling\n      samples. This is relevant when a sample or other material was used to generate\n      the new sample.\n    title: sample linkage\n    comments:\n    - 'This field allows multiple entries separated by ; (Examples: Soil collected\n      from the field will link with the soil used in an incubation. The soil a plant\n      was grown in links to the plant sample. An original culture sample was transferred\n      to a new vial and generated a new sample)'\n    examples:\n    - value: IGSN:DSJ0284\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 5\n    string_serialization: '{text}:{text}'\n    alias: sample_link\n    owner: Biosample\n    domain_of:\n    - Biosample\n    slot_group: Sample ID\n    range: string\n    recommended: true\n    multivalued: true\n  bulk_elect_conductivity:\n    name: bulk_elect_conductivity\n    description: Electrical conductivity is a measure of the ability to carry electric\n      current, which is mostly dictated by the chemistry of and amount of water.\n    title: bulk electrical conductivity\n    comments:\n    - Provide the value output of the field instrument.\n    examples:\n    - value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')\n      description: The conductivity measurement was 0.017 millisiemens per centimeter.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: bulk_elect_conductivity\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: QuantityValue\n  infiltrations:\n    name: infiltrations\n    description: The amount of time it takes to complete each infiltration activity\n    examples:\n    - value: '[''00:01:32'', ''00:00:53'']'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1\n    aliases:\n    - infiltration_1\n    - infiltration_2\n    rank: 1000\n    list_elements_ordered: true\n    alias: infiltrations\n    owner: Biosample\n    domain_of:\n    - Biosample\n    range: string\n    multivalued: true\n    pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$\n  id:\n    name: id\n    description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Biosample\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Biosample\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Biosample\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a biosample submitted to additional resources.\n      Matches the entity that has been submitted to NMDC\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Biosample\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Biosample\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Biosample\nunique_keys:\n  samp_name_unique_key:\n    unique_key_name: samp_name_unique_key\n    unique_key_slots:\n    - samp_name\nrules:\n- preconditions:\n    slot_conditions:\n      dna_cont_well:\n        name: dna_cont_well\n        pattern: .+\n  postconditions:\n    slot_conditions:\n      dna_cont_type:\n        name: dna_cont_type\n        equals_string: plate\n  description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n    have any value for their plate position.\n  title: dna_well_requires_plate\n- preconditions:\n    slot_conditions:\n      dna_cont_type:\n        name: dna_cont_type\n        equals_string: plate\n  postconditions:\n    slot_conditions:\n      dna_cont_well:\n        name: dna_cont_well\n        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  description: DNA samples in plates must have a plate position that matches the regex.\n    Note the requirement for an empty string in the tube case. Waiting for value_present\n    validation to be added to runtime\n  title: dna_plate_requires_well\n- preconditions:\n    slot_conditions:\n      rna_cont_well:\n        name: rna_cont_well\n        pattern: .+\n  postconditions:\n    slot_conditions:\n      rna_cont_type:\n        name: rna_cont_type\n        equals_string: plate\n  description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n    have any value for their plate position.\n  title: rna_well_requires_plate\n- preconditions:\n    slot_conditions:\n      rna_cont_type:\n        name: rna_cont_type\n        equals_string: plate\n  postconditions:\n    slot_conditions:\n      rna_cont_well:\n        name: rna_cont_well\n        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n  description: RNA samples in plates must have a plate position that matches the regex.\n    Note the requirement for an empty string in the tube case. Waiting for value_present\n    validation to be added to runtime\n  title: rna_plate_requires_well\n\n
"},{"location":"BiosampleCategoryEnum/","title":"Enum: BiosampleCategoryEnum","text":"

Funding-based, sample location-based, or experimental method-based defined categories

URI: BiosampleCategoryEnum

"},{"location":"BiosampleCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description LTER https://lternet.edu/ SIP None SFA https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance Science Focus Area projects funded through the Department of Energy Office of... FICUS https://jgi.doe.gov/user-programs/program-info/ficus-overview NEON https://www.neonscience.org"},{"location":"BiosampleCategoryEnum/#slots","title":"Slots","text":"Name Description biosample_categories"},{"location":"BiosampleCategoryEnum/#aliases","title":"Aliases","text":""},{"location":"BiosampleCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BiosampleCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"BiosampleCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: BiosampleCategoryEnum\ndescription: Funding-based, sample location-based, or experimental method-based defined\n  categories\nnotes:\n- Currently, these values can associated with biosamples via the biosample_categories\n  slot\n- They might also be applicable to other classes\n- They are intended to enable metadata search and or filtering, for example in the\n  NMDC data portal, https://data.microbiomedata.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- category tag\nrank: 1000\npermissible_values:\n  LTER:\n    text: LTER\n    meaning: https://lternet.edu/\n    title: National Science Foundation's Long Term Ecological Research Network\n  SIP:\n    text: SIP\n  SFA:\n    text: SFA\n    description: Science Focus Area projects funded through the Department of Energy\n      Office of Science Biological and Environmental Research Program\n    meaning: https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance\n    title: Department of Energy Office of Science Biological and Environmental Research\n      Program Laboratory Science Focus Areas\n  FICUS:\n    text: FICUS\n    meaning: https://jgi.doe.gov/user-programs/program-info/ficus-overview\n    title: Facilities Integrating Collaborations for User Science\n  NEON:\n    text: NEON\n    meaning: https://www.neonscience.org\n    title: National Science Foundation's National Ecological Observatory Network\n\n
"},{"location":"BioticRelationshipEnum/","title":"Enum: BioticRelationshipEnum","text":"

URI: BioticRelationshipEnum

"},{"location":"BioticRelationshipEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description free living None parasite None commensal None symbiont None"},{"location":"BioticRelationshipEnum/#slots","title":"Slots","text":"Name Description biotic_relationship Description of relationship(s) between the subject organism and other organis..."},{"location":"BioticRelationshipEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BioticRelationshipEnum/#schema-source","title":"Schema Source","text":""},{"location":"BioticRelationshipEnum/#linkml-source","title":"LinkML Source","text":"
name: biotic_relationship_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  free living:\n    text: free living\n  parasite:\n    text: parasite\n  commensal:\n    text: commensal\n  symbiont:\n    text: symbiont\n\n
"},{"location":"Boolean/","title":"Type: Boolean","text":"

A binary (true or false) value

URI: xsd:boolean

"},{"location":"Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Boolean/#schema-source","title":"Schema Source","text":""},{"location":"Boolean/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:boolean native nmdc:boolean exact schema:Boolean"},{"location":"BuildDocsEnum/","title":"Enum: BuildDocsEnum","text":"

URI: BuildDocsEnum

"},{"location":"BuildDocsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building information model None commissioning report None complaint logs None contract administration None cost estimate None janitorial schedules or logs None maintenance plans None schedule None sections None shop drawings None submittals None ventilation system None windows None"},{"location":"BuildDocsEnum/#slots","title":"Slots","text":"Name Description build_docs The building design, construction and operation documents"},{"location":"BuildDocsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildDocsEnum/#schema-source","title":"Schema Source","text":""},{"location":"BuildDocsEnum/#linkml-source","title":"LinkML Source","text":"
name: build_docs_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  building information model:\n    text: building information model\n  commissioning report:\n    text: commissioning report\n  complaint logs:\n    text: complaint logs\n  contract administration:\n    text: contract administration\n  cost estimate:\n    text: cost estimate\n  janitorial schedules or logs:\n    text: janitorial schedules or logs\n  maintenance plans:\n    text: maintenance plans\n  schedule:\n    text: schedule\n  sections:\n    text: sections\n  shop drawings:\n    text: shop drawings\n  submittals:\n    text: submittals\n  ventilation system:\n    text: ventilation system\n  windows:\n    text: windows\n\n
"},{"location":"BuildOccupTypeEnum/","title":"Enum: BuildOccupTypeEnum","text":"

URI: BuildOccupTypeEnum

"},{"location":"BuildOccupTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description office None market None restaurant None residence None school None residential None commercial None low rise None high rise None wood framed None health care None airport None sports complex None"},{"location":"BuildOccupTypeEnum/#slots","title":"Slots","text":"Name Description build_occup_type The primary function for which a building or discrete part of a building is i..."},{"location":"BuildOccupTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildOccupTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"BuildOccupTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: build_occup_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  office:\n    text: office\n  market:\n    text: market\n  restaurant:\n    text: restaurant\n  residence:\n    text: residence\n  school:\n    text: school\n  residential:\n    text: residential\n  commercial:\n    text: commercial\n  low rise:\n    text: low rise\n  high rise:\n    text: high rise\n  wood framed:\n    text: wood framed\n  health care:\n    text: health care\n  airport:\n    text: airport\n  sports complex:\n    text: sports complex\n\n
"},{"location":"BuildingSettingEnum/","title":"Enum: BuildingSettingEnum","text":"

URI: BuildingSettingEnum

"},{"location":"BuildingSettingEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description urban None suburban None exurban None rural None"},{"location":"BuildingSettingEnum/#slots","title":"Slots","text":"Name Description building_setting A location (geography) where a building is set"},{"location":"BuildingSettingEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildingSettingEnum/#schema-source","title":"Schema Source","text":""},{"location":"BuildingSettingEnum/#linkml-source","title":"LinkML Source","text":"
name: building_setting_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  urban:\n    text: urban\n  suburban:\n    text: suburban\n  exurban:\n    text: exurban\n  rural:\n    text: rural\n\n
"},{"location":"Bytes/","title":"Type: Bytes","text":"

An integer value that corresponds to a size in bytes

URI: xsd:long

"},{"location":"Bytes/#see-also","title":"See Also","text":""},{"location":"Bytes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Bytes/#schema-source","title":"Schema Source","text":""},{"location":"Bytes/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:long native nmdc:bytes"},{"location":"CalibrationInformation/","title":"Class: CalibrationInformation","text":"

A calibration object that is associated with a process.

URI: nmdc:CalibrationInformation

classDiagram\n  class CalibrationInformation\n  click CalibrationInformation href \"../CalibrationInformation\"\n    InformationObject <|-- CalibrationInformation\n      click InformationObject href \"../InformationObject\"\n\n\n\n  CalibrationInformation : alternative_identifiers\n\n  CalibrationInformation : calibration_object\n\n      CalibrationInformation --> \"0..1\" DataObject : calibration_object\n    click DataObject href \"../DataObject\"\n\n  CalibrationInformation : calibration_standard\n\n      CalibrationInformation --> \"0..1\" CalibrationStandardEnum : calibration_standard\n    click CalibrationStandardEnum href \"../CalibrationStandardEnum\"\n\n  CalibrationInformation : calibration_target\n\n      CalibrationInformation --> \"1\" CalibrationTargetEnum : calibration_target\n    click CalibrationTargetEnum href \"../CalibrationTargetEnum\"\n\n  CalibrationInformation : description\n\n  CalibrationInformation : id\n\n  CalibrationInformation : internal_calibration\n\n  CalibrationInformation : name\n\n  CalibrationInformation : type\n\n\n\n
"},{"location":"CalibrationInformation/#inheritance","title":"Inheritance","text":""},{"location":"CalibrationInformation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance calibration_object 0..1 DataObject the file containing calibration data object direct internal_calibration 1 Boolean whether internal calibration was used, if false, external calibration was use... direct calibration_target 1 CalibrationTargetEnum the target measurement of the calibration direct calibration_standard 0..1 CalibrationStandardEnum the reference standard(s) used for calibration direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"CalibrationInformation/#usages","title":"Usages","text":"used by used in type used MassSpectrometry has_calibration any_of[range] CalibrationInformation Database calibration_set range CalibrationInformation MetabolomicsAnalysis has_calibration any_of[range] CalibrationInformation NomAnalysis has_calibration any_of[range] CalibrationInformation"},{"location":"CalibrationInformation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationInformation/#schema-source","title":"Schema Source","text":""},{"location":"CalibrationInformation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:CalibrationInformation native nmdc:CalibrationInformation"},{"location":"CalibrationInformation/#linkml-source","title":"LinkML Source","text":""},{"location":"CalibrationInformation/#direct","title":"Direct","text":"
name: CalibrationInformation\ndescription: A calibration object that is associated with a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- calibration_object\n- internal_calibration\n- calibration_target\n- calibration_standard\nslot_usage:\n  internal_calibration:\n    name: internal_calibration\n    required: true\n  calibration_target:\n    name: calibration_target\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:CalibrationInformation\nrules:\n- preconditions:\n    slot_conditions:\n      calibration_target:\n        name: calibration_target\n        equals_string: retention_index\n  postconditions:\n    slot_conditions:\n      calibration_standard:\n        name: calibration_standard\n        required: true\n  description: If the calibration_target is retention_index, a calibration_standard\n    is required.\n  title: calibration_standard_if_rt\n- preconditions:\n    slot_conditions:\n      internal_calibration:\n        name: internal_calibration\n        id_prefixes:\n        - 'False'\n  postconditions:\n    slot_conditions:\n      calibration_object:\n        name: calibration_object\n        required: true\n  description: If internal_calibration is false, a calibration_object is required.\n  title: calibration_object_if_not_internal_calibration\n\n
"},{"location":"CalibrationInformation/#induced","title":"Induced","text":"
name: CalibrationInformation\ndescription: A calibration object that is associated with a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n  internal_calibration:\n    name: internal_calibration\n    required: true\n  calibration_target:\n    name: calibration_target\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  calibration_object:\n    name: calibration_object\n    description: the file containing calibration data object\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: calibration_object\n    owner: CalibrationInformation\n    domain_of:\n    - CalibrationInformation\n    range: DataObject\n  internal_calibration:\n    name: internal_calibration\n    description: whether internal calibration was used, if false, external calibration\n      was used\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: internal_calibration\n    owner: CalibrationInformation\n    domain_of:\n    - CalibrationInformation\n    range: boolean\n    required: true\n  calibration_target:\n    name: calibration_target\n    description: the target measurement of the calibration\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: calibration_target\n    owner: CalibrationInformation\n    domain_of:\n    - CalibrationInformation\n    range: CalibrationTargetEnum\n    required: true\n  calibration_standard:\n    name: calibration_standard\n    description: the reference standard(s) used for calibration\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: calibration_standard\n    owner: CalibrationInformation\n    domain_of:\n    - CalibrationInformation\n    range: CalibrationStandardEnum\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CalibrationInformation\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: CalibrationInformation\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: CalibrationInformation\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: CalibrationInformation\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: CalibrationInformation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:CalibrationInformation\nrules:\n- preconditions:\n    slot_conditions:\n      calibration_target:\n        name: calibration_target\n        equals_string: retention_index\n  postconditions:\n    slot_conditions:\n      calibration_standard:\n        name: calibration_standard\n        required: true\n  description: If the calibration_target is retention_index, a calibration_standard\n    is required.\n  title: calibration_standard_if_rt\n- preconditions:\n    slot_conditions:\n      internal_calibration:\n        name: internal_calibration\n        id_prefixes:\n        - 'False'\n  postconditions:\n    slot_conditions:\n      calibration_object:\n        name: calibration_object\n        required: true\n  description: If internal_calibration is false, a calibration_object is required.\n  title: calibration_object_if_not_internal_calibration\n\n
"},{"location":"CalibrationStandardEnum/","title":"Enum: CalibrationStandardEnum","text":"

URI: CalibrationStandardEnum

"},{"location":"CalibrationStandardEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fames None alkanes None"},{"location":"CalibrationStandardEnum/#slots","title":"Slots","text":"Name Description calibration_standard the reference standard(s) used for calibration"},{"location":"CalibrationStandardEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationStandardEnum/#schema-source","title":"Schema Source","text":""},{"location":"CalibrationStandardEnum/#linkml-source","title":"LinkML Source","text":"
name: CalibrationStandardEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  fames:\n    text: fames\n    aliases:\n    - FAMES\n  alkanes:\n    text: alkanes\n    aliases:\n    - Alkanes\n\n
"},{"location":"CalibrationTargetEnum/","title":"Enum: CalibrationTargetEnum","text":"

URI: CalibrationTargetEnum

"},{"location":"CalibrationTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mass_charge_ratio None retention_time None retention_index None"},{"location":"CalibrationTargetEnum/#slots","title":"Slots","text":"Name Description calibration_target the target measurement of the calibration"},{"location":"CalibrationTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationTargetEnum/#schema-source","title":"Schema Source","text":""},{"location":"CalibrationTargetEnum/#linkml-source","title":"LinkML Source","text":"
name: CalibrationTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  mass_charge_ratio:\n    text: mass_charge_ratio\n    title: m/z\n    aliases:\n    - Mass\n    - m/z\n  retention_time:\n    text: retention_time\n    aliases:\n    - RT\n  retention_index:\n    text: retention_index\n    aliases:\n    - RI\n\n
"},{"location":"CeilCondEnum/","title":"Enum: CeilCondEnum","text":"

URI: CeilCondEnum

"},{"location":"CeilCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"CeilCondEnum/#slots","title":"Slots","text":"Name Description ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide..."},{"location":"CeilCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"CeilCondEnum/#linkml-source","title":"LinkML Source","text":"
name: ceil_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  new:\n    text: new\n  visible wear:\n    text: visible wear\n  needs repair:\n    text: needs repair\n  damaged:\n    text: damaged\n  rupture:\n    text: rupture\n\n
"},{"location":"CeilFinishMatEnum/","title":"Enum: CeilFinishMatEnum","text":"

URI: CeilFinishMatEnum

"},{"location":"CeilFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drywall None mineral fibre None tiles None PVC None plasterboard None metal None fiberglass None stucco None mineral wool/calcium silicate None wood None"},{"location":"CeilFinishMatEnum/#slots","title":"Slots","text":"Name Description ceil_finish_mat The type of material used to finish a ceiling"},{"location":"CeilFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilFinishMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"CeilFinishMatEnum/#linkml-source","title":"LinkML Source","text":"
name: ceil_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  drywall:\n    text: drywall\n  mineral fibre:\n    text: mineral fibre\n  tiles:\n    text: tiles\n  PVC:\n    text: PVC\n  plasterboard:\n    text: plasterboard\n  metal:\n    text: metal\n  fiberglass:\n    text: fiberglass\n  stucco:\n    text: stucco\n  mineral wool/calcium silicate:\n    text: mineral wool/calcium silicate\n  wood:\n    text: wood\n\n
"},{"location":"CeilTextureEnum/","title":"Enum: CeilTextureEnum","text":"

URI: CeilTextureEnum

"},{"location":"CeilTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"CeilTextureEnum/#slots","title":"Slots","text":"Name Description ceil_texture The feel, appearance, or consistency of a ceiling surface"},{"location":"CeilTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTextureEnum/#schema-source","title":"Schema Source","text":""},{"location":"CeilTextureEnum/#linkml-source","title":"LinkML Source","text":"
name: ceil_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  crows feet:\n    text: crows feet\n  crows-foot stomp:\n    text: crows-foot stomp\n  double skip:\n    text: double skip\n  hawk and trowel:\n    text: hawk and trowel\n  knockdown:\n    text: knockdown\n  popcorn:\n    text: popcorn\n  orange peel:\n    text: orange peel\n  rosebud stomp:\n    text: rosebud stomp\n  Santa-Fe texture:\n    text: Santa-Fe texture\n  skip trowel:\n    text: skip trowel\n  smooth:\n    text: smooth\n  stomp knockdown:\n    text: stomp knockdown\n  swirl:\n    text: swirl\n\n
"},{"location":"CeilTypeEnum/","title":"Enum: CeilTypeEnum","text":"

URI: CeilTypeEnum

"},{"location":"CeilTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cathedral None dropped None concave None barrel-shaped None coffered None cove None stretched None"},{"location":"CeilTypeEnum/#slots","title":"Slots","text":"Name Description ceil_type The type of ceiling according to the ceiling's appearance or construction"},{"location":"CeilTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"CeilTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: ceil_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  cathedral:\n    text: cathedral\n  dropped:\n    text: dropped\n  concave:\n    text: concave\n  barrel-shaped:\n    text: barrel-shaped\n  coffered:\n    text: coffered\n  cove:\n    text: cove\n  stretched:\n    text: stretched\n\n
"},{"location":"Checklist/","title":"Subset: Checklist","text":"

A MIxS checklist. These can be combined with packages

URI: Checklist

"},{"location":"Checklist/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Checklist/#schema-source","title":"Schema Source","text":""},{"location":"ChecklistPackageCombination/","title":"Subset: ChecklistPackageCombination","text":"

A combination of a checklist and a package

URI: ChecklistPackageCombination

"},{"location":"ChecklistPackageCombination/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChecklistPackageCombination/#schema-source","title":"Schema Source","text":""},{"location":"ChemicalConversionCategoryEnum/","title":"Enum: ChemicalConversionCategoryEnum","text":"

URI: ChemicalConversionCategoryEnum

"},{"location":"ChemicalConversionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description addition None substitution None acid_base None reduction_oxidation None combustion None decomposition None protease_cleavage OBI:0600056 an enzymatic cleavage which relies on an enzyme with protease activity to act..."},{"location":"ChemicalConversionCategoryEnum/#slots","title":"Slots","text":"Name Description chemical_conversion_category The type of chemical conversion process"},{"location":"ChemicalConversionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalConversionCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ChemicalConversionCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ChemicalConversionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  addition:\n    text: addition\n  substitution:\n    text: substitution\n  acid_base:\n    text: acid_base\n  reduction_oxidation:\n    text: reduction_oxidation\n  combustion:\n    text: combustion\n  decomposition:\n    text: decomposition\n  protease_cleavage:\n    text: protease_cleavage\n    description: an enzymatic cleavage which relies on an enzyme with protease activity\n      to act on proteins and to produce polypeptides (protein fragments).\n    meaning: OBI:0600056\n\n
"},{"location":"ChemicalConversionProcess/","title":"Class: ChemicalConversionProcess","text":"

A process that results in the interconversion of chemical species by a reaction to transform the reagents into products.

__

URI: nmdc:ChemicalConversionProcess

classDiagram\n  class ChemicalConversionProcess\n  click ChemicalConversionProcess href \"../ChemicalConversionProcess\"\n    MaterialProcessing <|-- ChemicalConversionProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  ChemicalConversionProcess : alternative_identifiers\n\n  ChemicalConversionProcess : chemical_conversion_category\n\n      ChemicalConversionProcess --> \"0..1\" ChemicalConversionCategoryEnum : chemical_conversion_category\n    click ChemicalConversionCategoryEnum href \"../ChemicalConversionCategoryEnum\"\n\n  ChemicalConversionProcess : description\n\n  ChemicalConversionProcess : duration\n\n      ChemicalConversionProcess --> \"0..1\" QuantityValue : duration\n    click QuantityValue href \"../QuantityValue\"\n\n  ChemicalConversionProcess : end_date\n\n  ChemicalConversionProcess : has_failure_categorization\n\n      ChemicalConversionProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ChemicalConversionProcess : has_input\n\n      ChemicalConversionProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ChemicalConversionProcess : has_output\n\n      ChemicalConversionProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  ChemicalConversionProcess : id\n\n  ChemicalConversionProcess : instrument_used\n\n      ChemicalConversionProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  ChemicalConversionProcess : name\n\n  ChemicalConversionProcess : processing_institution\n\n      ChemicalConversionProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ChemicalConversionProcess : protocol_link\n\n      ChemicalConversionProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ChemicalConversionProcess : qc_comment\n\n  ChemicalConversionProcess : qc_status\n\n      ChemicalConversionProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ChemicalConversionProcess : start_date\n\n  ChemicalConversionProcess : substances_used\n\n      ChemicalConversionProcess --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  ChemicalConversionProcess : substances_volume\n\n      ChemicalConversionProcess --> \"0..1\" QuantityValue : substances_volume\n    click QuantityValue href \"../QuantityValue\"\n\n  ChemicalConversionProcess : temperature\n\n      ChemicalConversionProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  ChemicalConversionProcess : type\n\n\n\n
"},{"location":"ChemicalConversionProcess/#inheritance","title":"Inheritance","text":""},{"location":"ChemicalConversionProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance chemical_conversion_category 0..1 ChemicalConversionCategoryEnum The type of chemical conversion process direct duration 0..1 QuantityValue The elapsed time of an activity direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct substances_used * PortionOfSubstance The substances that are combined to enable a ChemicalConversionProcess direct substances_volume 0..1 QuantityValue The volume of the combined substances that was included in a ChemicalConversi... direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ChemicalConversionProcess/#aliases","title":"Aliases","text":""},{"location":"ChemicalConversionProcess/#comments","title":"Comments","text":""},{"location":"ChemicalConversionProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalConversionProcess/#schema-source","title":"Schema Source","text":""},{"location":"ChemicalConversionProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ChemicalConversionProcess native nmdc:ChemicalConversionProcess exact MISO:0000001"},{"location":"ChemicalConversionProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"ChemicalConversionProcess/#direct","title":"Direct","text":"
name: ChemicalConversionProcess\ndescription: 'A process that results in the interconversion of chemical species by\n  a reaction to transform the reagents into products.\n\n  '\ncomments:\n- The values of both has_reagents slot and has_input slot are considered the reagents\n  of a chemical process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical reaction\nexact_mappings:\n- MISO:0000001\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- chemical_conversion_category\n- duration\n- temperature\n- substances_used\n- substances_volume\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ChemicalConversionProcess\n\n
"},{"location":"ChemicalConversionProcess/#induced","title":"Induced","text":"
name: ChemicalConversionProcess\ndescription: 'A process that results in the interconversion of chemical species by\n  a reaction to transform the reagents into products.\n\n  '\ncomments:\n- The values of both has_reagents slot and has_input slot are considered the reagents\n  of a chemical process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical reaction\nexact_mappings:\n- MISO:0000001\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  chemical_conversion_category:\n    name: chemical_conversion_category\n    description: The type of chemical conversion process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: chemical_conversion_category\n    owner: ChemicalConversionProcess\n    domain_of:\n    - ChemicalConversionProcess\n    range: ChemicalConversionCategoryEnum\n  duration:\n    name: duration\n    description: The elapsed time of an activity.\n    examples:\n    - value: JsonObj(has_numeric_value=2, has_unit='hours')\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: duration\n    owner: ChemicalConversionProcess\n    domain_of:\n    - MixingProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: QuantityValue\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: ChemicalConversionProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  substances_used:\n    name: substances_used\n    description: The substances that are combined to enable a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: ChemicalConversionProcess\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  substances_volume:\n    name: substances_volume\n    description: The volume of the combined substances that was included in a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_volume\n    owner: ChemicalConversionProcess\n    domain_of:\n    - ChemicalConversionProcess\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: ChemicalConversionProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalConversionProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ChemicalConversionProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ChemicalConversionProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ChemicalConversionProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ChemicalConversionProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ChemicalConversionProcess\n\n
"},{"location":"ChemicalEntity/","title":"Class: ChemicalEntity","text":"

An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states

URI: nmdc:ChemicalEntity

classDiagram\n  class ChemicalEntity\n  click ChemicalEntity href \"../ChemicalEntity\"\n    OntologyClass <|-- ChemicalEntity\n      click OntologyClass href \"../OntologyClass\"\n\n\n\n  ChemicalEntity : alternative_identifiers\n\n  ChemicalEntity : alternative_names\n\n  ChemicalEntity : chemical_formula\n\n  ChemicalEntity : description\n\n  ChemicalEntity : id\n\n  ChemicalEntity : inchi\n\n  ChemicalEntity : inchi_key\n\n  ChemicalEntity : name\n\n  ChemicalEntity : smiles\n\n  ChemicalEntity : type\n\n\n\n
"},{"location":"ChemicalEntity/#inheritance","title":"Inheritance","text":""},{"location":"ChemicalEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance alternative_names * String A list of alternative names used to refer to the entity direct chemical_formula 0..1 String A generic grouping for molecular formulae and empirical formulae direct inchi 0..1 String direct inchi_key 0..1 String direct smiles * String A string encoding of a molecular graph, no chiral or isotopic information direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ChemicalEntity/#usages","title":"Usages","text":"used by used in type used Database chemical_entity_set range ChemicalEntity PortionOfSubstance known_as range ChemicalEntity MetaboliteIdentification metabolite_identified range ChemicalEntity"},{"location":"ChemicalEntity/#aliases","title":"Aliases","text":""},{"location":"ChemicalEntity/#comments","title":"Comments","text":""},{"location":"ChemicalEntity/#see-also","title":"See Also","text":""},{"location":"ChemicalEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalEntity/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"ChemicalEntity/#schema-source","title":"Schema Source","text":""},{"location":"ChemicalEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ChemicalEntity native nmdc:ChemicalEntity exact biolink:ChemicalSubstance"},{"location":"ChemicalEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"ChemicalEntity/#direct","title":"Direct","text":"
name: ChemicalEntity\nid_prefixes:\n- cas\n- CHEBI\n- CHEMBL.COMPOUND\n- DRUGBANK\n- HMDB\n- KEGG.COMPOUND\n- MESH\n- PUBCHEM.COMPOUND\ndescription: An atom or molecule that can be represented with a chemical formula.\n  Include lipids, glycans, natural products, drugs. There may be different terms for\n  distinct acid-base forms, protonation states\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n  to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nslots:\n- alternative_names\n- chemical_formula\n- inchi\n- inchi_key\n- smiles\nclass_uri: nmdc:ChemicalEntity\n\n
"},{"location":"ChemicalEntity/#induced","title":"Induced","text":"
name: ChemicalEntity\nid_prefixes:\n- cas\n- CHEBI\n- CHEMBL.COMPOUND\n- DRUGBANK\n- HMDB\n- KEGG.COMPOUND\n- MESH\n- PUBCHEM.COMPOUND\ndescription: An atom or molecule that can be represented with a chemical formula.\n  Include lipids, glycans, natural products, drugs. There may be different terms for\n  distinct acid-base forms, protonation states\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n  to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nattributes:\n  alternative_names:\n    name: alternative_names\n    description: A list of alternative names used to refer to the entity. The distinction\n      between name and alternative names is application-specific.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - dcterms:alternative\n    - skos:altLabel\n    rank: 1000\n    alias: alternative_names\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    - Study\n    range: string\n    multivalued: true\n  chemical_formula:\n    name: chemical_formula\n    description: A generic grouping for molecular formulae and empirical formulae\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: chemical_formula\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    range: string\n  inchi:\n    name: inchi\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: inchi\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    range: string\n  inchi_key:\n    name: inchi_key\n    notes:\n    - 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n      K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n      testing. J Cheminform. 4:12'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: inchi_key\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    range: string\n  smiles:\n    name: smiles\n    description: A string encoding of a molecular graph, no chiral or isotopic information.\n      There are usually a large number of valid SMILES which represent a given structure.\n      For example, CCO, OCC and C(O)C all specify the structure of ethanol.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: smiles\n    owner: ChemicalEntity\n    domain_of:\n    - ChemicalEntity\n    range: string\n    multivalued: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChemicalEntity\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ChemicalEntity\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ChemicalEntity\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ChemicalEntity\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ChemicalEntity\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ChemicalEntity\n\n
"},{"location":"ChromatographicCategoryEnum/","title":"Enum: ChromatographicCategoryEnum","text":"

URI: ChromatographicCategoryEnum

"},{"location":"ChromatographicCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description liquid_chromatography None gas_chromatography None solid_phase_extraction None"},{"location":"ChromatographicCategoryEnum/#slots","title":"Slots","text":"Name Description chromatographic_category The type of chromatography used in a process"},{"location":"ChromatographicCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChromatographicCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ChromatographicCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ChromatographicCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  liquid_chromatography:\n    text: liquid_chromatography\n    aliases:\n    - LC\n  gas_chromatography:\n    text: gas_chromatography\n    aliases:\n    - GC\n  solid_phase_extraction:\n    text: solid_phase_extraction\n    aliases:\n    - SPE\n\n
"},{"location":"ChromatographicSeparationProcess/","title":"Class: ChromatographicSeparationProcess","text":"

The process of using a selective partitioning of the analyte or interferent between two immiscible phases.

URI: nmdc:ChromatographicSeparationProcess

classDiagram\n  class ChromatographicSeparationProcess\n  click ChromatographicSeparationProcess href \"../ChromatographicSeparationProcess\"\n    MaterialProcessing <|-- ChromatographicSeparationProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  ChromatographicSeparationProcess : alternative_identifiers\n\n  ChromatographicSeparationProcess : chromatographic_category\n\n      ChromatographicSeparationProcess --> \"0..1\" ChromatographicCategoryEnum : chromatographic_category\n    click ChromatographicCategoryEnum href \"../ChromatographicCategoryEnum\"\n\n  ChromatographicSeparationProcess : description\n\n  ChromatographicSeparationProcess : end_date\n\n  ChromatographicSeparationProcess : has_failure_categorization\n\n      ChromatographicSeparationProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ChromatographicSeparationProcess : has_input\n\n      ChromatographicSeparationProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ChromatographicSeparationProcess : has_output\n\n      ChromatographicSeparationProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  ChromatographicSeparationProcess : id\n\n  ChromatographicSeparationProcess : instrument_used\n\n      ChromatographicSeparationProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  ChromatographicSeparationProcess : name\n\n  ChromatographicSeparationProcess : ordered_mobile_phases\n\n      ChromatographicSeparationProcess --> \"*\" MobilePhaseSegment : ordered_mobile_phases\n    click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n  ChromatographicSeparationProcess : processing_institution\n\n      ChromatographicSeparationProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ChromatographicSeparationProcess : protocol_link\n\n      ChromatographicSeparationProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ChromatographicSeparationProcess : qc_comment\n\n  ChromatographicSeparationProcess : qc_status\n\n      ChromatographicSeparationProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ChromatographicSeparationProcess : start_date\n\n  ChromatographicSeparationProcess : stationary_phase\n\n      ChromatographicSeparationProcess --> \"0..1\" StationaryPhaseEnum : stationary_phase\n    click StationaryPhaseEnum href \"../StationaryPhaseEnum\"\n\n  ChromatographicSeparationProcess : temperature\n\n      ChromatographicSeparationProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  ChromatographicSeparationProcess : type\n\n\n\n
"},{"location":"ChromatographicSeparationProcess/#inheritance","title":"Inheritance","text":""},{"location":"ChromatographicSeparationProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance chromatographic_category 0..1 ChromatographicCategoryEnum The type of chromatography used in a process direct ordered_mobile_phases * MobilePhaseSegment The solution(s) that moves through a chromatography column direct stationary_phase 0..1 StationaryPhaseEnum The material the stationary phase is comprised of used in chromatography direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ChromatographicSeparationProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChromatographicSeparationProcess/#schema-source","title":"Schema Source","text":""},{"location":"ChromatographicSeparationProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ChromatographicSeparationProcess native nmdc:ChromatographicSeparationProcess"},{"location":"ChromatographicSeparationProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"ChromatographicSeparationProcess/#direct","title":"Direct","text":"
name: ChromatographicSeparationProcess\ndescription: The process of using a selective partitioning of the analyte or interferent\n  between two immiscible phases.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- chromatographic_category\n- ordered_mobile_phases\n- stationary_phase\n- temperature\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ChromatographicSeparationProcess\n\n
"},{"location":"ChromatographicSeparationProcess/#induced","title":"Induced","text":"
name: ChromatographicSeparationProcess\ndescription: The process of using a selective partitioning of the analyte or interferent\n  between two immiscible phases.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  chromatographic_category:\n    name: chromatographic_category\n    description: The type of chromatography used in a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: chromatographic_category\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: ChromatographicCategoryEnum\n  ordered_mobile_phases:\n    name: ordered_mobile_phases\n    description: The solution(s) that moves through a chromatography column.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    list_elements_ordered: true\n    alias: ordered_mobile_phases\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: MobilePhaseSegment\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  stationary_phase:\n    name: stationary_phase\n    description: The material the stationary phase is comprised of used in chromatography.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: stationary_phase\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: StationaryPhaseEnum\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ChromatographicSeparationProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ChromatographicSeparationProcess\n\n
"},{"location":"ChromatographyConfiguration/","title":"Class: ChromatographyConfiguration","text":"

A set of parameters that define and control the actions of a chromatography process.

URI: nmdc:ChromatographyConfiguration

classDiagram\n  class ChromatographyConfiguration\n  click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n    Configuration <|-- ChromatographyConfiguration\n      click Configuration href \"../Configuration\"\n\n\n\n  ChromatographyConfiguration : alternative_identifiers\n\n  ChromatographyConfiguration : chromatographic_category\n\n      ChromatographyConfiguration --> \"0..1\" ChromatographicCategoryEnum : chromatographic_category\n    click ChromatographicCategoryEnum href \"../ChromatographicCategoryEnum\"\n\n  ChromatographyConfiguration : description\n\n  ChromatographyConfiguration : id\n\n  ChromatographyConfiguration : name\n\n  ChromatographyConfiguration : ordered_mobile_phases\n\n      ChromatographyConfiguration --> \"*\" MobilePhaseSegment : ordered_mobile_phases\n    click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n  ChromatographyConfiguration : stationary_phase\n\n      ChromatographyConfiguration --> \"0..1\" StationaryPhaseEnum : stationary_phase\n    click StationaryPhaseEnum href \"../StationaryPhaseEnum\"\n\n  ChromatographyConfiguration : temperature\n\n      ChromatographyConfiguration --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  ChromatographyConfiguration : type\n\n\n\n
"},{"location":"ChromatographyConfiguration/#inheritance","title":"Inheritance","text":""},{"location":"ChromatographyConfiguration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance chromatographic_category 0..1 ChromatographicCategoryEnum The type of chromatography used in a process direct ordered_mobile_phases * MobilePhaseSegment The solution(s) that moves through a chromatography column direct stationary_phase 0..1 StationaryPhaseEnum The material the stationary phase is comprised of used in chromatography direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 1 String A human readable label for an entity NamedThing description 1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ChromatographyConfiguration/#usages","title":"Usages","text":"used by used in type used MassSpectrometry has_chromatography_configuration range ChromatographyConfiguration"},{"location":"ChromatographyConfiguration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChromatographyConfiguration/#schema-source","title":"Schema Source","text":""},{"location":"ChromatographyConfiguration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ChromatographyConfiguration native nmdc:ChromatographyConfiguration"},{"location":"ChromatographyConfiguration/#linkml-source","title":"LinkML Source","text":""},{"location":"ChromatographyConfiguration/#direct","title":"Direct","text":"
name: ChromatographyConfiguration\ndescription: A set of parameters that define and control the actions of a chromatography\n  process.\nnotes:\n- This class is intended to represent a chromatography method file associated with\n  a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslots:\n- chromatographic_category\n- ordered_mobile_phases\n- stationary_phase\n- temperature\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ChromatographyConfiguration\n\n
"},{"location":"ChromatographyConfiguration/#induced","title":"Induced","text":"
name: ChromatographyConfiguration\ndescription: A set of parameters that define and control the actions of a chromatography\n  process.\nnotes:\n- This class is intended to represent a chromatography method file associated with\n  a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  chromatographic_category:\n    name: chromatographic_category\n    description: The type of chromatography used in a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: chromatographic_category\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: ChromatographicCategoryEnum\n  ordered_mobile_phases:\n    name: ordered_mobile_phases\n    description: The solution(s) that moves through a chromatography column.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    list_elements_ordered: true\n    alias: ordered_mobile_phases\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: MobilePhaseSegment\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  stationary_phase:\n    name: stationary_phase\n    description: The material the stationary phase is comprised of used in chromatography.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: stationary_phase\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ChromatographyConfiguration\n    - ChromatographicSeparationProcess\n    range: StationaryPhaseEnum\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ChromatographyConfiguration\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ChromatographyConfiguration\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n    required: true\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ChromatographyConfiguration\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n    required: true\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ChromatographyConfiguration\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ChromatographyConfiguration\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ChromatographyConfiguration\n\n
"},{"location":"CollectingBiosamplesFromSite/","title":"Class: Collecting Biosamples From Site (CollectingBiosamplesFromSite)","text":"

URI: nmdc:CollectingBiosamplesFromSite

classDiagram\n  class CollectingBiosamplesFromSite\n  click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n    PlannedProcess <|-- CollectingBiosamplesFromSite\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n\n  CollectingBiosamplesFromSite : alternative_identifiers\n\n  CollectingBiosamplesFromSite : description\n\n  CollectingBiosamplesFromSite : end_date\n\n  CollectingBiosamplesFromSite : has_failure_categorization\n\n      CollectingBiosamplesFromSite --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  CollectingBiosamplesFromSite : has_input\n\n      CollectingBiosamplesFromSite --> \"1..*\" Site : has_input\n    click Site href \"../Site\"\n\n  CollectingBiosamplesFromSite : has_output\n\n      CollectingBiosamplesFromSite --> \"1..*\" Biosample : has_output\n    click Biosample href \"../Biosample\"\n\n  CollectingBiosamplesFromSite : id\n\n  CollectingBiosamplesFromSite : name\n\n  CollectingBiosamplesFromSite : processing_institution\n\n      CollectingBiosamplesFromSite --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  CollectingBiosamplesFromSite : protocol_link\n\n      CollectingBiosamplesFromSite --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  CollectingBiosamplesFromSite : qc_comment\n\n  CollectingBiosamplesFromSite : qc_status\n\n      CollectingBiosamplesFromSite --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  CollectingBiosamplesFromSite : start_date\n\n  CollectingBiosamplesFromSite : type\n\n\n\n
"},{"location":"CollectingBiosamplesFromSite/#inheritance","title":"Inheritance","text":""},{"location":"CollectingBiosamplesFromSite/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_input 1..* Site An input to a process PlannedProcess has_output 1..* Biosample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"CollectingBiosamplesFromSite/#usages","title":"Usages","text":"used by used in type used Database collecting_biosamples_from_site_set range CollectingBiosamplesFromSite"},{"location":"CollectingBiosamplesFromSite/#comments","title":"Comments","text":""},{"location":"CollectingBiosamplesFromSite/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CollectingBiosamplesFromSite/#schema-source","title":"Schema Source","text":""},{"location":"CollectingBiosamplesFromSite/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:CollectingBiosamplesFromSite native nmdc:CollectingBiosamplesFromSite close OBI:0000744"},{"location":"CollectingBiosamplesFromSite/#linkml-source","title":"LinkML Source","text":""},{"location":"CollectingBiosamplesFromSite/#direct","title":"Direct","text":"
name: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n  has_input:\n    name: has_input\n    range: Site\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    range: Biosample\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:CollectingBiosamplesFromSite\n\n
"},{"location":"CollectingBiosamplesFromSite/#induced","title":"Induced","text":"
name: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n  has_input:\n    name: has_input\n    range: Site\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    range: Biosample\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: Site\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: Biosample\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: CollectingBiosamplesFromSite\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:CollectingBiosamplesFromSite\n\n
"},{"location":"Configuration/","title":"Class: Configuration","text":"

A set of parameters that define the actions of a process and is shared among multiple instances of the process.

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:Configuration

classDiagram\n  class Configuration\n  click Configuration href \"../Configuration\"\n    InformationObject <|-- Configuration\n      click InformationObject href \"../InformationObject\"\n\n\n    Configuration <|-- MassSpectrometryConfiguration\n      click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n    Configuration <|-- ChromatographyConfiguration\n      click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n\n\n\n  Configuration : alternative_identifiers\n\n  Configuration : description\n\n  Configuration : id\n\n  Configuration : name\n\n  Configuration : type\n\n\n\n
"},{"location":"Configuration/#inheritance","title":"Inheritance","text":""},{"location":"Configuration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Configuration/#usages","title":"Usages","text":"used by used in type used Database configuration_set range Configuration"},{"location":"Configuration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Configuration/#schema-source","title":"Schema Source","text":""},{"location":"Configuration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Configuration native nmdc:Configuration"},{"location":"Configuration/#linkml-source","title":"LinkML Source","text":""},{"location":"Configuration/#direct","title":"Direct","text":"
name: Configuration\ndescription: A set of parameters that define the actions of a process and is shared\n  among multiple instances of the process.\nnotes:\n- This class is intended to represent the parameters within a method file (or similar)\n  that control a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nabstract: true\nclass_uri: nmdc:Configuration\n\n
"},{"location":"Configuration/#induced","title":"Induced","text":"
name: Configuration\ndescription: A set of parameters that define the actions of a process and is shared\n  among multiple instances of the process.\nnotes:\n- This class is intended to represent the parameters within a method file (or similar)\n  that control a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Configuration\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Configuration\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Configuration\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Configuration\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Configuration\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Configuration\n\n
"},{"location":"ContainerCategoryEnum/","title":"Enum: ContainerCategoryEnum","text":"

The permitted types of containers used in processing metabolomic samples.

URI: ContainerCategoryEnum

"},{"location":"ContainerCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description v-bottom_conical_tube None falcon_tube None"},{"location":"ContainerCategoryEnum/#slots","title":"Slots","text":"Name Description contained_in A type of container"},{"location":"ContainerCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ContainerCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ContainerCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ContainerCategoryEnum\ndescription: The permitted types of containers used in processing metabolomic samples.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\npermissible_values:\n  v-bottom_conical_tube:\n    text: v-bottom_conical_tube\n  falcon_tube:\n    text: falcon_tube\n\n
"},{"location":"ControlledIdentifiedTermValue/","title":"Class: ControlledIdentifiedTermValue","text":"

A controlled term or class from an ontology, requiring the presence of term with an id

URI: nmdc:ControlledIdentifiedTermValue

classDiagram\n  class ControlledIdentifiedTermValue\n  click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n    ControlledTermValue <|-- ControlledIdentifiedTermValue\n      click ControlledTermValue href \"../ControlledTermValue\"\n\n\n\n  ControlledIdentifiedTermValue : has_raw_value\n\n  ControlledIdentifiedTermValue : term\n\n      ControlledIdentifiedTermValue --> \"1\" OntologyClass : term\n    click OntologyClass href \"../OntologyClass\"\n\n  ControlledIdentifiedTermValue : type\n\n\n\n
"},{"location":"ControlledIdentifiedTermValue/#inheritance","title":"Inheritance","text":""},{"location":"ControlledIdentifiedTermValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance term 1 OntologyClass pointer to an ontology class ControlledTermValue has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"ControlledIdentifiedTermValue/#usages","title":"Usages","text":"used by used in type used Biosample host_taxid range ControlledIdentifiedTermValue Biosample env_broad_scale range ControlledIdentifiedTermValue Biosample env_local_scale range ControlledIdentifiedTermValue Biosample env_medium range ControlledIdentifiedTermValue Biosample samp_taxon_id range ControlledIdentifiedTermValue GenomeFeature feature_category range ControlledIdentifiedTermValue FunctionalAnnotation feature_category range ControlledIdentifiedTermValue"},{"location":"ControlledIdentifiedTermValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ControlledIdentifiedTermValue/#schema-source","title":"Schema Source","text":""},{"location":"ControlledIdentifiedTermValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ControlledIdentifiedTermValue native nmdc:ControlledIdentifiedTermValue"},{"location":"ControlledIdentifiedTermValue/#linkml-source","title":"LinkML Source","text":""},{"location":"ControlledIdentifiedTermValue/#direct","title":"Direct","text":"
name: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n  term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n  term:\n    name: term\n    required: true\nclass_uri: nmdc:ControlledIdentifiedTermValue\n\n
"},{"location":"ControlledIdentifiedTermValue/#induced","title":"Induced","text":"
name: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n  term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n  term:\n    name: term\n    required: true\nattributes:\n  term:\n    name: term\n    description: pointer to an ontology class\n    notes:\n    - 'removed ''slot_uri: rdf:type'''\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: term\n    owner: ControlledIdentifiedTermValue\n    domain_of:\n    - ControlledTermValue\n    range: OntologyClass\n    required: true\n    inlined: true\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: ControlledIdentifiedTermValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ControlledIdentifiedTermValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ControlledIdentifiedTermValue\n\n
"},{"location":"ControlledTermValue/","title":"Class: ControlledTermValue","text":"

A controlled term or class from an ontology

URI: nmdc:ControlledTermValue

classDiagram\n  class ControlledTermValue\n  click ControlledTermValue href \"../ControlledTermValue\"\n    AttributeValue <|-- ControlledTermValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n    ControlledTermValue <|-- ControlledIdentifiedTermValue\n      click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n\n\n  ControlledTermValue : has_raw_value\n\n  ControlledTermValue : term\n\n      ControlledTermValue --> \"0..1\" OntologyClass : term\n    click OntologyClass href \"../OntologyClass\"\n\n  ControlledTermValue : type\n\n\n\n
"},{"location":"ControlledTermValue/#inheritance","title":"Inheritance","text":""},{"location":"ControlledTermValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance term 0..1 OntologyClass pointer to an ontology class direct has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"ControlledTermValue/#usages","title":"Usages","text":"used by used in type used Biosample chem_administration range ControlledTermValue Biosample experimental_factor range ControlledTermValue Biosample growth_facil range ControlledTermValue Biosample host_body_product range ControlledTermValue Biosample host_body_site range ControlledTermValue Biosample host_phenotype range ControlledTermValue Biosample plant_growth_med range ControlledTermValue Biosample plant_struc range ControlledTermValue Biosample samp_mat_process range ControlledTermValue"},{"location":"ControlledTermValue/#todos","title":"TODOs","text":""},{"location":"ControlledTermValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ControlledTermValue/#schema-source","title":"Schema Source","text":""},{"location":"ControlledTermValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ControlledTermValue native nmdc:ControlledTermValue"},{"location":"ControlledTermValue/#linkml-source","title":"LinkML Source","text":""},{"location":"ControlledTermValue/#direct","title":"Direct","text":"
name: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- term\nclass_uri: nmdc:ControlledTermValue\n\n
"},{"location":"ControlledTermValue/#induced","title":"Induced","text":"
name: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n  term:\n    name: term\n    description: pointer to an ontology class\n    notes:\n    - 'removed ''slot_uri: rdf:type'''\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: term\n    owner: ControlledTermValue\n    domain_of:\n    - ControlledTermValue\n    range: OntologyClass\n    inlined: true\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: ControlledTermValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ControlledTermValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ControlledTermValue\n\n
"},{"location":"CreditAssociation/","title":"Class: CreditAssociation","text":"

This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role and for a person value. Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0

URI: prov:Association

classDiagram\n  class CreditAssociation\n  click CreditAssociation href \"../CreditAssociation\"\n\n  CreditAssociation : applied_roles\n\n      CreditAssociation --> \"1..*\" CreditEnum : applied_roles\n    click CreditEnum href \"../CreditEnum\"\n\n  CreditAssociation : applies_to_person\n\n      CreditAssociation --> \"1\" PersonValue : applies_to_person\n    click PersonValue href \"../PersonValue\"\n\n  CreditAssociation : type\n\n\n\n
"},{"location":"CreditAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance applies_to_person 1 PersonValue direct applied_roles 1..* CreditEnum direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"CreditAssociation/#usages","title":"Usages","text":"used by used in type used Study has_credit_associations range CreditAssociation"},{"location":"CreditAssociation/#aliases","title":"Aliases","text":""},{"location":"CreditAssociation/#see-also","title":"See Also","text":""},{"location":"CreditAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CreditAssociation/#schema-source","title":"Schema Source","text":""},{"location":"CreditAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self prov:Association native nmdc:CreditAssociation"},{"location":"CreditAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"CreditAssociation/#direct","title":"Direct","text":"
name: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n  will be at least a slot for a CRediT Contributor Role and for a person value. Specifically\n  see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n  at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://casrai.org/credit/\naliases:\n- study role\n- credit table\n- associated researchers\nslots:\n- applies_to_person\n- applied_roles\n- type\nclass_uri: prov:Association\n\n
"},{"location":"CreditAssociation/#induced","title":"Induced","text":"
name: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n  will be at least a slot for a CRediT Contributor Role and for a person value. Specifically\n  see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n  at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://casrai.org/credit/\naliases:\n- study role\n- credit table\n- associated researchers\nattributes:\n  applies_to_person:\n    name: applies_to_person\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: applies_to_person\n    owner: CreditAssociation\n    domain_of:\n    - CreditAssociation\n    range: PersonValue\n    required: true\n  applied_roles:\n    name: applied_roles\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: 'Identify all CRediT roles associated with this contributor. CRediT\n          Information: https://info.orcid.org/credit-for-research-contribution ; CRediT:\n          https://credit.niso.org/'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: applied_roles\n    owner: CreditAssociation\n    domain_of:\n    - CreditAssociation\n    range: CreditEnum\n    required: true\n    multivalued: true\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: CreditAssociation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: prov:Association\n\n
"},{"location":"CreditEnum/","title":"Enum: CreditEnum","text":"

URI: CreditEnum

"},{"location":"CreditEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Conceptualization None Conceptualization Data curation None Data curation Formal Analysis None Formal Analysis Funding acquisition None Funding acquisition Investigation None Investigation Methodology None Methodology Project administration None Project administration Resources None Resources Software None Software Supervision None Supervision Validation None Validation Visualization None Visualization Writing original draft None Writing \u2013 original draft Writing review and editing None Writing \u2013 review & editing Principal Investigator OBI:0000103 principal investigator role Submitter EFO:0001741 the person(s) who enter study and biosample metadata into the NMDC submission..."},{"location":"CreditEnum/#slots","title":"Slots","text":"Name Description applied_roles"},{"location":"CreditEnum/#comments","title":"Comments","text":""},{"location":"CreditEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CreditEnum/#schema-source","title":"Schema Source","text":""},{"location":"CreditEnum/#linkml-source","title":"LinkML Source","text":"
name: CreditEnum\ncomments:\n- CreditEnums come from https://casrai.org/credit/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Conceptualization:\n    text: Conceptualization\n    description: Conceptualization\n  Data curation:\n    text: Data curation\n    description: Data curation\n  Formal Analysis:\n    text: Formal Analysis\n    description: Formal Analysis\n  Funding acquisition:\n    text: Funding acquisition\n    description: Funding acquisition\n  Investigation:\n    text: Investigation\n    description: Investigation\n  Methodology:\n    text: Methodology\n    description: Methodology\n  Project administration:\n    text: Project administration\n    description: Project administration\n  Resources:\n    text: Resources\n    description: Resources\n  Software:\n    text: Software\n    description: Software\n  Supervision:\n    text: Supervision\n    description: Supervision\n  Validation:\n    text: Validation\n    description: Validation\n  Visualization:\n    text: Visualization\n    description: Visualization\n  Writing original draft:\n    text: Writing original draft\n    description: Writing \u2013 original draft\n  Writing review and editing:\n    text: Writing review and editing\n    description: Writing \u2013 review & editing\n  Principal Investigator:\n    text: Principal Investigator\n    description: principal investigator role\n    meaning: OBI:0000103\n  Submitter:\n    text: Submitter\n    description: the person(s) who enter study and biosample metadata into the NMDC\n      submission portal\n    meaning: EFO:0001741\n\n
"},{"location":"CurLandUseEnum/","title":"Enum: CurLandUseEnum","text":"

URI: CurLandUseEnum

"},{"location":"CurLandUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description badlands None cities None conifers None crop trees None farmstead None gravel None hardwoods None hayland None horticultural plants None industrial areas None intermixed hardwood and conifers None marshlands None meadows None mines/quarries None mudflats None oil waste areas None pastureland None permanent snow or ice None rainforest None rangeland None roads/railroads None rock None row crops None saline seeps None salt flats None sand None shrub crops None shrub land None small grains None successional shrub land None swamp None tropical None tundra None vegetable crops None vine crops None"},{"location":"CurLandUseEnum/#slots","title":"Slots","text":"Name Description cur_land_use Present state of sample site"},{"location":"CurLandUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CurLandUseEnum/#schema-source","title":"Schema Source","text":""},{"location":"CurLandUseEnum/#linkml-source","title":"LinkML Source","text":"
name: cur_land_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  badlands:\n    text: badlands\n  cities:\n    text: cities\n  conifers:\n    text: conifers\n    annotations:\n      originally:\n        tag: originally\n        value: conifers (e.g. pine,spruce,fir,cypress)\n    examples:\n    - value: cypress\n    - value: fir\n    - value: pine\n    - value: spruce\n  crop trees:\n    text: crop trees\n    annotations:\n      originally:\n        tag: originally\n        value: crop trees (nuts,fruit,christmas trees,nursery trees)\n    examples:\n    - value: christmas trees\n    - value: fruit\n    - value: nursery trees\n    - value: nuts\n  farmstead:\n    text: farmstead\n  gravel:\n    text: gravel\n  hardwoods:\n    text: hardwoods\n    annotations:\n      originally:\n        tag: originally\n        value: hardwoods (e.g. oak,hickory,elm,aspen)\n    examples:\n    - value: aspen\n    - value: elm\n    - value: hickory\n    - value: oak\n  hayland:\n    text: hayland\n  horticultural plants:\n    text: horticultural plants\n    annotations:\n      originally:\n        tag: originally\n        value: horticultural plants (e.g. tulips)\n    examples:\n    - value: tulips\n  industrial areas:\n    text: industrial areas\n  intermixed hardwood and conifers:\n    text: intermixed hardwood and conifers\n  marshlands:\n    text: marshlands\n    annotations:\n      originally:\n        tag: originally\n        value: marshlands (grass,sedges,rushes)\n    examples:\n    - value: grass\n    - value: rushes\n    - value: sedgees\n  meadows:\n    text: meadows\n    annotations:\n      originally:\n        tag: originally\n        value: meadows (grasses,alfalfa,fescue,bromegrass,timothy)\n    examples:\n    - value: alfalfa\n    - value: bromegrass\n    - value: fescue\n    - value: grasses\n    - value: timothy\n  mines/quarries:\n    text: mines/quarries\n  mudflats:\n    text: mudflats\n  oil waste areas:\n    text: oil waste areas\n  pastureland:\n    text: pastureland\n    annotations:\n      originally:\n        tag: originally\n        value: pastureland (grasslands used for livestock grazing)\n    comments:\n    - grasslands used for livestock grazing\n  permanent snow or ice:\n    text: permanent snow or ice\n  rainforest:\n    text: rainforest\n    annotations:\n      originally:\n        tag: originally\n        value: rainforest (evergreen forest receiving greater than 406 cm annual rainfall)\n    comments:\n    - evergreen forest receiving greater than 406 cm annual rainfall\n  rangeland:\n    text: rangeland\n  roads/railroads:\n    text: roads/railroads\n  rock:\n    text: rock\n  row crops:\n    text: row crops\n  saline seeps:\n    text: saline seeps\n  salt flats:\n    text: salt flats\n  sand:\n    text: sand\n  shrub crops:\n    text: shrub crops\n    annotations:\n      originally:\n        tag: originally\n        value: shrub crops (blueberries,nursery ornamentals,filberts)\n    examples:\n    - value: blueberries\n    - value: filberts\n    - value: nursery ornamentals\n  shrub land:\n    text: shrub land\n    annotations:\n      originally:\n        tag: originally\n        value: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)\n    examples:\n    - value: creosote bush\n    - value: eucalyptus\n    - value: mesquite\n    - value: sage-brush\n    - value: shrub oak\n  small grains:\n    text: small grains\n  successional shrub land:\n    text: successional shrub land\n    annotations:\n      originally:\n        tag: originally\n        value: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub\n          dogwoods,blackberries)\n    examples:\n    - value: blackberries\n    - value: chokecherry\n    - value: hazels\n    - value: shrub dogwoods\n    - value: sumacs\n    - value: tree saplings\n  swamp:\n    text: swamp\n    annotations:\n      originally:\n        tag: originally\n        value: swamp (permanent or semi-permanent water body dominated by woody plants)\n    comments:\n    - permanent or semi-permanent water body dominated by woody plants\n  tropical:\n    text: tropical\n    annotations:\n      originally:\n        tag: originally\n        value: tropical (e.g. mangrove,palms)\n    examples:\n    - value: mangrove\n    - value: palms\n  tundra:\n    text: tundra\n    annotations:\n      originally:\n        tag: originally\n        value: tundra (mosses,lichens)\n    examples:\n    - value: lichens\n    - value: mosses\n  vegetable crops:\n    text: vegetable crops\n  vine crops:\n    text: vine crops\n    annotations:\n      originally:\n        tag: originally\n        value: vine crops (grapes)\n    examples:\n    - value: grapes\n\n
"},{"location":"Curie/","title":"Type: Curie","text":"

a compact URI

URI: xsd:string

"},{"location":"Curie/#comments","title":"Comments","text":""},{"location":"Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Curie/#schema-source","title":"Schema Source","text":""},{"location":"Curie/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:curie"},{"location":"DNASampleFormatEnum/","title":"Enum: DNASampleFormatEnum","text":"

URI: DNASampleFormatEnum

"},{"location":"DNASampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"DNASampleFormatEnum/#slots","title":"Slots","text":"Name Description dna_sample_format Solution in which the DNA sample has been suspended"},{"location":"DNASampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DNASampleFormatEnum/#schema-source","title":"Schema Source","text":""},{"location":"DNASampleFormatEnum/#linkml-source","title":"LinkML Source","text":"
name: DNASampleFormatEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  10 mM Tris-HCl:\n    text: 10 mM Tris-HCl\n  DNAStable:\n    text: DNAStable\n  Ethanol:\n    text: Ethanol\n  Low EDTA TE:\n    text: Low EDTA TE\n  MDA reaction buffer:\n    text: MDA reaction buffer\n  PBS:\n    text: PBS\n  Pellet:\n    text: Pellet\n  RNAStable:\n    text: RNAStable\n  TE:\n    text: TE\n  Water:\n    text: Water\n  Gentegra-DNA:\n    text: Gentegra-DNA\n  Gentegra-RNA:\n    text: Gentegra-RNA\n\n
"},{"location":"DataCategoryEnum/","title":"Enum: DataCategoryEnum","text":"

URI: DataCategoryEnum

"},{"location":"DataCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description instrument_data None Data generated by a DataGeneration PlannedProcess processed_data None Data generated by a WorkflowExecution PlannedProcess workflow_parameter_data None Data used as input into a workflow providing workflow specification"},{"location":"DataCategoryEnum/#slots","title":"Slots","text":"Name Description data_category The category of the file, such as instrument data from data generation or pro..."},{"location":"DataCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"DataCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: DataCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  instrument_data:\n    text: instrument_data\n    description: Data generated by a DataGeneration PlannedProcess\n  processed_data:\n    text: processed_data\n    description: Data generated by a WorkflowExecution PlannedProcess\n  workflow_parameter_data:\n    text: workflow_parameter_data\n    description: Data used as input into a workflow providing workflow specification.\n    related_mappings:\n    - edam.data:0949\n\n
"},{"location":"DataGeneration/","title":"Class: DataGeneration","text":"

The methods and processes used to generate omics data from a biosample or organism.

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:DataGeneration

classDiagram\n  class DataGeneration\n  click DataGeneration href \"../DataGeneration\"\n    PlannedProcess <|-- DataGeneration\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n    DataGeneration <|-- NucleotideSequencing\n      click NucleotideSequencing href \"../NucleotideSequencing\"\n    DataGeneration <|-- MassSpectrometry\n      click MassSpectrometry href \"../MassSpectrometry\"\n\n\n\n  DataGeneration : add_date\n\n  DataGeneration : alternative_identifiers\n\n  DataGeneration : analyte_category\n\n      DataGeneration --> \"1\" AnalyteCategoryEnum : analyte_category\n    click AnalyteCategoryEnum href \"../AnalyteCategoryEnum\"\n\n  DataGeneration : associated_studies\n\n      DataGeneration --> \"1..*\" Study : associated_studies\n    click Study href \"../Study\"\n\n  DataGeneration : description\n\n  DataGeneration : end_date\n\n  DataGeneration : has_failure_categorization\n\n      DataGeneration --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  DataGeneration : has_input\n\n      DataGeneration --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  DataGeneration : has_output\n\n      DataGeneration --> \"*\" DataObject : has_output\n    click DataObject href \"../DataObject\"\n\n  DataGeneration : id\n\n  DataGeneration : instrument_used\n\n      DataGeneration --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  DataGeneration : mod_date\n\n  DataGeneration : name\n\n  DataGeneration : principal_investigator\n\n      DataGeneration --> \"0..1\" PersonValue : principal_investigator\n    click PersonValue href \"../PersonValue\"\n\n  DataGeneration : processing_institution\n\n      DataGeneration --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  DataGeneration : protocol_link\n\n      DataGeneration --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  DataGeneration : qc_comment\n\n  DataGeneration : qc_status\n\n      DataGeneration --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  DataGeneration : start_date\n\n  DataGeneration : type\n\n\n\n
"},{"location":"DataGeneration/#inheritance","title":"Inheritance","text":""},{"location":"DataGeneration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance add_date 0..1 String The date on which the information was added to the database direct analyte_category 1 AnalyteCategoryEnum The type of analyte(s) that were measured in the data generation process and ... direct associated_studies 1..* Study The study associated with a resource direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing direct mod_date 0..1 String The last date on which the database information was modified direct principal_investigator 0..1 PersonValue Principal Investigator who led the study and/or generated the dataset direct has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * DataObject An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"DataGeneration/#usages","title":"Usages","text":"used by used in type used Database data_generation_set range DataGeneration MetagenomeAnnotation was_informed_by range DataGeneration FunctionalAnnotation was_generated_by any_of[range] DataGeneration DataObject was_generated_by any_of[range] DataGeneration WorkflowExecution was_informed_by range DataGeneration MetagenomeAssembly was_informed_by range DataGeneration MetatranscriptomeAssembly was_informed_by range DataGeneration MetatranscriptomeAnnotation was_informed_by range DataGeneration MetatranscriptomeExpressionAnalysis was_informed_by range DataGeneration MagsAnalysis was_informed_by range DataGeneration MetagenomeSequencing was_informed_by range DataGeneration ReadQcAnalysis was_informed_by range DataGeneration ReadBasedTaxonomyAnalysis was_informed_by range DataGeneration MetabolomicsAnalysis was_informed_by range DataGeneration MetaproteomicsAnalysis was_informed_by range DataGeneration NomAnalysis was_informed_by range DataGeneration"},{"location":"DataGeneration/#aliases","title":"Aliases","text":""},{"location":"DataGeneration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataGeneration/#schema-source","title":"Schema Source","text":""},{"location":"DataGeneration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:DataGeneration native nmdc:DataGeneration broad OBI:0000070, ISA:Assay"},{"location":"DataGeneration/#linkml-source","title":"LinkML Source","text":""},{"location":"DataGeneration/#direct","title":"Direct","text":"
name: DataGeneration\ndescription: The methods and processes used to generate omics data from a biosample\n  or organism.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: An experiment contains information about a sequencing experiment\n      including library and instrument details.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OmicsProcessing\n- assay\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nabstract: true\nslots:\n- add_date\n- analyte_category\n- associated_studies\n- instrument_used\n- mod_date\n- principal_investigator\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  associated_studies:\n    name: associated_studies\n    range: Study\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    range: DataObject\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:DataGeneration\n\n
"},{"location":"DataGeneration/#induced","title":"Induced","text":"
name: DataGeneration\ndescription: The methods and processes used to generate omics data from a biosample\n  or organism.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: An experiment contains information about a sequencing experiment\n      including library and instrument details.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OmicsProcessing\n- assay\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  associated_studies:\n    name: associated_studies\n    range: Study\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    range: DataObject\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  add_date:\n    name: add_date\n    description: The date on which the information was added to the database.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: add_date\n    owner: DataGeneration\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  analyte_category:\n    name: analyte_category\n    description: \"The type of analyte(s) that were measured in the data generation\\\n      \\ process and analyzed\\n  in the Workflow Chain\\n\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: analyte_category\n    owner: DataGeneration\n    domain_of:\n    - DataGeneration\n    range: AnalyteCategoryEnum\n    required: true\n  associated_studies:\n    name: associated_studies\n    description: The study associated with a resource.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: associated_studies\n    owner: DataGeneration\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: Study\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: DataGeneration\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  mod_date:\n    name: mod_date\n    description: The last date on which the database information was modified.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mod_date\n    owner: DataGeneration\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  principal_investigator:\n    name: principal_investigator\n    description: Principal Investigator who led the study and/or generated the dataset.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - PI\n    rank: 1000\n    alias: principal_investigator\n    owner: DataGeneration\n    domain_of:\n    - Study\n    - DataGeneration\n    range: PersonValue\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: DataObject\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: DataGeneration\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DataGeneration\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: DataGeneration\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: DataGeneration\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: DataGeneration\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: DataGeneration\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:DataGeneration\n\n
"},{"location":"DataObject/","title":"Class: DataObject","text":"

An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.

URI: nmdc:DataObject

classDiagram\n  class DataObject\n  click DataObject href \"../DataObject\"\n    InformationObject <|-- DataObject\n      click InformationObject href \"../InformationObject\"\n\n\n\n  DataObject : alternative_identifiers\n\n  DataObject : compression_type\n\n  DataObject : data_category\n\n      DataObject --> \"0..1\" DataCategoryEnum : data_category\n    click DataCategoryEnum href \"../DataCategoryEnum\"\n\n  DataObject : data_object_type\n\n      DataObject --> \"0..1\" FileTypeEnum : data_object_type\n    click FileTypeEnum href \"../FileTypeEnum\"\n\n  DataObject : description\n\n  DataObject : file_size_bytes\n\n  DataObject : id\n\n  DataObject : in_manifest\n\n      DataObject --> \"*\" Manifest : in_manifest\n    click Manifest href \"../Manifest\"\n\n  DataObject : insdc_experiment_identifiers\n\n  DataObject : md5_checksum\n\n  DataObject : name\n\n  DataObject : type\n\n  DataObject : url\n\n  DataObject : was_generated_by\n\n      DataObject --> \"0..1\" WorkflowExecution : was_generated_by\n    click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n
"},{"location":"DataObject/#inheritance","title":"Inheritance","text":""},{"location":"DataObject/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance compression_type 0..1 String If provided, specifies the compression type direct data_category 0..1 DataCategoryEnum The category of the file, such as instrument data from data generation or pro... direct data_object_type 0..1 FileTypeEnum The type of file represented by the data object direct file_size_bytes 0..1 Bytes Size of the file in bytes direct insdc_experiment_identifiers * ExternalIdentifier direct md5_checksum 0..1 String MD5 checksum of file (pre-compressed) direct url 0..1 String direct was_generated_by 0..1 WorkflowExecution\u00a0or\u00a0WorkflowExecution\u00a0or\u00a0DataGeneration direct in_manifest * Manifest direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 1 String A human readable label for an entity NamedThing description 1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"DataObject/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_output range DataObject MassSpectrometry has_output range DataObject Database data_object_set range DataObject DataGeneration has_output range DataObject CalibrationInformation calibration_object range DataObject"},{"location":"DataObject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataObject/#schema-source","title":"Schema Source","text":""},{"location":"DataObject/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:DataObject native nmdc:DataObject"},{"location":"DataObject/#linkml-source","title":"LinkML Source","text":""},{"location":"DataObject/#direct","title":"Direct","text":"
name: DataObject\ndescription: An object that primarily consists of symbols that represent information.   Files,\n  records, and omics data are examples of data objects.\nin_subset:\n- data object subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- compression_type\n- data_category\n- data_object_type\n- file_size_bytes\n- insdc_experiment_identifiers\n- md5_checksum\n- url\n- was_generated_by\n- in_manifest\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_generated_by:\n    name: was_generated_by\n    structured_pattern:\n      syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n      interpolated: true\nclass_uri: nmdc:DataObject\n\n
"},{"location":"DataObject/#induced","title":"Induced","text":"
name: DataObject\ndescription: An object that primarily consists of symbols that represent information.   Files,\n  records, and omics data are examples of data objects.\nin_subset:\n- data object subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_generated_by:\n    name: was_generated_by\n    structured_pattern:\n      syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n      interpolated: true\nattributes:\n  compression_type:\n    name: compression_type\n    description: If provided, specifies the compression type\n    todos:\n    - consider setting the range to an enum\n    examples:\n    - value: gzip\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: compression_type\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: string\n  data_category:\n    name: data_category\n    description: The category of the file, such as instrument data from data generation\n      or processed data from a workflow execution.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: data_category\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: DataCategoryEnum\n  data_object_type:\n    name: data_object_type\n    description: The type of file represented by the data object.\n    examples:\n    - value: FT ICR-MS Analysis Results\n    - value: GC-MS Metabolomics Results\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: data_object_type\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: FileTypeEnum\n  file_size_bytes:\n    name: file_size_bytes\n    description: Size of the file in bytes\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: file_size_bytes\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: bytes\n  insdc_experiment_identifiers:\n    name: insdc_experiment_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_experiment_identifiers\n    owner: DataObject\n    domain_of:\n    - NucleotideSequencing\n    - DataObject\n    range: external_identifier\n    multivalued: true\n    pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n  md5_checksum:\n    name: md5_checksum\n    description: MD5 checksum of file (pre-compressed)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: md5_checksum\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: string\n  url:\n    name: url\n    notes:\n    - See issue 207 - this clashes with the mixs field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: url\n    owner: DataObject\n    domain_of:\n    - ImageValue\n    - Protocol\n    - DataObject\n    range: string\n  was_generated_by:\n    name: was_generated_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasGeneratedBy\n    rank: 1000\n    alias: was_generated_by\n    owner: DataObject\n    domain_of:\n    - FunctionalAnnotation\n    - DataObject\n    range: WorkflowExecution\n    structured_pattern:\n      syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n      interpolated: true\n    any_of:\n    - range: WorkflowExecution\n    - range: DataGeneration\n  in_manifest:\n    name: in_manifest\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: in_manifest\n    owner: DataObject\n    domain_of:\n    - DataObject\n    range: Manifest\n    multivalued: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DataObject\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: DataObject\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n    required: true\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: DataObject\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n    required: true\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: DataObject\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: DataObject\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:DataObject\n\n
"},{"location":"DataObjectSubset/","title":"Subset: DataObjectSubset","text":"

Subset consisting of the data objects that either inputs or outputs of processes or workflows.

URI: DataObjectSubset

"},{"location":"DataObjectSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataObjectSubset/#schema-source","title":"Schema Source","text":""},{"location":"DataObjectSubset/#classes-in-subset","title":"Classes in subset","text":"Class Description DataObject An object that primarily consists of symbols that represent information"},{"location":"DataPortalSubset/","title":"Subset: DataPortalSubset","text":"

Subset consisting of entities that Kitware/nmdc-server use to populate the data portal.

URI: DataPortalSubset

"},{"location":"DataPortalSubset/#comments","title":"Comments","text":""},{"location":"DataPortalSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataPortalSubset/#schema-source","title":"Schema Source","text":""},{"location":"DataPortalSubset/#slots-in-subset","title":"Slots in subset","text":"Slot Description associated_dois A list of DOIs associated with a resource, such as a list of DOIS associated ... doi_category The resource type the corresponding doi resolves to doi_provider The authority, or organization, the DOI is associated with doi_value A digital object identifier, which is intended to persistantly identify some ..."},{"location":"Database/","title":"Class: Database","text":"

An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to collections.

URI: nmdc:Database

classDiagram\n  class Database\n  click Database href \"../Database\"\n\n  Database : biosample_set\n\n      Database --> \"*\" Biosample : biosample_set\n    click Biosample href \"../Biosample\"\n\n  Database : calibration_set\n\n      Database --> \"*\" CalibrationInformation : calibration_set\n    click CalibrationInformation href \"../CalibrationInformation\"\n\n  Database : chemical_entity_set\n\n      Database --> \"*\" ChemicalEntity : chemical_entity_set\n    click ChemicalEntity href \"../ChemicalEntity\"\n\n  Database : collecting_biosamples_from_site_set\n\n      Database --> \"*\" CollectingBiosamplesFromSite : collecting_biosamples_from_site_set\n    click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n\n  Database : configuration_set\n\n      Database --> \"*\" Configuration : configuration_set\n    click Configuration href \"../Configuration\"\n\n  Database : data_generation_set\n\n      Database --> \"*\" DataGeneration : data_generation_set\n    click DataGeneration href \"../DataGeneration\"\n\n  Database : data_object_set\n\n      Database --> \"*\" DataObject : data_object_set\n    click DataObject href \"../DataObject\"\n\n  Database : field_research_site_set\n\n      Database --> \"*\" FieldResearchSite : field_research_site_set\n    click FieldResearchSite href \"../FieldResearchSite\"\n\n  Database : functional_annotation_agg\n\n      Database --> \"*\" FunctionalAnnotationAggMember : functional_annotation_agg\n    click FunctionalAnnotationAggMember href \"../FunctionalAnnotationAggMember\"\n\n  Database : functional_annotation_set\n\n      Database --> \"*\" FunctionalAnnotation : functional_annotation_set\n    click FunctionalAnnotation href \"../FunctionalAnnotation\"\n\n  Database : genome_feature_set\n\n      Database --> \"*\" GenomeFeature : genome_feature_set\n    click GenomeFeature href \"../GenomeFeature\"\n\n  Database : instrument_set\n\n      Database --> \"*\" Instrument : instrument_set\n    click Instrument href \"../Instrument\"\n\n  Database : manifest_set\n\n      Database --> \"*\" Manifest : manifest_set\n    click Manifest href \"../Manifest\"\n\n  Database : material_processing_set\n\n      Database --> \"*\" MaterialProcessing : material_processing_set\n    click MaterialProcessing href \"../MaterialProcessing\"\n\n  Database : processed_sample_set\n\n      Database --> \"*\" ProcessedSample : processed_sample_set\n    click ProcessedSample href \"../ProcessedSample\"\n\n  Database : protocol_execution_set\n\n      Database --> \"*\" ProtocolExecution : protocol_execution_set\n    click ProtocolExecution href \"../ProtocolExecution\"\n\n  Database : storage_process_set\n\n      Database --> \"*\" StorageProcess : storage_process_set\n    click StorageProcess href \"../StorageProcess\"\n\n  Database : study_set\n\n      Database --> \"*\" Study : study_set\n    click Study href \"../Study\"\n\n  Database : workflow_execution_set\n\n      Database --> \"*\" WorkflowExecution : workflow_execution_set\n    click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n
"},{"location":"Database/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance biosample_set * Biosample This property links a database object to the set of samples within it direct calibration_set * CalibrationInformation This property links a database object to the set of calibrations within it direct chemical_entity_set * ChemicalEntity This property links a database object to the set of chemical entities within ... direct collecting_biosamples_from_site_set * CollectingBiosamplesFromSite direct configuration_set * Configuration This property links a database object to the set of configurations within it direct data_generation_set * DataGeneration This property links a database object to the set of data generations within i... direct data_object_set * DataObject This property links a database object to the set of data objects within it direct field_research_site_set * FieldResearchSite direct functional_annotation_agg * FunctionalAnnotationAggMember direct functional_annotation_set * FunctionalAnnotation This property links a database object to the set of all functional annotation... direct genome_feature_set * GenomeFeature This property links a database object to the set of all features direct instrument_set * Instrument This property links a database object to the set of instruments within it direct manifest_set * Manifest This property links a database object to the set of manifests within it direct material_processing_set * MaterialProcessing This property links a database object to the set of material processing withi... direct processed_sample_set * ProcessedSample This property links a database object to the set of processed samples within ... direct protocol_execution_set * ProtocolExecution This property links a database object to the set of protocol executions withi... direct storage_process_set * StorageProcess This property links a database object to the set of storage processes within ... direct study_set * Study This property links a database object to the set of studies within it direct workflow_execution_set * WorkflowExecution This property links a database object to the set of workflow executions direct"},{"location":"Database/#aliases","title":"Aliases","text":""},{"location":"Database/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Database/#schema-source","title":"Schema Source","text":""},{"location":"Database/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Database native nmdc:Database"},{"location":"Database/#linkml-source","title":"LinkML Source","text":""},{"location":"Database/#direct","title":"Direct","text":"
name: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n  to correspond to an actual managed database top level holder class. When translated\n  to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n  of interest. For MongoDB, the lists of objects that Database slots point to correspond\n  to **collections**.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nslots:\n- biosample_set\n- calibration_set\n- chemical_entity_set\n- collecting_biosamples_from_site_set\n- configuration_set\n- data_generation_set\n- data_object_set\n- field_research_site_set\n- functional_annotation_agg\n- functional_annotation_set\n- genome_feature_set\n- instrument_set\n- manifest_set\n- material_processing_set\n- processed_sample_set\n- protocol_execution_set\n- storage_process_set\n- study_set\n- workflow_execution_set\nclass_uri: nmdc:Database\ntree_root: true\n\n
"},{"location":"Database/#induced","title":"Induced","text":"
name: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n  to correspond to an actual managed database top level holder class. When translated\n  to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n  of interest. For MongoDB, the lists of objects that Database slots point to correspond\n  to **collections**.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nattributes:\n  biosample_set:\n    name: biosample_set\n    description: This property links a database object to the set of samples within\n      it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: biosample_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Biosample\n    multivalued: true\n    inlined_as_list: true\n  calibration_set:\n    name: calibration_set\n    description: This property links a database object to the set of calibrations\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: calibration_set\n    owner: Database\n    domain_of:\n    - Database\n    range: CalibrationInformation\n    multivalued: true\n    inlined_as_list: true\n  chemical_entity_set:\n    name: chemical_entity_set\n    description: This property links a database object to the set of chemical entities\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: chemical_entity_set\n    owner: Database\n    domain_of:\n    - Database\n    range: ChemicalEntity\n    multivalued: true\n    inlined_as_list: true\n  collecting_biosamples_from_site_set:\n    name: collecting_biosamples_from_site_set\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: collecting_biosamples_from_site_set\n    owner: Database\n    domain_of:\n    - Database\n    range: CollectingBiosamplesFromSite\n    multivalued: true\n    inlined_as_list: true\n  configuration_set:\n    name: configuration_set\n    description: This property links a database object to the set of configurations\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: configuration_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Configuration\n    multivalued: true\n    inlined_as_list: true\n  data_generation_set:\n    name: data_generation_set\n    description: This property links a database object to the set of data generations\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: data_generation_set\n    owner: Database\n    domain_of:\n    - Database\n    range: DataGeneration\n    multivalued: true\n    inlined_as_list: true\n  data_object_set:\n    name: data_object_set\n    description: This property links a database object to the set of data objects\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: data_object_set\n    owner: Database\n    domain_of:\n    - Database\n    range: DataObject\n    multivalued: true\n    inlined_as_list: true\n  field_research_site_set:\n    name: field_research_site_set\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: field_research_site_set\n    owner: Database\n    domain_of:\n    - Database\n    range: FieldResearchSite\n    multivalued: true\n    inlined_as_list: true\n  functional_annotation_agg:\n    name: functional_annotation_agg\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: functional_annotation_agg\n    owner: Database\n    domain_of:\n    - Database\n    range: FunctionalAnnotationAggMember\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  functional_annotation_set:\n    name: functional_annotation_set\n    description: This property links a database object to the set of all functional\n      annotations\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: functional_annotation_set\n    owner: Database\n    domain_of:\n    - Database\n    range: FunctionalAnnotation\n    multivalued: true\n    inlined_as_list: true\n  genome_feature_set:\n    name: genome_feature_set\n    description: This property links a database object to the set of all features\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: genome_feature_set\n    owner: Database\n    domain_of:\n    - Database\n    range: GenomeFeature\n    multivalued: true\n    inlined_as_list: true\n  instrument_set:\n    name: instrument_set\n    description: This property links a database object to the set of instruments within\n      it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: instrument_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Instrument\n    multivalued: true\n    inlined_as_list: true\n  manifest_set:\n    name: manifest_set\n    description: This property links a database object to the set of manifests within\n      it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: manifest_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Manifest\n    multivalued: true\n    inlined_as_list: true\n  material_processing_set:\n    name: material_processing_set\n    description: This property links a database object to the set of material processing\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: material_processing_set\n    owner: Database\n    domain_of:\n    - Database\n    range: MaterialProcessing\n    multivalued: true\n    inlined_as_list: true\n  processed_sample_set:\n    name: processed_sample_set\n    description: This property links a database object to the set of processed samples\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: processed_sample_set\n    owner: Database\n    domain_of:\n    - Database\n    range: ProcessedSample\n    multivalued: true\n    inlined_as_list: true\n  protocol_execution_set:\n    name: protocol_execution_set\n    description: This property links a database object to the set of protocol executions\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: protocol_execution_set\n    owner: Database\n    domain_of:\n    - Database\n    range: ProtocolExecution\n    multivalued: true\n    inlined_as_list: true\n  storage_process_set:\n    name: storage_process_set\n    description: This property links a database object to the set of storage processes\n      within it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: storage_process_set\n    owner: Database\n    domain_of:\n    - Database\n    range: StorageProcess\n    multivalued: true\n    inlined_as_list: true\n  study_set:\n    name: study_set\n    description: This property links a database object to the set of studies within\n      it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: study_set\n    owner: Database\n    domain_of:\n    - Database\n    range: Study\n    multivalued: true\n    inlined_as_list: true\n  workflow_execution_set:\n    name: workflow_execution_set\n    description: This property links a database object to the set of workflow executions.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    mixins:\n    - object_set\n    alias: workflow_execution_set\n    owner: Database\n    domain_of:\n    - Database\n    range: WorkflowExecution\n    multivalued: true\n    inlined_as_list: true\nclass_uri: nmdc:Database\ntree_root: true\n\n
"},{"location":"Date/","title":"Type: Date","text":"

a date (year, month and day) in an idealized calendar

URI: xsd:date

"},{"location":"Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Date/#schema-source","title":"Schema Source","text":""},{"location":"Date/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:date native nmdc:date exact schema:Date"},{"location":"DateOrDatetime/","title":"Type: DateOrDatetime","text":"

Either a date or a datetime

URI: linkml:DateOrDatetime

"},{"location":"DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"location":"DateOrDatetime/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:DateOrDatetime native nmdc:date_or_datetime"},{"location":"Datetime/","title":"Type: Datetime","text":"

The combination of a date and time

URI: xsd:dateTime

"},{"location":"Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Datetime/#schema-source","title":"Schema Source","text":""},{"location":"Datetime/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:dateTime native nmdc:datetime exact schema:DateTime"},{"location":"Decimal/","title":"Type: Decimal","text":"

A real number with arbitrary precision that conforms to the xsd:decimal specification

URI: xsd:decimal

"},{"location":"Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Decimal/#schema-source","title":"Schema Source","text":""},{"location":"Decimal/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:decimal native nmdc:decimal broad schema:Number"},{"location":"DecimalDegree/","title":"Type: DecimalDegree","text":"

A decimal degree expresses latitude or longitude as decimal fractions.

URI: xsd:decimal

"},{"location":"DecimalDegree/#see-also","title":"See Also","text":""},{"location":"DecimalDegree/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DecimalDegree/#schema-source","title":"Schema Source","text":""},{"location":"DecimalDegree/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:decimal native nmdc:decimal_degree"},{"location":"DeposEnvEnum/","title":"Enum: DeposEnvEnum","text":"

URI: DeposEnvEnum

"},{"location":"DeposEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Continental - Alluvial None Continental - Aeolian None Continental - Fluvial None Continental - Lacustrine None Transitional - Deltaic None Transitional - Tidal None Transitional - Lagoonal None Transitional - Beach None Transitional - Lake None Marine - Shallow None Marine - Deep None Marine - Reef None Other - Evaporite None Other - Glacial None Other - Volcanic None other None"},{"location":"DeposEnvEnum/#slots","title":"Slots","text":"Name Description depos_env Main depositional environment (https://en"},{"location":"DeposEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DeposEnvEnum/#schema-source","title":"Schema Source","text":""},{"location":"DeposEnvEnum/#linkml-source","title":"LinkML Source","text":"
name: depos_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Continental - Alluvial:\n    text: Continental - Alluvial\n  Continental - Aeolian:\n    text: Continental - Aeolian\n  Continental - Fluvial:\n    text: Continental - Fluvial\n  Continental - Lacustrine:\n    text: Continental - Lacustrine\n  Transitional - Deltaic:\n    text: Transitional - Deltaic\n  Transitional - Tidal:\n    text: Transitional - Tidal\n  Transitional - Lagoonal:\n    text: Transitional - Lagoonal\n  Transitional - Beach:\n    text: Transitional - Beach\n  Transitional - Lake:\n    text: Transitional - Lake\n  Marine - Shallow:\n    text: Marine - Shallow\n  Marine - Deep:\n    text: Marine - Deep\n  Marine - Reef:\n    text: Marine - Reef\n  Other - Evaporite:\n    text: Other - Evaporite\n  Other - Glacial:\n    text: Other - Glacial\n  Other - Volcanic:\n    text: Other - Volcanic\n  other:\n    text: other\n\n
"},{"location":"DirectInfusionEnum/","title":"Enum: DirectInfusionEnum","text":"

URI: DirectInfusionEnum

"},{"location":"DirectInfusionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description direct_infusion None autosampler None"},{"location":"DirectInfusionEnum/#slots","title":"Slots","text":"Name Description direct_infusion_category used when a processed sample is introduced into a mass spectrometer without c..."},{"location":"DirectInfusionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DirectInfusionEnum/#schema-source","title":"Schema Source","text":""},{"location":"DirectInfusionEnum/#linkml-source","title":"LinkML Source","text":"
name: DirectInfusionEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  direct_infusion:\n    text: direct_infusion\n    aliases:\n    - DI\n  autosampler:\n    text: autosampler\n\n
"},{"location":"DissolvingProcess/","title":"Class: DissolvingProcess","text":"

A mixing step where a soluble component is mixed with a liquid component.

__

URI: nmdc:DissolvingProcess

classDiagram\n  class DissolvingProcess\n  click DissolvingProcess href \"../DissolvingProcess\"\n    MaterialProcessing <|-- DissolvingProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  DissolvingProcess : alternative_identifiers\n\n  DissolvingProcess : description\n\n  DissolvingProcess : duration\n\n      DissolvingProcess --> \"0..1\" QuantityValue : duration\n    click QuantityValue href \"../QuantityValue\"\n\n  DissolvingProcess : end_date\n\n  DissolvingProcess : has_failure_categorization\n\n      DissolvingProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  DissolvingProcess : has_input\n\n      DissolvingProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  DissolvingProcess : has_output\n\n      DissolvingProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  DissolvingProcess : id\n\n  DissolvingProcess : instrument_used\n\n      DissolvingProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  DissolvingProcess : name\n\n  DissolvingProcess : processing_institution\n\n      DissolvingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  DissolvingProcess : protocol_link\n\n      DissolvingProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  DissolvingProcess : qc_comment\n\n  DissolvingProcess : qc_status\n\n      DissolvingProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  DissolvingProcess : start_date\n\n  DissolvingProcess : substances_used\n\n      DissolvingProcess --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  DissolvingProcess : temperature\n\n      DissolvingProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  DissolvingProcess : type\n\n\n\n
"},{"location":"DissolvingProcess/#inheritance","title":"Inheritance","text":""},{"location":"DissolvingProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance duration 0..1 QuantityValue The elapsed time of an activity direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct substances_used * PortionOfSubstance The substances that are combined to enable a ChemicalConversionProcess direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"DissolvingProcess/#aliases","title":"Aliases","text":""},{"location":"DissolvingProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DissolvingProcess/#schema-source","title":"Schema Source","text":""},{"location":"DissolvingProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:DissolvingProcess native nmdc:DissolvingProcess exact CHMO:0002773"},{"location":"DissolvingProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"DissolvingProcess/#direct","title":"Direct","text":"
name: DissolvingProcess\ndescription: 'A mixing step where a soluble component is mixed with a liquid component.\n\n  '\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Solubilization\nexact_mappings:\n- CHMO:0002773\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- duration\n- temperature\n- substances_used\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:DissolvingProcess\n\n
"},{"location":"DissolvingProcess/#induced","title":"Induced","text":"
name: DissolvingProcess\ndescription: 'A mixing step where a soluble component is mixed with a liquid component.\n\n  '\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Solubilization\nexact_mappings:\n- CHMO:0002773\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  duration:\n    name: duration\n    description: The elapsed time of an activity.\n    examples:\n    - value: JsonObj(has_numeric_value=2, has_unit='hours')\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: duration\n    owner: DissolvingProcess\n    domain_of:\n    - MixingProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: QuantityValue\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: DissolvingProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  substances_used:\n    name: substances_used\n    description: The substances that are combined to enable a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: DissolvingProcess\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: DissolvingProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: DissolvingProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DissolvingProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: DissolvingProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: DissolvingProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: DissolvingProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: DissolvingProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:DissolvingProcess\n\n
"},{"location":"Doi/","title":"Class: Doi","text":"

A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.

URI: nmdc:Doi

classDiagram\n  class Doi\n  click Doi href \"../Doi\"\n\n  Doi : doi_category\n\n      Doi --> \"1\" DoiCategoryEnum : doi_category\n    click DoiCategoryEnum href \"../DoiCategoryEnum\"\n\n  Doi : doi_provider\n\n      Doi --> \"0..1\" DoiProviderEnum : doi_provider\n    click DoiProviderEnum href \"../DoiProviderEnum\"\n\n  Doi : doi_value\n\n  Doi : type\n\n\n\n
"},{"location":"Doi/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance doi_value 1 Uriorcurie A digital object identifier, which is intended to persistantly identify some ... direct doi_provider 0..1 DoiProviderEnum The authority, or organization, the DOI is associated with direct doi_category 1 DoiCategoryEnum The resource type the corresponding doi resolves to direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"Doi/#usages","title":"Usages","text":"used by used in type used Study associated_dois range Doi"},{"location":"Doi/#aliases","title":"Aliases","text":""},{"location":"Doi/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Doi/#schema-source","title":"Schema Source","text":""},{"location":"Doi/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Doi native nmdc:Doi exact OBI:0002110"},{"location":"Doi/#linkml-source","title":"LinkML Source","text":""},{"location":"Doi/#direct","title":"Direct","text":"
name: Doi\ndescription: A centrally registered identifier symbol used to uniquely identify objects\n  given by the International DOI Foundation. The DOI system is particularly used for\n  electronic documents.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOIs\n- digital object identifiers\nexact_mappings:\n- OBI:0002110\nslots:\n- doi_value\n- doi_provider\n- doi_category\n- type\nclass_uri: nmdc:Doi\nrules:\n- preconditions:\n    slot_conditions:\n      doi_category:\n        name: doi_category\n        any_of:\n        - equals_string: dataset_doi\n        - equals_string: award_doi\n  postconditions:\n    slot_conditions:\n      doi_provider:\n        name: doi_provider\n        required: true\n  description: If doi_category is a publication_doi, then doi_provider is not required.\n    Otherwise, doi_provider is required.\n  title: dataset_award_dois_required\n\n
"},{"location":"Doi/#induced","title":"Induced","text":"
name: Doi\ndescription: A centrally registered identifier symbol used to uniquely identify objects\n  given by the International DOI Foundation. The DOI system is particularly used for\n  electronic documents.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOIs\n- digital object identifiers\nexact_mappings:\n- OBI:0002110\nattributes:\n  doi_value:\n    name: doi_value\n    description: A digital object identifier, which is intended to persistantly identify\n      some resource on the web.\n    examples:\n    - value: doi:10.46936/10.25585/60000880\n      description: The DOI links to an electronic document.\n    in_subset:\n    - data_portal_subset\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - DOI\n    - digital object identifier\n    exact_mappings:\n    - OBI:0002110\n    narrow_mappings:\n    - edam.data:1188\n    rank: 1000\n    alias: doi_value\n    owner: Doi\n    domain_of:\n    - Doi\n    range: uriorcurie\n    required: true\n    pattern: ^doi:10.\\d{2,9}/.*$\n  doi_provider:\n    name: doi_provider\n    description: The authority, or organization, the DOI is associated with.\n    examples:\n    - value: ess_dive\n      description: The corresponding DOI is associated with ESS-DIVE.\n    in_subset:\n    - data_portal_subset\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - NCIT:C74932\n    rank: 1000\n    alias: doi_provider\n    owner: Doi\n    domain_of:\n    - Doi\n    range: DoiProviderEnum\n  doi_category:\n    name: doi_category\n    description: The resource type the corresponding doi resolves to.\n    examples:\n    - value: dataset_doi\n      description: The corresponding DOI is a dataset resource type.\n    in_subset:\n    - data_portal_subset\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: doi_category\n    owner: Doi\n    domain_of:\n    - Doi\n    range: DoiCategoryEnum\n    required: true\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Doi\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Doi\nrules:\n- preconditions:\n    slot_conditions:\n      doi_category:\n        name: doi_category\n        any_of:\n        - equals_string: dataset_doi\n        - equals_string: award_doi\n  postconditions:\n    slot_conditions:\n      doi_provider:\n        name: doi_provider\n        required: true\n  description: If doi_category is a publication_doi, then doi_provider is not required.\n    Otherwise, doi_provider is required.\n  title: dataset_award_dois_required\n\n
"},{"location":"DoiCategoryEnum/","title":"Enum: DoiCategoryEnum","text":"

URI: DoiCategoryEnum

"},{"location":"DoiCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description award_doi None A type of DOI that resolves to a funding authority dataset_doi None A type of DOI that resolves to generated data publication_doi None A type of DOI that resolves to a publication data_management_plan_doi None A type of DOI that resolves to a data management plan"},{"location":"DoiCategoryEnum/#slots","title":"Slots","text":"Name Description doi_category The resource type the corresponding doi resolves to"},{"location":"DoiCategoryEnum/#comments","title":"Comments","text":""},{"location":"DoiCategoryEnum/#see-also","title":"See Also","text":""},{"location":"DoiCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoiCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoiCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: DoiCategoryEnum\ncomments:\n- See especially the resourceTypeGeneral section of the DataCite PDF, on pp48-53 as\n  of 2023-07-19\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://schema.datacite.org/meta/kernel-4.4/doc/DataCite-MetadataKernel_v4.4.pdf\n- https://api.crossref.org/types\nrank: 1000\npermissible_values:\n  award_doi:\n    text: award_doi\n    description: A type of DOI that resolves to a funding authority.\n  dataset_doi:\n    text: dataset_doi\n    description: A type of DOI that resolves to generated data.\n  publication_doi:\n    text: publication_doi\n    description: A type of DOI that resolves to a publication.\n  data_management_plan_doi:\n    text: data_management_plan_doi\n    description: A type of DOI that resolves to a data management plan.\n\n
"},{"location":"DoiProviderEnum/","title":"Enum: DoiProviderEnum","text":"

URI: DoiProviderEnum

"},{"location":"DoiProviderEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description emsl https://ror.org/04rc0xn13 jgi https://ror.org/04xm1d337 kbase https://ror.org/01znn6x10 osti https://ror.org/031478740 ess_dive https://ror.org/01t14bp54 massive None gsc None zenodo None edi https://ror.org/0330j0z60 figshare https://ror.org/041mxqs23"},{"location":"DoiProviderEnum/#slots","title":"Slots","text":"Name Description doi_provider The authority, or organization, the DOI is associated with"},{"location":"DoiProviderEnum/#see-also","title":"See Also","text":""},{"location":"DoiProviderEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoiProviderEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoiProviderEnum/#linkml-source","title":"LinkML Source","text":"
name: DoiProviderEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:DoiProviderEnum\n- nmdc:ProcessingInstitutionEnum\n- nmdc:ExecutionResourceEnum\nrank: 1000\npermissible_values:\n  emsl:\n    text: emsl\n    meaning: https://ror.org/04rc0xn13\n    title: EMSL\n    aliases:\n    - Environmental Molecular Sciences Laboratory\n    - EMSL\n  jgi:\n    text: jgi\n    meaning: https://ror.org/04xm1d337\n    title: JGI\n    aliases:\n    - Joint Genome Institute\n    - JGI\n  kbase:\n    text: kbase\n    meaning: https://ror.org/01znn6x10\n    title: KBase\n    aliases:\n    - KBase\n  osti:\n    text: osti\n    meaning: https://ror.org/031478740\n    title: OSTI\n    aliases:\n    - Office of Scientific and Technical Information\n    - OSTI\n  ess_dive:\n    text: ess_dive\n    meaning: https://ror.org/01t14bp54\n    title: ESS-DIVE\n    aliases:\n    - ESS-DIVE\n    - Environmental System Science Data Infrastructure for a Virtual Ecosystem\n  massive:\n    text: massive\n    title: MassIVE\n    aliases:\n    - MassIVE\n    - Mass Spectrometry Virtual Environment\n  gsc:\n    text: gsc\n    title: GSC\n    aliases:\n    - GSC\n    - Genomic Standards Consortium\n  zenodo:\n    text: zenodo\n    title: Zenodo\n    aliases:\n    - Zenodo\n  edi:\n    text: edi\n    meaning: https://ror.org/0330j0z60\n    title: EDI\n    aliases:\n    - EDI\n    - Environmental Data Initiative\n  figshare:\n    text: figshare\n    meaning: https://ror.org/041mxqs23\n    title: Figshare\n\n
"},{"location":"DoorCompTypeEnum/","title":"Enum: DoorCompTypeEnum","text":"

URI: DoorCompTypeEnum

"},{"location":"DoorCompTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metal covered None revolving None sliding None telescopic None"},{"location":"DoorCompTypeEnum/#slots","title":"Slots","text":"Name Description door_comp_type The composite type of the door"},{"location":"DoorCompTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCompTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorCompTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: door_comp_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  metal covered:\n    text: metal covered\n  revolving:\n    text: revolving\n  sliding:\n    text: sliding\n  telescopic:\n    text: telescopic\n\n
"},{"location":"DoorCondEnum/","title":"Enum: DoorCondEnum","text":"

URI: DoorCondEnum

"},{"location":"DoorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"DoorCondEnum/#slots","title":"Slots","text":"Name Description door_cond The phsical condition of the door"},{"location":"DoorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorCondEnum/#linkml-source","title":"LinkML Source","text":"
name: door_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  damaged:\n    text: damaged\n  needs repair:\n    text: needs repair\n  new:\n    text: new\n  rupture:\n    text: rupture\n  visible wear:\n    text: visible wear\n\n
"},{"location":"DoorDirectEnum/","title":"Enum: DoorDirectEnum","text":"

URI: DoorDirectEnum

"},{"location":"DoorDirectEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description inward None outward None sideways None"},{"location":"DoorDirectEnum/#slots","title":"Slots","text":"Name Description door_direct The direction the door opens"},{"location":"DoorDirectEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorDirectEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorDirectEnum/#linkml-source","title":"LinkML Source","text":"
name: door_direct_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  inward:\n    text: inward\n  outward:\n    text: outward\n  sideways:\n    text: sideways\n\n
"},{"location":"DoorLocEnum/","title":"Enum: DoorLocEnum","text":"

URI: DoorLocEnum

"},{"location":"DoorLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"DoorLocEnum/#slots","title":"Slots","text":"Name Description door_loc The relative location of the door in the room"},{"location":"DoorLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorLocEnum/#linkml-source","title":"LinkML Source","text":"
name: door_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n\n
"},{"location":"DoorMatEnum/","title":"Enum: DoorMatEnum","text":"

URI: DoorMatEnum

"},{"location":"DoorMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aluminum None cellular PVC None engineered plastic None fiberboard None fiberglass None metal None thermoplastic alloy None vinyl None wood None wood/plastic composite None"},{"location":"DoorMatEnum/#slots","title":"Slots","text":"Name Description door_mat The material the door is composed of"},{"location":"DoorMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorMatEnum/#linkml-source","title":"LinkML Source","text":"
name: door_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  aluminum:\n    text: aluminum\n  cellular PVC:\n    text: cellular PVC\n  engineered plastic:\n    text: engineered plastic\n  fiberboard:\n    text: fiberboard\n  fiberglass:\n    text: fiberglass\n  metal:\n    text: metal\n  thermoplastic alloy:\n    text: thermoplastic alloy\n  vinyl:\n    text: vinyl\n  wood:\n    text: wood\n  wood/plastic composite:\n    text: wood/plastic composite\n\n
"},{"location":"DoorMoveEnum/","title":"Enum: DoorMoveEnum","text":"

URI: DoorMoveEnum

"},{"location":"DoorMoveEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None folding None revolving None rolling shutter None sliding None swinging None"},{"location":"DoorMoveEnum/#slots","title":"Slots","text":"Name Description door_move The type of movement of the door"},{"location":"DoorMoveEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMoveEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorMoveEnum/#linkml-source","title":"LinkML Source","text":"
name: door_move_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  collapsible:\n    text: collapsible\n  folding:\n    text: folding\n  revolving:\n    text: revolving\n  rolling shutter:\n    text: rolling shutter\n  sliding:\n    text: sliding\n  swinging:\n    text: swinging\n\n
"},{"location":"DoorTypeEnum/","title":"Enum: DoorTypeEnum","text":"

URI: DoorTypeEnum

"},{"location":"DoorTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description composite None metal None wooden None"},{"location":"DoorTypeEnum/#slots","title":"Slots","text":"Name Description door_type The type of door material"},{"location":"DoorTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: door_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  composite:\n    text: composite\n  metal:\n    text: metal\n  wooden:\n    text: wooden\n\n
"},{"location":"DoorTypeMetalEnum/","title":"Enum: DoorTypeMetalEnum","text":"

URI: DoorTypeMetalEnum

"},{"location":"DoorTypeMetalEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None corrugated steel None hollow None rolling shutters None steel plate None"},{"location":"DoorTypeMetalEnum/#slots","title":"Slots","text":"Name Description door_type_metal The type of metal door"},{"location":"DoorTypeMetalEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeMetalEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorTypeMetalEnum/#linkml-source","title":"LinkML Source","text":"
name: door_type_metal_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  collapsible:\n    text: collapsible\n  corrugated steel:\n    text: corrugated steel\n  hollow:\n    text: hollow\n  rolling shutters:\n    text: rolling shutters\n  steel plate:\n    text: steel plate\n\n
"},{"location":"DoorTypeWoodEnum/","title":"Enum: DoorTypeWoodEnum","text":"

URI: DoorTypeWoodEnum

"},{"location":"DoorTypeWoodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bettened and ledged None battened None ledged and braced None ledged and framed None ledged, braced and frame None framed and paneled None glashed or sash None flush None louvered None wire gauged None"},{"location":"DoorTypeWoodEnum/#slots","title":"Slots","text":"Name Description door_type_wood The type of wood door"},{"location":"DoorTypeWoodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeWoodEnum/#schema-source","title":"Schema Source","text":""},{"location":"DoorTypeWoodEnum/#linkml-source","title":"LinkML Source","text":"
name: door_type_wood_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  bettened and ledged:\n    text: bettened and ledged\n  battened:\n    text: battened\n  ledged and braced:\n    text: ledged and braced\n  ledged and framed:\n    text: ledged and framed\n  ledged, braced and frame:\n    text: ledged, braced and frame\n  framed and paneled:\n    text: framed and paneled\n  glashed or sash:\n    text: glashed or sash\n  flush:\n    text: flush\n  louvered:\n    text: louvered\n  wire gauged:\n    text: wire gauged\n\n
"},{"location":"Double/","title":"Type: Double","text":"

A real number that conforms to the xsd:double specification

URI: xsd:double

"},{"location":"Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Double/#schema-source","title":"Schema Source","text":""},{"location":"Double/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:double native nmdc:double close schema:Float"},{"location":"DrainageClassEnum/","title":"Enum: DrainageClassEnum","text":"

URI: DrainageClassEnum

"},{"location":"DrainageClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description very poorly None poorly None somewhat poorly None moderately well None well None excessively drained None"},{"location":"DrainageClassEnum/#slots","title":"Slots","text":"Name Description drainage_class Drainage classification from a standard system such as the USDA system"},{"location":"DrainageClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrainageClassEnum/#schema-source","title":"Schema Source","text":""},{"location":"DrainageClassEnum/#linkml-source","title":"LinkML Source","text":"
name: drainage_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  very poorly:\n    text: very poorly\n  poorly:\n    text: poorly\n  somewhat poorly:\n    text: somewhat poorly\n  moderately well:\n    text: moderately well\n  well:\n    text: well\n  excessively drained:\n    text: excessively drained\n\n
"},{"location":"DrawingsEnum/","title":"Enum: DrawingsEnum","text":"

URI: DrawingsEnum

"},{"location":"DrawingsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None building navigation map None diagram None sketch None"},{"location":"DrawingsEnum/#slots","title":"Slots","text":"Name Description drawings The buildings architectural drawings; if design is chosen, indicate phase-con..."},{"location":"DrawingsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrawingsEnum/#schema-source","title":"Schema Source","text":""},{"location":"DrawingsEnum/#linkml-source","title":"LinkML Source","text":"
name: drawings_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  operation:\n    text: operation\n  as built:\n    text: as built\n  construction:\n    text: construction\n  bid:\n    text: bid\n  design:\n    text: design\n  building navigation map:\n    text: building navigation map\n  diagram:\n    text: diagram\n  sketch:\n    text: sketch\n\n
"},{"location":"EluentIntroductionCategoryEnum/","title":"Enum: EluentIntroductionCategoryEnum","text":"

URI: EluentIntroductionCategoryEnum

"},{"location":"EluentIntroductionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description liquid_chromatography None The processed sample is introduced into the mass spectrometer through a liqui... gas_chromatography None The processed sample is introduced into the mass spectrometer through a gas c... direct_infusion_syringe None The processed sample is introduced into the mass spectrometer through a direc... direct_infusion_autosampler None The processed sample is introduced into the mass spectrometer through a direc..."},{"location":"EluentIntroductionCategoryEnum/#slots","title":"Slots","text":"Name Description eluent_introduction_category A high-level categorization for how the processed sample is introduced into a..."},{"location":"EluentIntroductionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"EluentIntroductionCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"EluentIntroductionCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: EluentIntroductionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  liquid_chromatography:\n    text: liquid_chromatography\n    description: The processed sample is introduced into the mass spectrometer through\n      a liquid chromatography process.\n    aliases:\n    - LC\n  gas_chromatography:\n    text: gas_chromatography\n    description: The processed sample is introduced into the mass spectrometer through\n      a gas chromatography process.\n    aliases:\n    - GC\n  direct_infusion_syringe:\n    text: direct_infusion_syringe\n    description: The processed sample is introduced into the mass spectrometer through\n      a direct infusion process using a syringe.\n  direct_infusion_autosampler:\n    text: direct_infusion_autosampler\n    description: The processed sample is introduced into the mass spectrometer through\n      a direct infusion process using an autosampler.\n\n
"},{"location":"Environment/","title":"Subset: Environment","text":"

URI: Environment

"},{"location":"Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Environment/#schema-source","title":"Schema Source","text":""},{"location":"EnvironmentalMaterialTerm/","title":"Class: EnvironmentalMaterialTerm (DEPRECATED)

URI: nmdc:EnvironmentalMaterialTerm

classDiagram\n  class EnvironmentalMaterialTerm\n  click EnvironmentalMaterialTerm href \"../EnvironmentalMaterialTerm\"\n    OntologyClass <|-- EnvironmentalMaterialTerm\n      click OntologyClass href \"../OntologyClass\"\n\n\n\n  EnvironmentalMaterialTerm : alternative_identifiers\n\n  EnvironmentalMaterialTerm : description\n\n  EnvironmentalMaterialTerm : id\n\n  EnvironmentalMaterialTerm : name\n\n  EnvironmentalMaterialTerm : type\n\n\n\n
","text":""},{"location":"EnvironmentalMaterialTerm/#inheritance","title":"Inheritance","text":""},{"location":"EnvironmentalMaterialTerm/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"EnvironmentalMaterialTerm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"EnvironmentalMaterialTerm/#schema-source","title":"Schema Source","text":""},{"location":"EnvironmentalMaterialTerm/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:EnvironmentalMaterialTerm native nmdc:EnvironmentalMaterialTerm"},{"location":"EnvironmentalMaterialTerm/#linkml-source","title":"LinkML Source","text":""},{"location":"EnvironmentalMaterialTerm/#direct","title":"Direct","text":"
name: EnvironmentalMaterialTerm\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nclass_uri: nmdc:EnvironmentalMaterialTerm\n\n
"},{"location":"EnvironmentalMaterialTerm/#induced","title":"Induced","text":"
name: EnvironmentalMaterialTerm\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: EnvironmentalMaterialTerm\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:EnvironmentalMaterialTerm\n\n
"},{"location":"EukEval/","title":"Class: EukEval","text":"

This class contains information pertaining to evaluating if a Metagenome-Assembled Genome (MAG) is eukaryotic.

URI: nmdc:EukEval

classDiagram\n  class EukEval\n  click EukEval href \"../EukEval\"\n\n  EukEval : completeness\n\n  EukEval : contamination\n\n  EukEval : ncbi_lineage\n\n  EukEval : ncbi_lineage_tax_ids\n\n  EukEval : type\n\n\n\n
"},{"location":"EukEval/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance type 1 Uriorcurie the class_uri of the class that has been instantiated direct completeness 0..1 Float direct contamination 0..1 Float direct ncbi_lineage_tax_ids 0..1 String Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId) direct ncbi_lineage 0..1 String Comma delimited ordered list of NCBI taxonomy names direct"},{"location":"EukEval/#usages","title":"Usages","text":"used by used in type used MagBin eukaryotic_evaluation range EukEval"},{"location":"EukEval/#comments","title":"Comments","text":""},{"location":"EukEval/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"EukEval/#schema-source","title":"Schema Source","text":""},{"location":"EukEval/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:EukEval native nmdc:EukEval"},{"location":"EukEval/#linkml-source","title":"LinkML Source","text":""},{"location":"EukEval/#direct","title":"Direct","text":"
name: EukEval\ndescription: This class contains information pertaining to evaluating if a Metagenome-Assembled\n  Genome (MAG) is eukaryotic.\ncomments:\n- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information\n  for this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- type\n- completeness\n- contamination\n- ncbi_lineage_tax_ids\n- ncbi_lineage\nclass_uri: nmdc:EukEval\n\n
"},{"location":"EukEval/#induced","title":"Induced","text":"
name: EukEval\ndescription: This class contains information pertaining to evaluating if a Metagenome-Assembled\n  Genome (MAG) is eukaryotic.\ncomments:\n- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information\n  for this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: EukEval\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  completeness:\n    name: completeness\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: completeness\n    owner: EukEval\n    domain_of:\n    - EukEval\n    - MagBin\n    range: float\n  contamination:\n    name: contamination\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: contamination\n    owner: EukEval\n    domain_of:\n    - EukEval\n    - MagBin\n    range: float\n  ncbi_lineage_tax_ids:\n    name: ncbi_lineage_tax_ids\n    description: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)\n    comments:\n    - Example 1-131567-2759-2611352-33682-191814-2603949\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: ncbi_lineage_tax_ids\n    owner: EukEval\n    domain_of:\n    - EukEval\n    range: string\n    pattern: ^\\d+(-\\d+)*$\n  ncbi_lineage:\n    name: ncbi_lineage\n    description: Comma delimited ordered list of NCBI taxonomy names.\n    comments:\n    - Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: ncbi_lineage\n    owner: EukEval\n    domain_of:\n    - EukEval\n    range: string\nclass_uri: nmdc:EukEval\n\n
"},{"location":"ExecutionResourceEnum/","title":"Enum: ExecutionResourceEnum","text":"

URI: ExecutionResourceEnum

"},{"location":"ExecutionResourceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description NERSC-Cori None NERSC Cori supercomputer NERSC-Perlmutter None NERSC Perlmutter supercomputer EMSL None Environmental Molecular Sciences Laboratory EMSL-RZR None Environmental Molecular Sciences Laboratory RZR cluster JGI None Joint Genome Institute LANL-B-div None LANL Bioscience Division"},{"location":"ExecutionResourceEnum/#slots","title":"Slots","text":"Name Description execution_resource The computing resource or facility where the workflow was executed"},{"location":"ExecutionResourceEnum/#see-also","title":"See Also","text":""},{"location":"ExecutionResourceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExecutionResourceEnum/#schema-source","title":"Schema Source","text":""},{"location":"ExecutionResourceEnum/#linkml-source","title":"LinkML Source","text":"
name: ExecutionResourceEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:DoiProviderEnum\n- nmdc:ProcessingInstitutionEnum\n- nmdc:ExecutionResourceEnum\nrank: 1000\npermissible_values:\n  NERSC-Cori:\n    text: NERSC-Cori\n    description: NERSC Cori supercomputer\n    aliases:\n    - Cori\n  NERSC-Perlmutter:\n    text: NERSC-Perlmutter\n    description: NERSC Perlmutter supercomputer\n    aliases:\n    - Perlmutter\n    - Saul\n  EMSL:\n    text: EMSL\n    description: Environmental Molecular Sciences Laboratory\n  EMSL-RZR:\n    text: EMSL-RZR\n    description: Environmental Molecular Sciences Laboratory RZR cluster\n    aliases:\n    - RZR\n  JGI:\n    text: JGI\n    description: Joint Genome Institute\n  LANL-B-div:\n    text: LANL-B-div\n    description: LANL Bioscience Division\n    aliases:\n    - B-div\n\n
"},{"location":"ExtWallOrientEnum/","title":"Enum: ExtWallOrientEnum","text":"

URI: ExtWallOrientEnum

"},{"location":"ExtWallOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWallOrientEnum/#slots","title":"Slots","text":"Name Description ext_wall_orient The orientation of the exterior wall"},{"location":"ExtWallOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWallOrientEnum/#schema-source","title":"Schema Source","text":""},{"location":"ExtWallOrientEnum/#linkml-source","title":"LinkML Source","text":"
name: ext_wall_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n  northeast:\n    text: northeast\n  southeast:\n    text: southeast\n  southwest:\n    text: southwest\n  northwest:\n    text: northwest\n\n
"},{"location":"ExtWindowOrientEnum/","title":"Enum: ExtWindowOrientEnum","text":"

URI: ExtWindowOrientEnum

"},{"location":"ExtWindowOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWindowOrientEnum/#slots","title":"Slots","text":"Name Description ext_window_orient The compass direction the exterior window of the room is facing"},{"location":"ExtWindowOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWindowOrientEnum/#schema-source","title":"Schema Source","text":""},{"location":"ExtWindowOrientEnum/#linkml-source","title":"LinkML Source","text":"
name: ext_window_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n  northeast:\n    text: northeast\n  southeast:\n    text: southeast\n  southwest:\n    text: southwest\n  northwest:\n    text: northwest\n\n
"},{"location":"ExternalIdentifier/","title":"Type: ExternalIdentifier","text":"

A CURIE representing an external identifier

URI: xsd:anyURI

"},{"location":"ExternalIdentifier/#see-also","title":"See Also","text":""},{"location":"ExternalIdentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExternalIdentifier/#schema-source","title":"Schema Source","text":""},{"location":"ExternalIdentifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:anyURI native nmdc:external_identifier"},{"location":"Extraction/","title":"Class: Extraction","text":"

A material separation in which a desired component of an input material is separated from the remainder.

URI: nmdc:Extraction

classDiagram\n  class Extraction\n  click Extraction href \"../Extraction\"\n    MaterialProcessing <|-- Extraction\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  Extraction : alternative_identifiers\n\n  Extraction : description\n\n  Extraction : end_date\n\n  Extraction : extraction_targets\n\n      Extraction --> \"*\" ExtractionTargetEnum : extraction_targets\n    click ExtractionTargetEnum href \"../ExtractionTargetEnum\"\n\n  Extraction : has_failure_categorization\n\n      Extraction --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  Extraction : has_input\n\n      Extraction --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  Extraction : has_output\n\n      Extraction --> \"1..*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  Extraction : id\n\n  Extraction : input_mass\n\n      Extraction --> \"0..1\" QuantityValue : input_mass\n    click QuantityValue href \"../QuantityValue\"\n\n  Extraction : instrument_used\n\n      Extraction --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  Extraction : name\n\n  Extraction : processing_institution\n\n      Extraction --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  Extraction : protocol_link\n\n      Extraction --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  Extraction : qc_comment\n\n  Extraction : qc_status\n\n      Extraction --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  Extraction : start_date\n\n  Extraction : substances_used\n\n      Extraction --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  Extraction : type\n\n  Extraction : volume\n\n      Extraction --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"Extraction/#inheritance","title":"Inheritance","text":""},{"location":"Extraction/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance substances_used * PortionOfSubstance The substances that are combined to enable a ChemicalConversionProcess direct extraction_targets * ExtractionTargetEnum Provides the target biomolecule that has been separated from a sample during ... direct input_mass 0..1 QuantityValue Total mass of sample used in activity direct volume 0..1 QuantityValue The volume of the solvent/solute being used, not the input direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output 1..* ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Extraction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Extraction/#schema-source","title":"Schema Source","text":""},{"location":"Extraction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Extraction native nmdc:Extraction exact OBI:0302884"},{"location":"Extraction/#linkml-source","title":"LinkML Source","text":""},{"location":"Extraction/#direct","title":"Direct","text":"
name: Extraction\ndescription: A material separation in which a desired component of an input material\n  is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: MaterialProcessing\nslots:\n- substances_used\n- extraction_targets\n- input_mass\n- volume\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The volume of the solvent/solute being used, not the input.\nclass_uri: nmdc:Extraction\n\n
"},{"location":"Extraction/#induced","title":"Induced","text":"
name: Extraction\ndescription: A material separation in which a desired component of an input material\n  is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: MaterialProcessing\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The volume of the solvent/solute being used, not the input.\nattributes:\n  substances_used:\n    name: substances_used\n    description: The substances that are combined to enable a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: Extraction\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  extraction_targets:\n    name: extraction_targets\n    description: Provides the target biomolecule that has been separated from a sample\n      during an extraction process.\n    notes:\n    - todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)\n    from_schema: https://w3id.org/nmdc/nmdc\n    narrow_mappings:\n    - NCIT:C177560\n    - MIXS:0000037\n    rank: 1000\n    alias: extraction_targets\n    owner: Extraction\n    domain_of:\n    - Extraction\n    range: ExtractionTargetEnum\n    multivalued: true\n  input_mass:\n    name: input_mass\n    description: Total mass of sample used in activity.\n    title: sample mass used\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - sample mass\n    - sample weight\n    exact_mappings:\n    - MS:1000004\n    narrow_mappings:\n    - MIXS:0000111\n    rank: 1000\n    alias: input_mass\n    owner: Extraction\n    domain_of:\n    - Extraction\n    range: QuantityValue\n  volume:\n    name: volume\n    description: The volume of the solvent/solute being used, not the input.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: Extraction\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: Extraction\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: Extraction\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Extraction\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Extraction\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Extraction\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Extraction\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Extraction\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Extraction\n\n
"},{"location":"ExtractionTargetEnum/","title":"Enum: ExtractionTargetEnum","text":"

URI: ExtractionTargetEnum

"},{"location":"ExtractionTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None metabolite None protein None lipid None"},{"location":"ExtractionTargetEnum/#slots","title":"Slots","text":"Name Description extraction_targets Provides the target biomolecule that has been separated from a sample during ..."},{"location":"ExtractionTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtractionTargetEnum/#schema-source","title":"Schema Source","text":""},{"location":"ExtractionTargetEnum/#linkml-source","title":"LinkML Source","text":"
name: ExtractionTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  DNA:\n    text: DNA\n  RNA:\n    text: RNA\n  metabolite:\n    text: metabolite\n  protein:\n    text: protein\n  lipid:\n    text: lipid\n\n
"},{"location":"FailureCategorization/","title":"Class: FailureCategorization","text":"

URI: nmdc:FailureCategorization

classDiagram\n  class FailureCategorization\n  click FailureCategorization href \"../FailureCategorization\"\n\n  FailureCategorization : qc_failure_what\n\n      FailureCategorization --> \"0..1\" FailureWhatEnum : qc_failure_what\n    click FailureWhatEnum href \"../FailureWhatEnum\"\n\n  FailureCategorization : qc_failure_where\n\n      FailureCategorization --> \"0..1\" FailureWhereEnum : qc_failure_where\n    click FailureWhereEnum href \"../FailureWhereEnum\"\n\n  FailureCategorization : type\n\n\n\n
"},{"location":"FailureCategorization/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance qc_failure_what 0..1 FailureWhatEnum Provides a summary about what caused a lab or workflow process to fail direct qc_failure_where 0..1 FailureWhereEnum Describes the nmdc schema class that corresonds to where the failure occurred direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"FailureCategorization/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_failure_categorization range FailureCategorization MassSpectrometry has_failure_categorization range FailureCategorization Pooling has_failure_categorization range FailureCategorization Extraction has_failure_categorization range FailureCategorization LibraryPreparation has_failure_categorization range FailureCategorization CollectingBiosamplesFromSite has_failure_categorization range FailureCategorization ProtocolExecution has_failure_categorization range FailureCategorization SubSamplingProcess has_failure_categorization range FailureCategorization MixingProcess has_failure_categorization range FailureCategorization FiltrationProcess has_failure_categorization range FailureCategorization StorageProcess has_failure_categorization range FailureCategorization ChromatographicSeparationProcess has_failure_categorization range FailureCategorization DissolvingProcess has_failure_categorization range FailureCategorization ChemicalConversionProcess has_failure_categorization range FailureCategorization MetagenomeAnnotation has_failure_categorization range FailureCategorization MaterialProcessing has_failure_categorization range FailureCategorization PlannedProcess has_failure_categorization range FailureCategorization DataGeneration has_failure_categorization range FailureCategorization WorkflowExecution has_failure_categorization range FailureCategorization MetagenomeAssembly has_failure_categorization range FailureCategorization MetatranscriptomeAssembly has_failure_categorization range FailureCategorization MetatranscriptomeAnnotation has_failure_categorization range FailureCategorization MetatranscriptomeExpressionAnalysis has_failure_categorization range FailureCategorization MagsAnalysis has_failure_categorization range FailureCategorization MetagenomeSequencing has_failure_categorization range FailureCategorization ReadQcAnalysis has_failure_categorization range FailureCategorization ReadBasedTaxonomyAnalysis has_failure_categorization range FailureCategorization MetabolomicsAnalysis has_failure_categorization range FailureCategorization MetaproteomicsAnalysis has_failure_categorization range FailureCategorization NomAnalysis has_failure_categorization range FailureCategorization"},{"location":"FailureCategorization/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FailureCategorization/#schema-source","title":"Schema Source","text":""},{"location":"FailureCategorization/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FailureCategorization native nmdc:FailureCategorization"},{"location":"FailureCategorization/#linkml-source","title":"LinkML Source","text":""},{"location":"FailureCategorization/#direct","title":"Direct","text":"
name: FailureCategorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- qc_failure_what\n- qc_failure_where\n- type\nclass_uri: nmdc:FailureCategorization\n\n
"},{"location":"FailureCategorization/#induced","title":"Induced","text":"
name: FailureCategorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  qc_failure_what:\n    name: qc_failure_what\n    description: Provides a summary about what caused a lab or workflow process to\n      fail\n    comments:\n    - For example, low read count from a sequencer, malformed fastq files, etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_failure_what\n    owner: FailureCategorization\n    domain_of:\n    - FailureCategorization\n    range: FailureWhatEnum\n  qc_failure_where:\n    name: qc_failure_where\n    description: Describes the nmdc schema class that corresonds to where the failure\n      occurred. Most commonly this would be the same as Class that generated the results.\n    comments:\n    - If the assembly size was too small to proceed to annotation failure_where would\n      be MetagenomeAssembly.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_failure_where\n    owner: FailureCategorization\n    domain_of:\n    - FailureCategorization\n    range: FailureWhereEnum\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FailureCategorization\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FailureCategorization\n\n
"},{"location":"FailureWhatEnum/","title":"Enum: FailureWhatEnum","text":"

The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.

URI: FailureWhatEnum

"},{"location":"FailureWhatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low_read_count None Number of output reads is not sufficient to continue to the next analysis ste... malformed_data None Workflow failure reading input or writing the output file(s) assembly_size_too_small None The size of the metagenome or metatranscriptome assembly is too small to proc... no_valid_data_generated None A process ran but did not produce any output other None A lab process or analysis workflow has failed in a way that has not been capt..."},{"location":"FailureWhatEnum/#slots","title":"Slots","text":"Name Description qc_failure_what Provides a summary about what caused a lab or workflow process to fail"},{"location":"FailureWhatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FailureWhatEnum/#schema-source","title":"Schema Source","text":""},{"location":"FailureWhatEnum/#linkml-source","title":"LinkML Source","text":"
name: FailureWhatEnum\ndescription: The permitted values for describing where a failure occurred during processing\n  in the lab during analysis workflows.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  low_read_count:\n    text: low_read_count\n    description: Number of output reads is not sufficient to continue to the next\n      analysis step.\n  malformed_data:\n    text: malformed_data\n    description: Workflow failure reading input or writing the output file(s).\n  assembly_size_too_small:\n    text: assembly_size_too_small\n    description: The size of the metagenome or metatranscriptome assembly is too small\n      to proceed to the next analysis workflow.\n  no_valid_data_generated:\n    text: no_valid_data_generated\n    description: A process ran but did not produce any output. Ie binning ran but\n      did not produce any medium or high quality bins.\n  other:\n    text: other\n    description: A lab process or analysis workflow has failed in a way that has not\n      been captured by the available values yet. Please use slot 'qc_comment' to specify\n      details.\n\n
"},{"location":"FailureWhereEnum/","title":"Enum: FailureWhereEnum","text":"

The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.

URI: FailureWhereEnum

"},{"location":"FailureWhereEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description NucleotideSequencing None A failure has occurred during nucleotide sequencing, a data generation proces... MassSpectrometry None A failure has occurred during mass spectrometry, a data generation process Pooling None A failure has occurred in pooling, a lab process Extraction None A failure has occurred in extraction, a lab process LibraryPreparation None A failure has occurred in library preparation, a lab process MetagenomeAssembly None A failure has occurred in metagenome assembly, a workflow process MetatranscriptomeExpressionAnalysis None A failure has occurred in metatranscriptome expression analysis, a workflow p... MagsAnalysis None A failure has occurred in binning, a workflow process to generate metagenome-... ReadQcAnalysis None A failure has occurred in read qc, a workflow process ReadBasedTaxonomyAnalysis None A failure has occurred in reads based taxonomy, a workflow process MetagenomeAnnotation None A failure has occurred in annotation, a workflow process MetatranscriptomeAssembly None A failure has occurred in assembly, a workflow process MetatranscriptomeAnnotation None A failure has occurred in annotation, a workflow process MetabolomicsAnalysis None A failure has occurred in analyzing metabolomics data MetaproteomicsAnalysis None A failure has occurred in analyzing metaproteomics data NomAnalysis None A failure has occurred in analyzing NOM data"},{"location":"FailureWhereEnum/#slots","title":"Slots","text":"Name Description qc_failure_where Describes the nmdc schema class that corresonds to where the failure occurred"},{"location":"FailureWhereEnum/#comments","title":"Comments","text":""},{"location":"FailureWhereEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FailureWhereEnum/#schema-source","title":"Schema Source","text":""},{"location":"FailureWhereEnum/#linkml-source","title":"LinkML Source","text":"
name: FailureWhereEnum\ndescription: The permitted values for describing where in the process, either a lab\n  or analysis workflow step, the failure occurred.\ncomments:\n- At Chris' recommendation permissible values for this enumeration are the same as\n  Class names.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  NucleotideSequencing:\n    text: NucleotideSequencing\n    description: A failure has occurred during nucleotide sequencing, a data generation\n      process.\n  MassSpectrometry:\n    text: MassSpectrometry\n    description: A failure has occurred during mass spectrometry, a data generation\n      process.\n  Pooling:\n    text: Pooling\n    description: A failure has occurred in pooling, a lab process.\n  Extraction:\n    text: Extraction\n    description: A failure has occurred in extraction, a lab process.\n  LibraryPreparation:\n    text: LibraryPreparation\n    description: A failure has occurred in library preparation, a lab process.\n  MetagenomeAssembly:\n    text: MetagenomeAssembly\n    description: A failure has occurred in metagenome assembly, a workflow process.\n  MetatranscriptomeExpressionAnalysis:\n    text: MetatranscriptomeExpressionAnalysis\n    description: A failure has occurred in metatranscriptome expression analysis,\n      a workflow process.\n  MagsAnalysis:\n    text: MagsAnalysis\n    description: A failure has occurred in binning, a workflow process to generate\n      metagenome-assembled genomes (MAGS).\n  ReadQcAnalysis:\n    text: ReadQcAnalysis\n    description: A failure has occurred in read qc, a workflow process.\n  ReadBasedTaxonomyAnalysis:\n    text: ReadBasedTaxonomyAnalysis\n    description: A failure has occurred in reads based taxonomy, a workflow process.\n  MetagenomeAnnotation:\n    text: MetagenomeAnnotation\n    description: A failure has occurred in annotation, a workflow process.\n  MetatranscriptomeAssembly:\n    text: MetatranscriptomeAssembly\n    description: A failure has occurred in assembly, a workflow process.\n  MetatranscriptomeAnnotation:\n    text: MetatranscriptomeAnnotation\n    description: A failure has occurred in annotation, a workflow process.\n  MetabolomicsAnalysis:\n    text: MetabolomicsAnalysis\n    description: A failure has occurred in analyzing metabolomics data.\n  MetaproteomicsAnalysis:\n    text: MetaproteomicsAnalysis\n    description: A failure has occurred in analyzing metaproteomics data.\n  NomAnalysis:\n    text: NomAnalysis\n    description: A failure has occurred in analyzing NOM data.\n\n
"},{"location":"FaoClassEnum/","title":"Enum: FaoClassEnum","text":"

URI: FaoClassEnum

"},{"location":"FaoClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Acrisols None Andosols None Arenosols None Cambisols None Chernozems None Ferralsols None Fluvisols None Gleysols None Greyzems None Gypsisols None Histosols None Kastanozems None Lithosols None Luvisols None Nitosols None Phaeozems None Planosols None Podzols None Podzoluvisols None Rankers None Regosols None Rendzinas None Solonchaks None Solonetz None Vertisols None Yermosols None"},{"location":"FaoClassEnum/#slots","title":"Slots","text":"Name Description fao_class Soil classification from the FAO World Reference Database for Soil Resources"},{"location":"FaoClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FaoClassEnum/#schema-source","title":"Schema Source","text":""},{"location":"FaoClassEnum/#linkml-source","title":"LinkML Source","text":"
name: fao_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Acrisols:\n    text: Acrisols\n  Andosols:\n    text: Andosols\n  Arenosols:\n    text: Arenosols\n  Cambisols:\n    text: Cambisols\n  Chernozems:\n    text: Chernozems\n  Ferralsols:\n    text: Ferralsols\n  Fluvisols:\n    text: Fluvisols\n  Gleysols:\n    text: Gleysols\n  Greyzems:\n    text: Greyzems\n  Gypsisols:\n    text: Gypsisols\n  Histosols:\n    text: Histosols\n  Kastanozems:\n    text: Kastanozems\n  Lithosols:\n    text: Lithosols\n  Luvisols:\n    text: Luvisols\n  Nitosols:\n    text: Nitosols\n  Phaeozems:\n    text: Phaeozems\n  Planosols:\n    text: Planosols\n  Podzols:\n    text: Podzols\n  Podzoluvisols:\n    text: Podzoluvisols\n  Rankers:\n    text: Rankers\n  Regosols:\n    text: Regosols\n  Rendzinas:\n    text: Rendzinas\n  Solonchaks:\n    text: Solonchaks\n  Solonetz:\n    text: Solonetz\n  Vertisols:\n    text: Vertisols\n  Yermosols:\n    text: Yermosols\n\n
"},{"location":"FieldResearchSite/","title":"Class: Field Research Site (FieldResearchSite)","text":"

A site, outside of a laboratory, from which biosamples may be collected.

URI: nmdc:FieldResearchSite

classDiagram\n  class FieldResearchSite\n  click FieldResearchSite href \"../FieldResearchSite\"\n    Site <|-- FieldResearchSite\n      click Site href \"../Site\"\n\n\n\n  FieldResearchSite : alternative_identifiers\n\n  FieldResearchSite : cur_vegetation\n\n      FieldResearchSite --> \"0..1\" TextValue : cur_vegetation\n    click TextValue href \"../TextValue\"\n\n  FieldResearchSite : description\n\n  FieldResearchSite : elev\n\n  FieldResearchSite : geo_loc_name\n\n      FieldResearchSite --> \"0..1\" TextValue : geo_loc_name\n    click TextValue href \"../TextValue\"\n\n  FieldResearchSite : habitat\n\n  FieldResearchSite : id\n\n  FieldResearchSite : lat_lon\n\n      FieldResearchSite --> \"0..1\" GeolocationValue : lat_lon\n    click GeolocationValue href \"../GeolocationValue\"\n\n  FieldResearchSite : local_class\n\n      FieldResearchSite --> \"0..1\" TextValue : local_class\n    click TextValue href \"../TextValue\"\n\n  FieldResearchSite : name\n\n  FieldResearchSite : part_of\n\n      FieldResearchSite --> \"*\" FieldResearchSite : part_of\n    click FieldResearchSite href \"../FieldResearchSite\"\n\n  FieldResearchSite : soil_type\n\n      FieldResearchSite --> \"0..1\" TextValue : soil_type\n    click TextValue href \"../TextValue\"\n\n  FieldResearchSite : type\n\n\n\n
"},{"location":"FieldResearchSite/#inheritance","title":"Inheritance","text":""},{"location":"FieldResearchSite/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance cur_vegetation 0..1 TextValue Vegetation classification from one or more standard classification systems, o... direct elev 0..1 Float Elevation of the sampling site is its height above a fixed reference point, m... direct geo_loc_name 0..1 TextValue The geographical origin of the sample as defined by the country or sea name f... direct habitat 0..1 String direct lat_lon 0..1 GeolocationValue The geographical origin of the sample as defined by latitude and longitude direct local_class 0..1 TextValue Soil classification based on local soil classification system direct part_of * FieldResearchSite Links a resource to another resource that either logically or physically incl... direct soil_type 0..1 TextValue Description of the soil type or classification direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"FieldResearchSite/#usages","title":"Usages","text":"used by used in type used Database field_research_site_set range FieldResearchSite FieldResearchSite part_of range FieldResearchSite Biosample collected_from range FieldResearchSite"},{"location":"FieldResearchSite/#aliases","title":"Aliases","text":""},{"location":"FieldResearchSite/#comments","title":"Comments","text":""},{"location":"FieldResearchSite/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FieldResearchSite/#schema-source","title":"Schema Source","text":""},{"location":"FieldResearchSite/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FieldResearchSite native nmdc:FieldResearchSite"},{"location":"FieldResearchSite/#linkml-source","title":"LinkML Source","text":""},{"location":"FieldResearchSite/#direct","title":"Direct","text":"
name: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n  the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n  same plant were obtained at the same site. In this case, the site would correspond\n  to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslots:\n- cur_vegetation\n- elev\n- geo_loc_name\n- habitat\n- lat_lon\n- local_class\n- part_of\n- soil_type\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  part_of:\n    name: part_of\n    range: FieldResearchSite\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:FieldResearchSite\n\n
"},{"location":"FieldResearchSite/#induced","title":"Induced","text":"
name: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n  the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n  same plant were obtained at the same site. In this case, the site would correspond\n  to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  part_of:\n    name: part_of\n    range: FieldResearchSite\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  cur_vegetation:\n    name: cur_vegetation\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: current vegetation type\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Vegetation classification from one or more standard classification\n      systems, or agricultural crop\n    title: current vegetation\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - current vegetation\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000312\n    alias: cur_vegetation\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  elev:\n    name: elev\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: measurement value\n    description: Elevation of the sampling site is its height above a fixed reference\n      point, most commonly the mean sea level. Elevation is mainly used when referring\n      to points on the earth's surface, while altitude is used for points above the\n      surface, such as an aircraft in flight or a spacecraft in orbit.\n    title: elevation\n    examples:\n    - value: 100 meter\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - elevation\n    rank: 1000\n    is_a: environment field\n    slot_uri: MIXS:0000093\n    alias: elev\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: float\n    multivalued: false\n  geo_loc_name:\n    name: geo_loc_name\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n          name'\n    description: The geographical origin of the sample as defined by the country or\n      sea name followed by specific region name. Country or sea names should be chosen\n      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n      (http://purl.bioontology.org/ontology/GAZ)\n    title: geographic location (country and/or sea,region)\n    examples:\n    - value: 'USA: Maryland, Bethesda'\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - geographic location (country and/or sea,region)\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{term}: {term}, {text}'\n    slot_uri: MIXS:0000010\n    alias: geo_loc_name\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  habitat:\n    name: habitat\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: habitat\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: string\n  lat_lon:\n    name: lat_lon\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: decimal degrees,  limit to 8 decimal points\n    description: The geographical origin of the sample as defined by latitude and\n      longitude. The values should be reported in decimal degrees and in WGS84 system\n    title: geographic location (latitude and longitude)\n    examples:\n    - value: 50.586825 6.408977\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - geographic location (latitude and longitude)\n    rank: 1000\n    is_a: environment field\n    string_serialization: '{float} {float}'\n    slot_uri: MIXS:0000009\n    alias: lat_lon\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: GeolocationValue\n    multivalued: false\n  local_class:\n    name: local_class\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: local classification name\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Soil classification based on local soil classification system\n    title: soil_taxonomic/local classification\n    examples:\n    - value: ''\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil_taxonomic/local classification\n    rank: 1000\n    is_a: core field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000330\n    alias: local_class\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  part_of:\n    name: part_of\n    description: Links a resource to another resource that either logically or physically\n      includes it.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - is part of\n    rank: 1000\n    slot_uri: dcterms:isPartOf\n    alias: part_of\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Study\n    range: FieldResearchSite\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  soil_type:\n    name: soil_type\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: ENVO_00001998\n      occurrence:\n        tag: occurrence\n        value: '1'\n    description: Description of the soil type or classification. This field accepts\n      terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms\n      can be separated by pipes.\n    title: soil type\n    examples:\n    - value: plinthosol [ENVO:00002250]\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - soil type\n    rank: 1000\n    is_a: core field\n    string_serialization: '{termLabel} {[termID]}'\n    slot_uri: MIXS:0000332\n    alias: soil_type\n    owner: FieldResearchSite\n    domain_of:\n    - FieldResearchSite\n    - Biosample\n    range: TextValue\n    multivalued: false\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: FieldResearchSite\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: FieldResearchSite\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: FieldResearchSite\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: FieldResearchSite\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FieldResearchSite\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FieldResearchSite\n\n
"},{"location":"FileTypeEnum/","title":"Enum: FileTypeEnum","text":"

URI: FileTypeEnum

"},{"location":"FileTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Reference Calibration File None A file that contains data used to calibrate a natural organic matter or metab... Metagenome Raw Reads None Interleaved paired-end raw sequencing data Metagenome Raw Read 1 None Read 1 raw sequencing data, aka forward reads Metagenome Raw Read 2 None Read 2 raw sequencing data, aka reverse reads FT ICR-MS Analysis Results None FT ICR-MS-based molecular formula assignment results table GC-MS Metabolomics Results None GC-MS-based metabolite assignment results table Metaproteomics Workflow Statistics None Aggregate workflow statistics file Protein Report None Filtered protein report file Peptide Report None Filtered peptide report file Unfiltered Metaproteomics Results None MSGFjobs and MASIC output file Read Count and RPKM None Annotation read count and RPKM per feature JSON QC non-rRNA R2 None QC removed rRNA reads (R2) fastq QC non-rRNA R1 None QC removed rRNA reads (R1) fastq Metagenome Bins None Metagenome bin contigs fasta Metagenome HQMQ Bins Compression File None Compressed file containing high qulaity and medium quality metagenome bins an... Metagenome LQ Bins Compression File None Compressed file containing low quality metagenome bins and associated files Metagenome Bins Info File None File containing version information on the binning workflow CheckM Statistics None CheckM statistics report Metagenome Bins Heatmap None The Heatmap presents the pdf file containing the KO analysis results for meta... Metagenome Bins Barplot None The Bar chart presents the pdf file containing the KO analysis results for me... Metagenome Bins Krona Plot None The Krona plot presents the HTML file containing the KO analysis results for ... Read Based Analysis Info File None File containing reads based analysis information GTDBTK Bacterial Summary None GTDBTK bacterial summary GTDBTK Archaeal Summary None GTDBTK archaeal summary GOTTCHA2 Krona Plot None GOTTCHA2 krona plot HTML file GOTTCHA2 Classification Report None GOTTCHA2 classification report file GOTTCHA2 Report Full None GOTTCHA2 report file Kraken2 Krona Plot None Kraken2 krona plot HTML file Centrifuge Krona Plot None Centrifuge krona plot HTML file Centrifuge output report file None Centrifuge output report file Kraken2 Classification Report None Kraken2 output report file Kraken2 Taxonomic Classification None Kraken2 output read classification file Centrifuge Classification Report None Centrifuge output report file Centrifuge Taxonomic Classification None Centrifuge output read classification file Structural Annotation GFF None GFF3 format file with structural annotations Structural Annotation Stats Json None Structural annotations stats json Functional Annotation GFF None GFF3 format file with functional annotations Annotation Info File None File containing annotation info Annotation Amino Acid FASTA None FASTA amino acid file for annotated proteins Annotation Enzyme Commission None Tab delimited file for EC annotation Annotation KEGG Orthology None Tab delimited file for KO annotation Assembly Info File None File containing assembly info Assembly Coverage BAM None Sorted bam file of reads mapping back to the final assembly Assembly AGP None An AGP format file that describes the assembly Assembly Scaffolds None Final assembly scaffolds fasta Assembly Contigs None Final assembly contigs fasta Assembly Coverage Stats None Assembled contigs coverage information Contig Mapping File None Contig mappings between contigs and scaffolds Error Corrected Reads None Error corrected reads fastq Filtered Sequencing Reads None Reads QC result fastq (clean data) Read Filtering Info File None File containing read filtering information QC Statistics Extended None Extended report including methods and results for read filtering QC Statistics None Reads QC summary statistics TIGRFam Annotation GFF None GFF3 format file with TIGRfam CRT Annotation GFF None GFF3 format file with CRT Genemark Annotation GFF None GFF3 format file with Genemark Prodigal Annotation GFF None GFF3 format file with Prodigal TRNA Annotation GFF None GFF3 format file with TRNA Misc Annotation GFF None GFF3 format file with Misc RFAM Annotation GFF None GFF3 format file with RFAM TMRNA Annotation GFF None GFF3 format file with TMRNA Crispr Terms None Crispr Terms Product Names None Product names file Gene Phylogeny tsv None Gene Phylogeny tsv Scaffold Lineage tsv None phylogeny at the scaffold level Clusters of Orthologous Groups (COG) Annotation GFF None GFF3 format file with COGs KO_EC Annotation GFF None GFF3 format file with KO_EC CATH FunFams (Functional Families) Annotation GFF None GFF3 format file with CATH FunFams SUPERFam Annotation GFF None GFF3 format file with SUPERFam SMART Annotation GFF None GFF3 format file with SMART Pfam Annotation GFF None GFF3 format file with Pfam Annotation Statistics None Annotation statistics report Direct Infusion FT ICR-MS Raw Data None Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance mass spect... LC-DDA-MS/MS Raw Data None Liquid chromatographically separated MS1 and Data-Dependent MS2 binary instru... Configuration toml None A configuration toml file used by various programs to store settings that are... LC-MS Lipidomics Results None LC-MS-based lipid assignment results table Contaminants Amino Acid FASTA None FASTA amino acid file for contaminant proteins commonly observed in proteomic... Analysis Tool Parameter File None A configuration file used by a single computational software tool that stores... Workflow Operation Summary None A human readable record of analysis steps applied during an instance of a wor... Metatranscriptome Expression None Metatranscriptome expression values and read counts for gene features predict... Metatranscriptome Expression Intergenic None Metatranscriptome expression values and read counts for intergenic regions Metatranscriptome Expression Info File None File containing version information on the expression workflow rRNA Filtered Sequencing Reads None File containing ribosomal reads from the read qc filtering step BAI File None An index file found in the same directory as the binary alignment map (BAM) f..."},{"location":"FileTypeEnum/#slots","title":"Slots","text":"Name Description data_object_type The type of file represented by the data object"},{"location":"FileTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FileTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"FileTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: FileTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Reference Calibration File:\n    text: Reference Calibration File\n    description: A file that contains data used to calibrate a natural organic matter\n      or metabalomics analysis.\n  Metagenome Raw Reads:\n    text: Metagenome Raw Reads\n    description: Interleaved paired-end raw sequencing data\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: ^\\.fastq(\\.gz)?$\n  Metagenome Raw Read 1:\n    text: Metagenome Raw Read 1\n    description: Read 1 raw sequencing data, aka forward reads\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: ^.+_R1\\.fastq(\\.gz)?$\n    examples:\n    - value: BMI_H25VYBGXH_19S_31WellG1_R1.fastq.gz\n  Metagenome Raw Read 2:\n    text: Metagenome Raw Read 2\n    description: Read 2 raw sequencing data, aka reverse reads\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: ^.+_R2\\.fastq(\\.gz)?$\n    examples:\n    - value: BMI_H25VYBGXH_19S_31WellG1_R2.fastq.gz\n  FT ICR-MS Analysis Results:\n    text: FT ICR-MS Analysis Results\n    description: FT ICR-MS-based molecular formula assignment results table\n  GC-MS Metabolomics Results:\n    text: GC-MS Metabolomics Results\n    description: GC-MS-based metabolite assignment results table\n  Metaproteomics Workflow Statistics:\n    text: Metaproteomics Workflow Statistics\n    description: Aggregate workflow statistics file\n  Protein Report:\n    text: Protein Report\n    description: Filtered protein report file\n  Peptide Report:\n    text: Peptide Report\n    description: Filtered peptide report file\n  Unfiltered Metaproteomics Results:\n    text: Unfiltered Metaproteomics Results\n    description: MSGFjobs and MASIC output file\n  Read Count and RPKM:\n    text: Read Count and RPKM\n    description: Annotation read count and RPKM per feature JSON\n  QC non-rRNA R2:\n    text: QC non-rRNA R2\n    description: QC removed rRNA reads (R2) fastq\n  QC non-rRNA R1:\n    text: QC non-rRNA R1\n    description: QC removed rRNA reads (R1) fastq\n  Metagenome Bins:\n    text: Metagenome Bins\n    description: Metagenome bin contigs fasta\n  Metagenome HQMQ Bins Compression File:\n    text: Metagenome HQMQ Bins Compression File\n    description: Compressed file containing high qulaity and medium quality metagenome\n      bins and associated files\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_hqmq_bin.zip'\n  Metagenome LQ Bins Compression File:\n    text: Metagenome LQ Bins Compression File\n    description: Compressed file containing low quality metagenome bins and associated\n      files\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_lq_bin.zip'\n  Metagenome Bins Info File:\n    text: Metagenome Bins Info File\n    description: File containing version information on the binning workflow\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_bin.info'\n  CheckM Statistics:\n    text: CheckM Statistics\n    description: CheckM statistics report\n  Metagenome Bins Heatmap:\n    text: Metagenome Bins Heatmap\n    description: The Heatmap presents the pdf file containing the KO analysis results\n      for metagenome bins\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_heatmap.pdf'\n  Metagenome Bins Barplot:\n    text: Metagenome Bins Barplot\n    description: The Bar chart presents the pdf file containing the KO analysis results\n      for metagenome bins\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_barplot.pdf'\n  Metagenome Bins Krona Plot:\n    text: Metagenome Bins Krona Plot\n    description: The Krona plot presents the HTML file containing the KO analysis\n      results for metagenome bins\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[mag_wf_activity_id]_kronaplot.html'\n  Read Based Analysis Info File:\n    text: Read Based Analysis Info File\n    description: File containing reads based analysis information\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: profiler.info\n  GTDBTK Bacterial Summary:\n    text: GTDBTK Bacterial Summary\n    description: GTDBTK bacterial summary\n  GTDBTK Archaeal Summary:\n    text: GTDBTK Archaeal Summary\n    description: GTDBTK archaeal summary\n  GOTTCHA2 Krona Plot:\n    text: GOTTCHA2 Krona Plot\n    description: GOTTCHA2 krona plot HTML file\n  GOTTCHA2 Classification Report:\n    text: GOTTCHA2 Classification Report\n    description: GOTTCHA2 classification report file\n  GOTTCHA2 Report Full:\n    text: GOTTCHA2 Report Full\n    description: GOTTCHA2 report file\n  Kraken2 Krona Plot:\n    text: Kraken2 Krona Plot\n    description: Kraken2 krona plot HTML file\n  Centrifuge Krona Plot:\n    text: Centrifuge Krona Plot\n    description: Centrifuge krona plot HTML file\n  Centrifuge output report file:\n    text: Centrifuge output report file\n    description: Centrifuge output report file\n  Kraken2 Classification Report:\n    text: Kraken2 Classification Report\n    description: Kraken2 output report file\n  Kraken2 Taxonomic Classification:\n    text: Kraken2 Taxonomic Classification\n    description: Kraken2 output read classification file\n  Centrifuge Classification Report:\n    text: Centrifuge Classification Report\n    description: Centrifuge output report file\n  Centrifuge Taxonomic Classification:\n    text: Centrifuge Taxonomic Classification\n    description: Centrifuge output read classification file\n  Structural Annotation GFF:\n    text: Structural Annotation GFF\n    description: GFF3 format file with structural annotations\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_structural_annotation.gff'\n  Structural Annotation Stats Json:\n    text: Structural Annotation Stats Json\n    description: Structural annotations stats json\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_structural_annotation_stats.json'\n  Functional Annotation GFF:\n    text: Functional Annotation GFF\n    description: GFF3 format file with functional annotations\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_functional_annotation.gff'\n  Annotation Info File:\n    text: Annotation Info File\n    description: File containing annotation info\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_imgap.info'\n  Annotation Amino Acid FASTA:\n    text: Annotation Amino Acid FASTA\n    description: FASTA amino acid file for annotated proteins\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_proteins.faa'\n  Annotation Enzyme Commission:\n    text: Annotation Enzyme Commission\n    description: Tab delimited file for EC annotation\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_ec.tsv'\n  Annotation KEGG Orthology:\n    text: Annotation KEGG Orthology\n    description: Tab delimited file for KO annotation\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_ko.tsv'\n  Assembly Info File:\n    text: Assembly Info File\n    description: File containing assembly info\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: README.txt\n  Assembly Coverage BAM:\n    text: Assembly Coverage BAM\n    description: Sorted bam file of reads mapping back to the final assembly\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_pairedMapped.sam.gz'\n  Assembly AGP:\n    text: Assembly AGP\n    description: An AGP format file that describes the assembly\n  Assembly Scaffolds:\n    text: Assembly Scaffolds\n    description: Final assembly scaffolds fasta\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_assembly.contigs.fasta'\n  Assembly Contigs:\n    text: Assembly Contigs\n    description: Final assembly contigs fasta\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: assembly.contigs.fasta\n  Assembly Coverage Stats:\n    text: Assembly Coverage Stats\n    description: Assembled contigs coverage information\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_pairedMapped_sorted.bam.cov'\n  Contig Mapping File:\n    text: Contig Mapping File\n    description: Contig mappings between contigs and scaffolds\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_contig_names_mapping.tsv'\n  Error Corrected Reads:\n    text: Error Corrected Reads\n    description: Error corrected reads fastq\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: input.corr.fastq.gz\n  Filtered Sequencing Reads:\n    text: Filtered Sequencing Reads\n    description: Reads QC result fastq (clean data)\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '/.+?(?=filter)/filter-METAGENOME.fastq.gz '\n  Read Filtering Info File:\n    text: Read Filtering Info File\n    description: File containing read filtering information\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[rqc_wf_activity_id]_readsQC.info'\n  QC Statistics Extended:\n    text: QC Statistics Extended\n    description: Extended report including methods and results for read filtering\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: /.+?(?=filter)/filtered-report.txt\n  QC Statistics:\n    text: QC Statistics\n    description: Reads QC summary statistics\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[rqc_wf_activity_id]_filterStats2.txt'\n  TIGRFam Annotation GFF:\n    text: TIGRFam Annotation GFF\n    description: GFF3 format file with TIGRfam\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_tigrfam.gff'\n  CRT Annotation GFF:\n    text: CRT Annotation GFF\n    description: GFF3 format file with CRT\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_crt.gff'\n  Genemark Annotation GFF:\n    text: Genemark Annotation GFF\n    description: GFF3 format file with Genemark\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_genemark.gff'\n  Prodigal Annotation GFF:\n    text: Prodigal Annotation GFF\n    description: GFF3 format file with Prodigal\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_prodigal.gff'\n  TRNA Annotation GFF:\n    text: TRNA Annotation GFF\n    description: GFF3 format file with TRNA\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_trna.gff'\n  Misc Annotation GFF:\n    text: Misc Annotation GFF\n    description: GFF3 format file with Misc\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff'\n  RFAM Annotation GFF:\n    text: RFAM Annotation GFF\n    description: GFF3 format file with RFAM\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_rfam.gff'\n  TMRNA Annotation GFF:\n    text: TMRNA Annotation GFF\n    description: GFF3 format file with TMRNA\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_rfam_ncrna_tmrna.gff'\n  Crispr Terms:\n    text: Crispr Terms\n    description: Crispr Terms\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_crt.crisprs'\n  Product Names:\n    text: Product Names\n    description: Product names file\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_product_names.tsv'\n  Gene Phylogeny tsv:\n    text: Gene Phylogeny tsv\n    description: Gene Phylogeny tsv\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_gene_phylogeny.tsv'\n  Scaffold Lineage tsv:\n    text: Scaffold Lineage tsv\n    description: phylogeny at the scaffold level\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_scaffold_lineage.tsv'\n  Clusters of Orthologous Groups (COG) Annotation GFF:\n    text: Clusters of Orthologous Groups (COG) Annotation GFF\n    description: GFF3 format file with COGs\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_cog.gff'\n  KO_EC Annotation GFF:\n    text: KO_EC Annotation GFF\n    description: GFF3 format file with KO_EC\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_ko_ec.gff'\n  CATH FunFams (Functional Families) Annotation GFF:\n    text: CATH FunFams (Functional Families) Annotation GFF\n    description: GFF3 format file with CATH FunFams\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_cath_funfam.gff'\n  SUPERFam Annotation GFF:\n    text: SUPERFam Annotation GFF\n    description: GFF3 format file with SUPERFam\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_supfam.gff'\n  SMART Annotation GFF:\n    text: SMART Annotation GFF\n    description: GFF3 format file with SMART\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_smart.gff'\n  Pfam Annotation GFF:\n    text: Pfam Annotation GFF\n    description: GFF3 format file with Pfam\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '[GOLD-AP]_pfam.gff'\n  Annotation Statistics:\n    text: Annotation Statistics\n    description: Annotation statistics report\n  Direct Infusion FT ICR-MS Raw Data:\n    text: Direct Infusion FT ICR-MS Raw Data\n    description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance\n      mass spectrometry raw data acquired in broadband full scan mode\n  LC-DDA-MS/MS Raw Data:\n    text: LC-DDA-MS/MS Raw Data\n    description: Liquid chromatographically separated MS1 and Data-Dependent MS2 binary\n      instrument file\n  Configuration toml:\n    text: Configuration toml\n    description: A configuration toml file used by various programs to store settings\n      that are specific to their respective software.\n    broad_mappings:\n    - edam.format:4005\n  LC-MS Lipidomics Results:\n    text: LC-MS Lipidomics Results\n    description: LC-MS-based lipid assignment results table.\n  Contaminants Amino Acid FASTA:\n    text: Contaminants Amino Acid FASTA\n    description: FASTA amino acid file for contaminant proteins commonly observed\n      in proteomics data.\n  Analysis Tool Parameter File:\n    text: Analysis Tool Parameter File\n    description: A configuration file used by a single computational software tool\n      that stores settings that are specific to that tool.\n  Workflow Operation Summary:\n    text: Workflow Operation Summary\n    description: A human readable record of analysis steps applied during an instance\n      of a workflow operation.\n  Metatranscriptome Expression:\n    text: Metatranscriptome Expression\n    description: Metatranscriptome expression values and read counts for gene features\n      predicted on contigs\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*.rnaseq_gea.txt'\n  Metatranscriptome Expression Intergenic:\n    text: Metatranscriptome Expression Intergenic\n    description: Metatranscriptome expression values and read counts for intergenic\n      regions.\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*.rnaseq_gea.intergenic.txt'\n  Metatranscriptome Expression Info File:\n    text: Metatranscriptome Expression Info File\n    description: File containing version information on the expression workflow\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*_readcount.info'\n  rRNA Filtered Sequencing Reads:\n    text: rRNA Filtered Sequencing Reads\n    description: File containing ribosomal reads from the read qc filtering step.\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*.rRNA.fastq.gz'\n  BAI File:\n    text: BAI File\n    description: An index file found in the same directory as the binary alignment\n      map (BAM) file, a compressed binary version of a sequence alignment/map (SAM)\n      file.\n    annotations:\n      file_name_pattern:\n        tag: file_name_pattern\n        value: '*.pairedMapped_sorted.bam.bai'\n    exact_mappings:\n    - NCIT:C190163\n\n
"},{"location":"FilterTypeEnum/","title":"Enum: FilterTypeEnum","text":"

URI: FilterTypeEnum

"},{"location":"FilterTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description particulate air filter None chemical air filter None low-MERV pleated media None HEPA None electrostatic None gas-phase or ultraviolet air treatments None"},{"location":"FilterTypeEnum/#slots","title":"Slots","text":"Name Description filter_type A device which removes solid particulates or airborne molecular contaminants"},{"location":"FilterTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FilterTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"FilterTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: filter_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  particulate air filter:\n    text: particulate air filter\n  chemical air filter:\n    text: chemical air filter\n  low-MERV pleated media:\n    text: low-MERV pleated media\n  HEPA:\n    text: HEPA\n  electrostatic:\n    text: electrostatic\n  gas-phase or ultraviolet air treatments:\n    text: gas-phase or ultraviolet air treatments\n\n
"},{"location":"FiltrationProcess/","title":"Class: FiltrationProcess","text":"

The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.

URI: nmdc:FiltrationProcess

classDiagram\n  class FiltrationProcess\n  click FiltrationProcess href \"../FiltrationProcess\"\n    MaterialProcessing <|-- FiltrationProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  FiltrationProcess : alternative_identifiers\n\n  FiltrationProcess : conditionings\n\n  FiltrationProcess : container_size\n\n      FiltrationProcess --> \"0..1\" QuantityValue : container_size\n    click QuantityValue href \"../QuantityValue\"\n\n  FiltrationProcess : description\n\n  FiltrationProcess : end_date\n\n  FiltrationProcess : filter_material\n\n  FiltrationProcess : filter_pore_size\n\n      FiltrationProcess --> \"0..1\" QuantityValue : filter_pore_size\n    click QuantityValue href \"../QuantityValue\"\n\n  FiltrationProcess : filtration_category\n\n  FiltrationProcess : has_failure_categorization\n\n      FiltrationProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  FiltrationProcess : has_input\n\n      FiltrationProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  FiltrationProcess : has_output\n\n      FiltrationProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  FiltrationProcess : id\n\n  FiltrationProcess : instrument_used\n\n      FiltrationProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  FiltrationProcess : is_pressurized\n\n  FiltrationProcess : name\n\n  FiltrationProcess : processing_institution\n\n      FiltrationProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  FiltrationProcess : protocol_link\n\n      FiltrationProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  FiltrationProcess : qc_comment\n\n  FiltrationProcess : qc_status\n\n      FiltrationProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  FiltrationProcess : separation_method\n\n      FiltrationProcess --> \"0..1\" SeparationMethodEnum : separation_method\n    click SeparationMethodEnum href \"../SeparationMethodEnum\"\n\n  FiltrationProcess : start_date\n\n  FiltrationProcess : type\n\n  FiltrationProcess : volume\n\n      FiltrationProcess --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"FiltrationProcess/#inheritance","title":"Inheritance","text":""},{"location":"FiltrationProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance conditionings * String Preliminary treatment of either phase with a suitable solution of the other p... direct container_size 0..1 QuantityValue The volume of the container an analyte is stored in or an activity takes plac... direct filter_material 0..1 String A porous material on which solid particles present in air or other fluid whic... direct filter_pore_size 0..1 QuantityValue A quantitative or qualitative measurement of the physical dimensions of the p... direct filtration_category 0..1 String The type of conditioning applied to a filter, device, etc direct is_pressurized 0..1 Boolean Whether or not pressure was applied to a thing or process direct separation_method 0..1 SeparationMethodEnum The method that was used to separate a substance from a solution or mixture direct volume 0..1 QuantityValue The volume of sample filtered direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"FiltrationProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FiltrationProcess/#schema-source","title":"Schema Source","text":""},{"location":"FiltrationProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FiltrationProcess native nmdc:FiltrationProcess related CHMO:0001640"},{"location":"FiltrationProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"FiltrationProcess/#direct","title":"Direct","text":"
name: FiltrationProcess\ndescription: The process of segregation of phases; e.g. the separation of suspended\n  solids from a liquid or gas, usually by forcing a carrier gas or liquid through\n  a porous medium.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- CHMO:0001640\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslots:\n- conditionings\n- container_size\n- filter_material\n- filter_pore_size\n- filtration_category\n- is_pressurized\n- separation_method\n- volume\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The volume of sample filtered.\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:FiltrationProcess\n\n
"},{"location":"FiltrationProcess/#induced","title":"Induced","text":"
name: FiltrationProcess\ndescription: The process of segregation of phases; e.g. the separation of suspended\n  solids from a liquid or gas, usually by forcing a carrier gas or liquid through\n  a porous medium.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- CHMO:0001640\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The volume of sample filtered.\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  conditionings:\n    name: conditionings\n    description: Preliminary treatment of either phase with a suitable solution of\n      the other phase (in the absence of main extractable solute(s)) so that when\n      the subsequent equilibration is carried out changes in the (volume) phase ratio\n      or in the concentrations of other components are minimized.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    list_elements_ordered: true\n    alias: conditionings\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: string\n    multivalued: true\n  container_size:\n    name: container_size\n    description: The volume of the container an analyte is stored in or an activity\n      takes place in\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: container_size\n    owner: FiltrationProcess\n    domain_of:\n    - SubSamplingProcess\n    - FiltrationProcess\n    range: QuantityValue\n  filter_material:\n    name: filter_material\n    description: A porous material on which solid particles present in air or other\n      fluid which flows through it are largely caught and retained.\n    comments:\n    - 'Filters are made with a variety of materials: cellulose and derivatives, glass\n      fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous\n      or be made so by mechanical or other means. Membrane/ceramic filters are prepared\n      with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene,\n      polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement.\n      The pores constitute 80\u201385% of the filter volume commonly and several pore sizes\n      are available for air sampling (0.45\u22120.8 \u03bcm are commonly employed).'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: filter_material\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: string\n  filter_pore_size:\n    name: filter_pore_size\n    description: A quantitative or qualitative measurement of the physical dimensions\n      of the pores in a material.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: filter_pore_size\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: QuantityValue\n  filtration_category:\n    name: filtration_category\n    description: The type of conditioning applied to a filter, device, etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: filtration_category\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: string\n  is_pressurized:\n    name: is_pressurized\n    description: Whether or not pressure was applied to a thing or process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: is_pressurized\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: boolean\n  separation_method:\n    name: separation_method\n    description: The method that was used to separate a substance from a solution\n      or mixture.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: separation_method\n    owner: FiltrationProcess\n    domain_of:\n    - FiltrationProcess\n    range: SeparationMethodEnum\n  volume:\n    name: volume\n    description: The volume of sample filtered.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: FiltrationProcess\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: FiltrationProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: FiltrationProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: FiltrationProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: FiltrationProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: FiltrationProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: FiltrationProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FiltrationProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FiltrationProcess\n\n
"},{"location":"Float/","title":"Type: Float","text":"

A real number that conforms to the xsd:float specification

URI: xsd:float

"},{"location":"Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Float/#schema-source","title":"Schema Source","text":""},{"location":"Float/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:float native nmdc:float exact schema:Float"},{"location":"FloorCondEnum/","title":"Enum: FloorCondEnum","text":"

URI: FloorCondEnum

"},{"location":"FloorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"FloorCondEnum/#slots","title":"Slots","text":"Name Description floor_cond The physical condition of the floor at the time of sampling; photos or video ..."},{"location":"FloorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"FloorCondEnum/#linkml-source","title":"LinkML Source","text":"
name: floor_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  new:\n    text: new\n  visible wear:\n    text: visible wear\n  needs repair:\n    text: needs repair\n  damaged:\n    text: damaged\n  rupture:\n    text: rupture\n\n
"},{"location":"FloorFinishMatEnum/","title":"Enum: FloorFinishMatEnum","text":"

URI: FloorFinishMatEnum

"},{"location":"FloorFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description tile None wood strip or parquet None carpet None rug None laminate wood None lineoleum None vinyl composition tile None sheet vinyl None stone None bamboo None cork None terrazo None concrete None none None sealed None clear finish None paint None none or unfinished None"},{"location":"FloorFinishMatEnum/#slots","title":"Slots","text":"Name Description floor_finish_mat The floor covering type; the finished surface that is walked on"},{"location":"FloorFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorFinishMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"FloorFinishMatEnum/#linkml-source","title":"LinkML Source","text":"
name: floor_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  tile:\n    text: tile\n  wood strip or parquet:\n    text: wood strip or parquet\n  carpet:\n    text: carpet\n  rug:\n    text: rug\n  laminate wood:\n    text: laminate wood\n  lineoleum:\n    text: lineoleum\n  vinyl composition tile:\n    text: vinyl composition tile\n  sheet vinyl:\n    text: sheet vinyl\n  stone:\n    text: stone\n  bamboo:\n    text: bamboo\n  cork:\n    text: cork\n  terrazo:\n    text: terrazo\n  concrete:\n    text: concrete\n  none:\n    text: none\n  sealed:\n    text: sealed\n  clear finish:\n    text: clear finish\n  paint:\n    text: paint\n  none or unfinished:\n    text: none or unfinished\n\n
"},{"location":"FloorStrucEnum/","title":"Enum: FloorStrucEnum","text":"

URI: FloorStrucEnum

"},{"location":"FloorStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description balcony None floating floor None glass floor None raised floor None sprung floor None wood-framed None concrete None"},{"location":"FloorStrucEnum/#slots","title":"Slots","text":"Name Description floor_struc Refers to the structural elements and subfloor upon which the finish flooring..."},{"location":"FloorStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorStrucEnum/#schema-source","title":"Schema Source","text":""},{"location":"FloorStrucEnum/#linkml-source","title":"LinkML Source","text":"
name: floor_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  balcony:\n    text: balcony\n  floating floor:\n    text: floating floor\n  glass floor:\n    text: glass floor\n  raised floor:\n    text: raised floor\n  sprung floor:\n    text: sprung floor\n  wood-framed:\n    text: wood-framed\n  concrete:\n    text: concrete\n\n
"},{"location":"FloorWaterMoldEnum/","title":"Enum: FloorWaterMoldEnum","text":"

URI: FloorWaterMoldEnum

"},{"location":"FloorWaterMoldEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mold odor None wet floor None water stains None wall discoloration None floor discoloration None ceiling discoloration None peeling paint or wallpaper None bulging walls None condensation None"},{"location":"FloorWaterMoldEnum/#slots","title":"Slots","text":"Name Description floor_water_mold Signs of the presence of mold or mildew in a room"},{"location":"FloorWaterMoldEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorWaterMoldEnum/#schema-source","title":"Schema Source","text":""},{"location":"FloorWaterMoldEnum/#linkml-source","title":"LinkML Source","text":"
name: floor_water_mold_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  mold odor:\n    text: mold odor\n  wet floor:\n    text: wet floor\n  water stains:\n    text: water stains\n  wall discoloration:\n    text: wall discoloration\n  floor discoloration:\n    text: floor discoloration\n  ceiling discoloration:\n    text: ceiling discoloration\n  peeling paint or wallpaper:\n    text: peeling paint or wallpaper\n  bulging walls:\n    text: bulging walls\n  condensation:\n    text: condensation\n\n
"},{"location":"FreqCleanEnum/","title":"Enum: FreqCleanEnum","text":"

URI: FreqCleanEnum

"},{"location":"FreqCleanEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Daily None Weekly None Monthly None Quarterly None Annually None other None"},{"location":"FreqCleanEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FreqCleanEnum/#schema-source","title":"Schema Source","text":""},{"location":"FreqCleanEnum/#linkml-source","title":"LinkML Source","text":"
name: freq_clean_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Daily:\n    text: Daily\n  Weekly:\n    text: Weekly\n  Monthly:\n    text: Monthly\n  Quarterly:\n    text: Quarterly\n  Annually:\n    text: Annually\n  other:\n    text: other\n\n
"},{"location":"FunctionalAnnotation/","title":"Class: FunctionalAnnotation","text":"

An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods

URI: nmdc:FunctionalAnnotation

classDiagram\n  class FunctionalAnnotation\n  click FunctionalAnnotation href \"../FunctionalAnnotation\"\n\n  FunctionalAnnotation : feature_category\n\n      FunctionalAnnotation --> \"0..1\" ControlledIdentifiedTermValue : feature_category\n    click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n  FunctionalAnnotation : has_function\n\n  FunctionalAnnotation : subject\n\n      FunctionalAnnotation --> \"0..1\" GeneProduct : subject\n    click GeneProduct href \"../GeneProduct\"\n\n  FunctionalAnnotation : type\n\n  FunctionalAnnotation : was_generated_by\n\n      FunctionalAnnotation --> \"0..1\" MetagenomeAnnotation : was_generated_by\n    click MetagenomeAnnotation href \"../MetagenomeAnnotation\"\n\n\n\n
"},{"location":"FunctionalAnnotation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_function 0..1 String direct subject 0..1 GeneProduct direct was_generated_by 0..1 MetagenomeAnnotation\u00a0or\u00a0WorkflowExecution\u00a0or\u00a0DataGeneration provenance for the annotation direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct feature_category 0..1 ControlledIdentifiedTermValue A Sequence Ontology term that describes the category of a feature direct"},{"location":"FunctionalAnnotation/#usages","title":"Usages","text":"used by used in type used Database functional_annotation_set range FunctionalAnnotation"},{"location":"FunctionalAnnotation/#see-also","title":"See Also","text":""},{"location":"FunctionalAnnotation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FunctionalAnnotation/#schema-source","title":"Schema Source","text":""},{"location":"FunctionalAnnotation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FunctionalAnnotation native nmdc:FunctionalAnnotation narrow biolink:GeneToGoTermAssociation"},{"location":"FunctionalAnnotation/#linkml-source","title":"LinkML Source","text":""},{"location":"FunctionalAnnotation/#direct","title":"Direct","text":"
name: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n  by a gene product,  or which the gene product plays an active role in. Functional\n  annotations can be assigned manually by curators, or automatically in workflows.  In\n  the context of NMDC, all function annotation is performed automatically, typically\n  using HMM or Blast type methods\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslots:\n- has_function\n- subject\n- was_generated_by\n- type\n- feature_category\nslot_usage:\n  has_function:\n    name: has_function\n    notes:\n    - Still missing patterns for COG and RetroRules\n    - These patterns are not yet tied to the listed prefixes. A discussion about that\n      possibility had been started, including the question of whether these lists\n      are intended to be open examples or closed\n  was_generated_by:\n    name: was_generated_by\n    description: provenance for the annotation.\n    notes:\n    - To be consistent with the rest of the NMDC schema we use the PROV annotation\n      model, rather than GPAD\n    range: MetagenomeAnnotation\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\nclass_uri: nmdc:FunctionalAnnotation\n\n
"},{"location":"FunctionalAnnotation/#induced","title":"Induced","text":"
name: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n  by a gene product,  or which the gene product plays an active role in. Functional\n  annotations can be assigned manually by curators, or automatically in workflows.  In\n  the context of NMDC, all function annotation is performed automatically, typically\n  using HMM or Blast type methods\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslot_usage:\n  has_function:\n    name: has_function\n    notes:\n    - Still missing patterns for COG and RetroRules\n    - These patterns are not yet tied to the listed prefixes. A discussion about that\n      possibility had been started, including the question of whether these lists\n      are intended to be open examples or closed\n  was_generated_by:\n    name: was_generated_by\n    description: provenance for the annotation.\n    notes:\n    - To be consistent with the rest of the NMDC schema we use the PROV annotation\n      model, rather than GPAD\n    range: MetagenomeAnnotation\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\nattributes:\n  has_function:\n    name: has_function\n    notes:\n    - Still missing patterns for COG and RetroRules\n    - These patterns are not yet tied to the listed prefixes. A discussion about that\n      possibility had been started, including the question of whether these lists\n      are intended to be open examples or closed\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_function\n    owner: FunctionalAnnotation\n    domain_of:\n    - FunctionalAnnotation\n    range: string\n    pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n  subject:\n    name: subject\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: subject\n    owner: FunctionalAnnotation\n    domain_of:\n    - FunctionalAnnotation\n    range: GeneProduct\n  was_generated_by:\n    name: was_generated_by\n    description: provenance for the annotation.\n    notes:\n    - To be consistent with the rest of the NMDC schema we use the PROV annotation\n      model, rather than GPAD\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasGeneratedBy\n    rank: 1000\n    alias: was_generated_by\n    owner: FunctionalAnnotation\n    domain_of:\n    - FunctionalAnnotation\n    - DataObject\n    range: MetagenomeAnnotation\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n    any_of:\n    - range: WorkflowExecution\n    - range: DataGeneration\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FunctionalAnnotation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  feature_category:\n    name: feature_category\n    description: A Sequence Ontology term that describes the category of a feature\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: feature_category\n    owner: FunctionalAnnotation\n    domain_of:\n    - GenomeFeature\n    - FunctionalAnnotation\n    range: ControlledIdentifiedTermValue\nclass_uri: nmdc:FunctionalAnnotation\n\n
"},{"location":"FunctionalAnnotationAggMember/","title":"Class: FunctionalAnnotationAggMember","text":"

URI: nmdc:FunctionalAnnotationAggMember

classDiagram\n  class FunctionalAnnotationAggMember\n  click FunctionalAnnotationAggMember href \"../FunctionalAnnotationAggMember\"\n\n  FunctionalAnnotationAggMember : count\n\n  FunctionalAnnotationAggMember : gene_function_id\n\n  FunctionalAnnotationAggMember : metagenome_annotation_id\n\n      FunctionalAnnotationAggMember --> \"1\" WorkflowExecution : metagenome_annotation_id\n    click WorkflowExecution href \"../WorkflowExecution\"\n\n  FunctionalAnnotationAggMember : type\n\n\n\n
"},{"location":"FunctionalAnnotationAggMember/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance metagenome_annotation_id 1 WorkflowExecution\u00a0or\u00a0MetagenomeAnnotation\u00a0or\u00a0MetatranscriptomeAnnotation The identifier for the analysis activity that generated the functional annota... direct gene_function_id 1 Uriorcurie The identifier for the gene function direct count 1 Integer direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"FunctionalAnnotationAggMember/#usages","title":"Usages","text":"used by used in type used Database functional_annotation_agg range FunctionalAnnotationAggMember"},{"location":"FunctionalAnnotationAggMember/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FunctionalAnnotationAggMember/#schema-source","title":"Schema Source","text":""},{"location":"FunctionalAnnotationAggMember/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FunctionalAnnotationAggMember native nmdc:FunctionalAnnotationAggMember"},{"location":"FunctionalAnnotationAggMember/#linkml-source","title":"LinkML Source","text":""},{"location":"FunctionalAnnotationAggMember/#direct","title":"Direct","text":"
name: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- metagenome_annotation_id\n- gene_function_id\n- count\n- type\nslot_usage:\n  metagenome_annotation_id:\n    name: metagenome_annotation_id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\nclass_uri: nmdc:FunctionalAnnotationAggMember\n\n
"},{"location":"FunctionalAnnotationAggMember/#induced","title":"Induced","text":"
name: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n  metagenome_annotation_id:\n    name: metagenome_annotation_id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\nattributes:\n  metagenome_annotation_id:\n    name: metagenome_annotation_id\n    description: The identifier for the analysis activity that generated the functional\n      annotation results, where the analysis activity is an instance of the/an appropriate\n      subclass of WorkflowExecution\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: metagenome_annotation_id\n    owner: FunctionalAnnotationAggMember\n    domain_of:\n    - FunctionalAnnotationAggMember\n    range: WorkflowExecution\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(wfmgan|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n    any_of:\n    - range: MetagenomeAnnotation\n    - range: MetatranscriptomeAnnotation\n  gene_function_id:\n    name: gene_function_id\n    description: The identifier for the gene function.\n    examples:\n    - value: KEGG.ORTHOLOGY:K00627\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gene_function_id\n    owner: FunctionalAnnotationAggMember\n    domain_of:\n    - FunctionalAnnotationAggMember\n    range: uriorcurie\n    required: true\n  count:\n    name: count\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: count\n    owner: FunctionalAnnotationAggMember\n    domain_of:\n    - FunctionalAnnotationAggMember\n    range: integer\n    required: true\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FunctionalAnnotationAggMember\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FunctionalAnnotationAggMember\n\n
"},{"location":"FunctionalAnnotationTerm/","title":"Class: FunctionalAnnotationTerm","text":"

Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:FunctionalAnnotationTerm

classDiagram\n  class FunctionalAnnotationTerm\n  click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n    OntologyClass <|-- FunctionalAnnotationTerm\n      click OntologyClass href \"../OntologyClass\"\n\n\n    FunctionalAnnotationTerm <|-- Pathway\n      click Pathway href \"../Pathway\"\n    FunctionalAnnotationTerm <|-- OrthologyGroup\n      click OrthologyGroup href \"../OrthologyGroup\"\n\n\n\n  FunctionalAnnotationTerm : alternative_identifiers\n\n  FunctionalAnnotationTerm : description\n\n  FunctionalAnnotationTerm : id\n\n  FunctionalAnnotationTerm : name\n\n  FunctionalAnnotationTerm : type\n\n\n\n
"},{"location":"FunctionalAnnotationTerm/#inheritance","title":"Inheritance","text":""},{"location":"FunctionalAnnotationTerm/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"FunctionalAnnotationTerm/#aliases","title":"Aliases","text":""},{"location":"FunctionalAnnotationTerm/#todos","title":"TODOs","text":""},{"location":"FunctionalAnnotationTerm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FunctionalAnnotationTerm/#schema-source","title":"Schema Source","text":""},{"location":"FunctionalAnnotationTerm/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:FunctionalAnnotationTerm native nmdc:FunctionalAnnotationTerm"},{"location":"FunctionalAnnotationTerm/#linkml-source","title":"LinkML Source","text":""},{"location":"FunctionalAnnotationTerm/#direct","title":"Direct","text":"
name: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n  a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming (Duncan, 2021-04-02)\n- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup\n  subclasses.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nclass_uri: nmdc:FunctionalAnnotationTerm\n\n
"},{"location":"FunctionalAnnotationTerm/#induced","title":"Induced","text":"
name: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n  a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming (Duncan, 2021-04-02)\n- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup\n  subclasses.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: FunctionalAnnotationTerm\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:FunctionalAnnotationTerm\n\n
"},{"location":"FurnitureEnum/","title":"Enum: FurnitureEnum","text":"

URI: FurnitureEnum

"},{"location":"FurnitureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None chair None desks None"},{"location":"FurnitureEnum/#slots","title":"Slots","text":"Name Description furniture The types of furniture present in the sampled room"},{"location":"FurnitureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FurnitureEnum/#schema-source","title":"Schema Source","text":""},{"location":"FurnitureEnum/#linkml-source","title":"LinkML Source","text":"
name: furniture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  cabinet:\n    text: cabinet\n  chair:\n    text: chair\n  desks:\n    text: desks\n\n
"},{"location":"GenderRestroomEnum/","title":"Enum: GenderRestroomEnum","text":"

URI: GenderRestroomEnum

"},{"location":"GenderRestroomEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description all gender None female None gender neurtral None male None male and female None unisex None"},{"location":"GenderRestroomEnum/#slots","title":"Slots","text":"Name Description gender_restroom The gender type of the restroom"},{"location":"GenderRestroomEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GenderRestroomEnum/#schema-source","title":"Schema Source","text":""},{"location":"GenderRestroomEnum/#linkml-source","title":"LinkML Source","text":"
name: gender_restroom_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  all gender:\n    text: all gender\n  female:\n    text: female\n  gender neurtral:\n    text: gender neurtral\n  male:\n    text: male\n  male and female:\n    text: male and female\n  unisex:\n    text: unisex\n\n
"},{"location":"GeneProduct/","title":"Class: GeneProduct","text":"

A molecule encoded by a gene that has an evolved function

URI: nmdc:GeneProduct

classDiagram\n  class GeneProduct\n  click GeneProduct href \"../GeneProduct\"\n    NamedThing <|-- GeneProduct\n      click NamedThing href \"../NamedThing\"\n\n\n\n  GeneProduct : alternative_identifiers\n\n  GeneProduct : description\n\n  GeneProduct : id\n\n  GeneProduct : name\n\n  GeneProduct : type\n\n\n\n
"},{"location":"GeneProduct/#inheritance","title":"Inheritance","text":""},{"location":"GeneProduct/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"GeneProduct/#usages","title":"Usages","text":"used by used in type used PeptideQuantification all_proteins range GeneProduct PeptideQuantification best_protein range GeneProduct ProteinQuantification all_proteins range GeneProduct ProteinQuantification best_protein range GeneProduct GenomeFeature encodes range GeneProduct FunctionalAnnotation subject range GeneProduct"},{"location":"GeneProduct/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GeneProduct/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"GeneProduct/#schema-source","title":"Schema Source","text":""},{"location":"GeneProduct/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:GeneProduct native nmdc:GeneProduct exact biolink:GeneProduct"},{"location":"GeneProduct/#linkml-source","title":"LinkML Source","text":""},{"location":"GeneProduct/#direct","title":"Direct","text":"
name: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nclass_uri: nmdc:GeneProduct\n\n
"},{"location":"GeneProduct/#induced","title":"Induced","text":"
name: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: GeneProduct\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: GeneProduct\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: GeneProduct\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: GeneProduct\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: GeneProduct\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:GeneProduct\n\n
"},{"location":"GenomeFeature/","title":"Class: GenomeFeature","text":"

A feature localized to an interval along a genome

URI: nmdc:GenomeFeature

classDiagram\n  class GenomeFeature\n  click GenomeFeature href \"../GenomeFeature\"\n\n  GenomeFeature : encodes\n\n      GenomeFeature --> \"0..1\" GeneProduct : encodes\n    click GeneProduct href \"../GeneProduct\"\n\n  GenomeFeature : end\n\n  GenomeFeature : feature_category\n\n      GenomeFeature --> \"0..1\" ControlledIdentifiedTermValue : feature_category\n    click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n  GenomeFeature : feature_type\n\n  GenomeFeature : phase\n\n  GenomeFeature : seqid\n\n  GenomeFeature : start\n\n  GenomeFeature : strand\n\n  GenomeFeature : type\n\n\n\n
"},{"location":"GenomeFeature/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance encodes 0..1 GeneProduct The gene product encoded by this feature direct end 1 Integer The end of the feature in positive 1-based integer coordinates direct feature_type 0..1 String TODO: Yuri to write direct phase 0..1 Integer The phase for a coding sequence entity direct seqid 1 String The ID of the landmark used to establish the coordinate system for the curren... direct start 1 Integer The start of the feature in positive 1-based integer coordinates direct strand 0..1 String The strand on which a feature is located direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct feature_category 0..1 ControlledIdentifiedTermValue A Sequence Ontology term that describes the category of a feature direct"},{"location":"GenomeFeature/#usages","title":"Usages","text":"used by used in type used Database genome_feature_set range GenomeFeature"},{"location":"GenomeFeature/#comments","title":"Comments","text":""},{"location":"GenomeFeature/#see-also","title":"See Also","text":""},{"location":"GenomeFeature/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GenomeFeature/#schema-source","title":"Schema Source","text":""},{"location":"GenomeFeature/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:GenomeFeature native nmdc:GenomeFeature"},{"location":"GenomeFeature/#linkml-source","title":"LinkML Source","text":""},{"location":"GenomeFeature/#direct","title":"Direct","text":"
name: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslots:\n- encodes\n- end\n- feature_type\n- phase\n- seqid\n- start\n- strand\n- type\n- feature_category\nslot_usage:\n  seqid:\n    name: seqid\n    required: true\n  start:\n    name: start\n    required: true\n  end:\n    name: end\n    required: true\nclass_uri: nmdc:GenomeFeature\n\n
"},{"location":"GenomeFeature/#induced","title":"Induced","text":"
name: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslot_usage:\n  seqid:\n    name: seqid\n    required: true\n  start:\n    name: start\n    required: true\n  end:\n    name: end\n    required: true\nattributes:\n  encodes:\n    name: encodes\n    description: The gene product encoded by this feature. Typically this is used\n      for a CDS feature or gene feature which will encode a protein. It can also be\n      used by a nc transcript ot gene feature that encoded a ncRNA\n    todos:\n    - If we revert Reaction back into the schema, that would be a reasonable domain\n      for this slot\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: encodes\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: GeneProduct\n  end:\n    name: end\n    description: The end of the feature in positive 1-based integer coordinates\n    comments:\n    - '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n      feature,  end = the position of the end + the length of the landmark feature.\"'\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - biolink:end_interbase_coordinate\n    rank: 1000\n    is_a: gff_coordinate\n    alias: end\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: integer\n    required: true\n    minimum_value: 1\n  feature_type:\n    name: feature_type\n    description: 'TODO: Yuri to write'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: feature_type\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: string\n  phase:\n    name: phase\n    description: The phase for a coding sequence entity. For example, phase of a CDS\n      as represented in a GFF3 with a value of 0, 1 or 2.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - biolink:phase\n    rank: 1000\n    alias: phase\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: integer\n    minimum_value: 0\n    maximum_value: 2\n  seqid:\n    name: seqid\n    description: The ID of the landmark used to establish the coordinate system for\n      the current feature.\n    todos:\n    - change range from string to object\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: seqid\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: string\n    required: true\n  start:\n    name: start\n    description: The start of the feature in positive 1-based integer coordinates\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - biolink:start_interbase_coordinate\n    rank: 1000\n    is_a: gff_coordinate\n    alias: start\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: integer\n    required: true\n    minimum_value: 1\n  strand:\n    name: strand\n    description: The strand on which a feature is located. Has a value of '+' (sense\n      strand or forward strand) or  '-' (anti-sense strand or reverse strand).\n    todos:\n    - set the range to an enum?\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - biolink:strand\n    rank: 1000\n    alias: strand\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: GenomeFeature\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  feature_category:\n    name: feature_category\n    description: A Sequence Ontology term that describes the category of a feature\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: feature_category\n    owner: GenomeFeature\n    domain_of:\n    - GenomeFeature\n    - FunctionalAnnotation\n    range: ControlledIdentifiedTermValue\nclass_uri: nmdc:GenomeFeature\n\n
"},{"location":"GeolocationValue/","title":"Class: GeolocationValue","text":"

A normalized value for a location on the earth's surface

URI: nmdc:GeolocationValue

classDiagram\n  class GeolocationValue\n  click GeolocationValue href \"../GeolocationValue\"\n    AttributeValue <|-- GeolocationValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  GeolocationValue : has_raw_value\n\n  GeolocationValue : latitude\n\n  GeolocationValue : longitude\n\n  GeolocationValue : type\n\n\n\n
"},{"location":"GeolocationValue/#inheritance","title":"Inheritance","text":""},{"location":"GeolocationValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance latitude 1 DecimalDegree latitude direct longitude 1 DecimalDegree longitude direct has_raw_value 0..1 String The raw value for a geolocation should follow {latitude} {longitude} AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"GeolocationValue/#usages","title":"Usages","text":"used by used in type used FieldResearchSite lat_lon range GeolocationValue Biosample lat_lon range GeolocationValue"},{"location":"GeolocationValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GeolocationValue/#schema-source","title":"Schema Source","text":""},{"location":"GeolocationValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:GeolocationValue native nmdc:GeolocationValue undefined schema:GeoCoordinates"},{"location":"GeolocationValue/#linkml-source","title":"LinkML Source","text":""},{"location":"GeolocationValue/#direct","title":"Direct","text":"
name: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslots:\n- latitude\n- longitude\nslot_usage:\n  has_raw_value:\n    name: has_raw_value\n    description: The raw value for a geolocation should follow {latitude} {longitude}\n  latitude:\n    name: latitude\n    required: true\n  longitude:\n    name: longitude\n    required: true\nclass_uri: nmdc:GeolocationValue\n\n
"},{"location":"GeolocationValue/#induced","title":"Induced","text":"
name: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslot_usage:\n  has_raw_value:\n    name: has_raw_value\n    description: The raw value for a geolocation should follow {latitude} {longitude}\n  latitude:\n    name: latitude\n    required: true\n  longitude:\n    name: longitude\n    required: true\nattributes:\n  latitude:\n    name: latitude\n    description: latitude\n    examples:\n    - value: '-33.460524'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - schema:latitude\n    rank: 1000\n    slot_uri: wgs84:lat\n    alias: latitude\n    owner: GeolocationValue\n    domain_of:\n    - GeolocationValue\n    range: decimal degree\n    required: true\n  longitude:\n    name: longitude\n    description: longitude\n    examples:\n    - value: '150.168149'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - schema:longitude\n    rank: 1000\n    slot_uri: wgs84:long\n    alias: longitude\n    owner: GeolocationValue\n    domain_of:\n    - GeolocationValue\n    range: decimal degree\n    required: true\n  has_raw_value:\n    name: has_raw_value\n    description: The raw value for a geolocation should follow {latitude} {longitude}\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: GeolocationValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: GeolocationValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:GeolocationValue\n\n
"},{"location":"GrowthHabitEnum/","title":"Enum: GrowthHabitEnum","text":"

URI: GrowthHabitEnum

"},{"location":"GrowthHabitEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description erect None semi-erect None spreading None prostrate None"},{"location":"GrowthHabitEnum/#slots","title":"Slots","text":"Name Description growth_habit Characteristic shape, appearance or growth form of a plant species"},{"location":"GrowthHabitEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GrowthHabitEnum/#schema-source","title":"Schema Source","text":""},{"location":"GrowthHabitEnum/#linkml-source","title":"LinkML Source","text":"
name: growth_habit_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  erect:\n    text: erect\n  semi-erect:\n    text: semi-erect\n  spreading:\n    text: spreading\n  prostrate:\n    text: prostrate\n\n
"},{"location":"HandidnessEnum/","title":"Enum: HandidnessEnum","text":"

URI: HandidnessEnum

"},{"location":"HandidnessEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ambidexterity None left handedness None mixed-handedness None right handedness None"},{"location":"HandidnessEnum/#slots","title":"Slots","text":"Name Description handidness The handidness of the individual sampled"},{"location":"HandidnessEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HandidnessEnum/#schema-source","title":"Schema Source","text":""},{"location":"HandidnessEnum/#linkml-source","title":"LinkML Source","text":"
name: handidness_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  ambidexterity:\n    text: ambidexterity\n  left handedness:\n    text: left handedness\n  mixed-handedness:\n    text: mixed-handedness\n  right handedness:\n    text: right handedness\n\n
"},{"location":"HcProducedEnum/","title":"Enum: HcProducedEnum","text":"

URI: HcProducedEnum

"},{"location":"HcProducedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil None Gas-Condensate None Gas None Bitumen None Coalbed Methane None other None"},{"location":"HcProducedEnum/#slots","title":"Slots","text":"Name Description hc_produced Main hydrocarbon type produced from resource (i"},{"location":"HcProducedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcProducedEnum/#schema-source","title":"Schema Source","text":""},{"location":"HcProducedEnum/#linkml-source","title":"LinkML Source","text":"
name: hc_produced_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Oil:\n    text: Oil\n  Gas-Condensate:\n    text: Gas-Condensate\n  Gas:\n    text: Gas\n  Bitumen:\n    text: Bitumen\n  Coalbed Methane:\n    text: Coalbed Methane\n  other:\n    text: other\n\n
"},{"location":"HcrEnum/","title":"Enum: HcrEnum","text":"

URI: HcrEnum

"},{"location":"HcrEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil Reservoir None Gas Reservoir None Oil Sand None Coalbed None Shale None Tight Oil Reservoir None Tight Gas Reservoir None other None"},{"location":"HcrEnum/#slots","title":"Slots","text":"Name Description hcr Main Hydrocarbon Resource type"},{"location":"HcrEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrEnum/#schema-source","title":"Schema Source","text":""},{"location":"HcrEnum/#linkml-source","title":"LinkML Source","text":"
name: hcr_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Oil Reservoir:\n    text: Oil Reservoir\n  Gas Reservoir:\n    text: Gas Reservoir\n  Oil Sand:\n    text: Oil Sand\n  Coalbed:\n    text: Coalbed\n  Shale:\n    text: Shale\n  Tight Oil Reservoir:\n    text: Tight Oil Reservoir\n  Tight Gas Reservoir:\n    text: Tight Gas Reservoir\n  other:\n    text: other\n\n
"},{"location":"HcrGeolAgeEnum/","title":"Enum: HcrGeolAgeEnum","text":"

URI: HcrGeolAgeEnum

"},{"location":"HcrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"HcrGeolAgeEnum/#slots","title":"Slots","text":"Name Description hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en"},{"location":"HcrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrGeolAgeEnum/#schema-source","title":"Schema Source","text":""},{"location":"HcrGeolAgeEnum/#linkml-source","title":"LinkML Source","text":"
name: hcr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Archean:\n    text: Archean\n  Cambrian:\n    text: Cambrian\n  Carboniferous:\n    text: Carboniferous\n  Cenozoic:\n    text: Cenozoic\n  Cretaceous:\n    text: Cretaceous\n  Devonian:\n    text: Devonian\n  Jurassic:\n    text: Jurassic\n  Mesozoic:\n    text: Mesozoic\n  Neogene:\n    text: Neogene\n  Ordovician:\n    text: Ordovician\n  Paleogene:\n    text: Paleogene\n  Paleozoic:\n    text: Paleozoic\n  Permian:\n    text: Permian\n  Precambrian:\n    text: Precambrian\n  Proterozoic:\n    text: Proterozoic\n  Silurian:\n    text: Silurian\n  Triassic:\n    text: Triassic\n  other:\n    text: other\n\n
"},{"location":"HeatCoolTypeEnum/","title":"Enum: HeatCoolTypeEnum","text":"

URI: HeatCoolTypeEnum

"},{"location":"HeatCoolTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description radiant system None heat pump None forced air system None steam forced heat None wood stove None"},{"location":"HeatCoolTypeEnum/#slots","title":"Slots","text":"Name Description heat_cool_type Methods of conditioning or heating a room or building"},{"location":"HeatCoolTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatCoolTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"HeatCoolTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: heat_cool_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  radiant system:\n    text: radiant system\n  heat pump:\n    text: heat pump\n  forced air system:\n    text: forced air system\n  steam forced heat:\n    text: steam forced heat\n  wood stove:\n    text: wood stove\n\n
"},{"location":"HeatDelivLocEnum/","title":"Enum: HeatDelivLocEnum","text":"

URI: HeatDelivLocEnum

"},{"location":"HeatDelivLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"HeatDelivLocEnum/#slots","title":"Slots","text":"Name Description heat_deliv_loc The location of heat delivery within the room"},{"location":"HeatDelivLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatDelivLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"HeatDelivLocEnum/#linkml-source","title":"LinkML Source","text":"
name: heat_deliv_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n\n
"},{"location":"HostSexEnum/","title":"Enum: HostSexEnum","text":"

URI: HostSexEnum

"},{"location":"HostSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description female None hermaphrodite None male None neuter None"},{"location":"HostSexEnum/#slots","title":"Slots","text":"Name Description host_sex Gender or physical sex of the host"},{"location":"HostSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HostSexEnum/#schema-source","title":"Schema Source","text":""},{"location":"HostSexEnum/#linkml-source","title":"LinkML Source","text":"
name: host_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  female:\n    text: female\n  hermaphrodite:\n    text: hermaphrodite\n  male:\n    text: male\n  neuter:\n    text: neuter\n\n
"},{"location":"ImageValue/","title":"Class: ImageValue","text":"

An attribute value representing an image.

URI: nmdc:ImageValue

classDiagram\n  class ImageValue\n  click ImageValue href \"../ImageValue\"\n    AttributeValue <|-- ImageValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  ImageValue : description\n\n  ImageValue : display_order\n\n  ImageValue : has_raw_value\n\n  ImageValue : type\n\n  ImageValue : url\n\n\n\n
"},{"location":"ImageValue/#inheritance","title":"Inheritance","text":""},{"location":"ImageValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance url 0..1 String direct description 0..1 String a human-readable description of a thing direct display_order 0..1 Integer When rendering information, this attribute to specify the order in which the ... direct has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"ImageValue/#usages","title":"Usages","text":"used by used in type used Study study_image range ImageValue"},{"location":"ImageValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ImageValue/#schema-source","title":"Schema Source","text":""},{"location":"ImageValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ImageValue native nmdc:ImageValue"},{"location":"ImageValue/#linkml-source","title":"LinkML Source","text":""},{"location":"ImageValue/#direct","title":"Direct","text":"
name: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- url\n- description\n- display_order\nclass_uri: nmdc:ImageValue\n\n
"},{"location":"ImageValue/#induced","title":"Induced","text":"
name: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n  url:\n    name: url\n    notes:\n    - See issue 207 - this clashes with the mixs field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: url\n    owner: ImageValue\n    domain_of:\n    - ImageValue\n    - Protocol\n    - DataObject\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ImageValue\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  display_order:\n    name: display_order\n    description: When rendering information, this attribute to specify the order in\n      which the information should be rendered.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: display_order\n    owner: ImageValue\n    domain_of:\n    - ImageValue\n    range: integer\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: ImageValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ImageValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ImageValue\n\n
"},{"location":"IndoorSpaceEnum/","title":"Enum: IndoorSpaceEnum","text":"

URI: IndoorSpaceEnum

"},{"location":"IndoorSpaceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bedroom None office None bathroom None foyer None kitchen None locker room None hallway None elevator None"},{"location":"IndoorSpaceEnum/#slots","title":"Slots","text":"Name Description indoor_space A distinguishable space within a structure, the purpose for which discrete ar..."},{"location":"IndoorSpaceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSpaceEnum/#schema-source","title":"Schema Source","text":""},{"location":"IndoorSpaceEnum/#linkml-source","title":"LinkML Source","text":"
name: indoor_space_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  bedroom:\n    text: bedroom\n  office:\n    text: office\n  bathroom:\n    text: bathroom\n  foyer:\n    text: foyer\n  kitchen:\n    text: kitchen\n  locker room:\n    text: locker room\n  hallway:\n    text: hallway\n  elevator:\n    text: elevator\n\n
"},{"location":"IndoorSurfEnum/","title":"Enum: IndoorSurfEnum","text":"

URI: IndoorSurfEnum

"},{"location":"IndoorSurfEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None ceiling None counter top None door None shelving None vent cover None window None wall None"},{"location":"IndoorSurfEnum/#slots","title":"Slots","text":"Name Description indoor_surf Type of indoor surface"},{"location":"IndoorSurfEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSurfEnum/#schema-source","title":"Schema Source","text":""},{"location":"IndoorSurfEnum/#linkml-source","title":"LinkML Source","text":"
name: indoor_surf_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  cabinet:\n    text: cabinet\n  ceiling:\n    text: ceiling\n  counter top:\n    text: counter top\n  door:\n    text: door\n  shelving:\n    text: shelving\n  vent cover:\n    text: vent cover\n  window:\n    text: window\n  wall:\n    text: wall\n\n
"},{"location":"InformationObject/","title":"Class: InformationObject","text":"

Any data or knowledge that reduces uncertainty or enhances understanding about a system, process, or entity.

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:InformationObject

classDiagram\n  class InformationObject\n  click InformationObject href \"../InformationObject\"\n    NamedThing <|-- InformationObject\n      click NamedThing href \"../NamedThing\"\n\n\n    InformationObject <|-- Configuration\n      click Configuration href \"../Configuration\"\n    InformationObject <|-- Manifest\n      click Manifest href \"../Manifest\"\n    InformationObject <|-- DataObject\n      click DataObject href \"../DataObject\"\n    InformationObject <|-- CalibrationInformation\n      click CalibrationInformation href \"../CalibrationInformation\"\n\n\n\n  InformationObject : alternative_identifiers\n\n  InformationObject : description\n\n  InformationObject : id\n\n  InformationObject : name\n\n  InformationObject : type\n\n\n\n
"},{"location":"InformationObject/#inheritance","title":"Inheritance","text":""},{"location":"InformationObject/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"InformationObject/#comments","title":"Comments","text":""},{"location":"InformationObject/#see-also","title":"See Also","text":""},{"location":"InformationObject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InformationObject/#schema-source","title":"Schema Source","text":""},{"location":"InformationObject/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:InformationObject native nmdc:InformationObject"},{"location":"InformationObject/#linkml-source","title":"LinkML Source","text":""},{"location":"InformationObject/#direct","title":"Direct","text":"
name: InformationObject\ndescription: Any data or knowledge that reduces uncertainty or enhances understanding\n  about a system, process, or entity.\ncomments:\n- The direct subclasses of NamedThing should aggregate the relevant classes and make\n  them uniform. PlannedProcess and MaterialEntity are clearly disjoint. Let's do the\n  same thing for our modelling of things that don't consist of matter and aren't processes.\n- InformationObjects may include embedded data or links to external resources via\n  the url slot\n- May appear as output from a process, inputs into a process, or both\n- All slots relating one class to a InformationObject should be is_a sub-properties\n  of has_input or has_output, if they are multivalued or otherwise organized\n- Historically information about many classes has been inlined into the class. This\n  is an alternative pattern.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:AttributeValue\nis_a: NamedThing\nabstract: true\nclass_uri: nmdc:InformationObject\n\n
"},{"location":"InformationObject/#induced","title":"Induced","text":"
name: InformationObject\ndescription: Any data or knowledge that reduces uncertainty or enhances understanding\n  about a system, process, or entity.\ncomments:\n- The direct subclasses of NamedThing should aggregate the relevant classes and make\n  them uniform. PlannedProcess and MaterialEntity are clearly disjoint. Let's do the\n  same thing for our modelling of things that don't consist of matter and aren't processes.\n- InformationObjects may include embedded data or links to external resources via\n  the url slot\n- May appear as output from a process, inputs into a process, or both\n- All slots relating one class to a InformationObject should be is_a sub-properties\n  of has_input or has_output, if they are multivalued or otherwise organized\n- Historically information about many classes has been inlined into the class. This\n  is an alternative pattern.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:AttributeValue\nis_a: NamedThing\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: InformationObject\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: InformationObject\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: InformationObject\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: InformationObject\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: InformationObject\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:InformationObject\n\n
"},{"location":"Instrument/","title":"Class: Instrument","text":"

A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.

URI: nmdc:Instrument

classDiagram\n  class Instrument\n  click Instrument href \"../Instrument\"\n    MaterialEntity <|-- Instrument\n      click MaterialEntity href \"../MaterialEntity\"\n\n\n\n  Instrument : alternative_identifiers\n\n  Instrument : description\n\n  Instrument : id\n\n  Instrument : model\n\n      Instrument --> \"0..1\" InstrumentModelEnum : model\n    click InstrumentModelEnum href \"../InstrumentModelEnum\"\n\n  Instrument : name\n\n  Instrument : type\n\n  Instrument : vendor\n\n      Instrument --> \"0..1\" InstrumentVendorEnum : vendor\n    click InstrumentVendorEnum href \"../InstrumentVendorEnum\"\n\n\n\n
"},{"location":"Instrument/#inheritance","title":"Inheritance","text":""},{"location":"Instrument/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance vendor 0..1 InstrumentVendorEnum direct model 0..1 InstrumentModelEnum direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Instrument/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing instrument_used range Instrument MassSpectrometry instrument_used range Instrument Database instrument_set range Instrument Pooling instrument_used range Instrument Extraction instrument_used range Instrument LibraryPreparation instrument_used range Instrument SubSamplingProcess instrument_used range Instrument MixingProcess instrument_used range Instrument FiltrationProcess instrument_used range Instrument ChromatographicSeparationProcess instrument_used range Instrument DissolvingProcess instrument_used range Instrument ChemicalConversionProcess instrument_used range Instrument MaterialProcessing instrument_used range Instrument DataGeneration instrument_used range Instrument"},{"location":"Instrument/#aliases","title":"Aliases","text":""},{"location":"Instrument/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Instrument/#schema-source","title":"Schema Source","text":""},{"location":"Instrument/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Instrument native nmdc:Instrument exact OBI:0000968"},{"location":"Instrument/#linkml-source","title":"LinkML Source","text":""},{"location":"Instrument/#direct","title":"Direct","text":"
name: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n  investigation, but is not a reagent.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000968\nis_a: MaterialEntity\nslots:\n- vendor\n- model\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:Instrument\n\n
"},{"location":"Instrument/#induced","title":"Induced","text":"
name: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n  investigation, but is not a reagent.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000968\nis_a: MaterialEntity\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  vendor:\n    name: vendor\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: vendor\n    owner: Instrument\n    domain_of:\n    - Instrument\n    range: InstrumentVendorEnum\n  model:\n    name: model\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: model\n    owner: Instrument\n    domain_of:\n    - Instrument\n    range: InstrumentModelEnum\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Instrument\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Instrument\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Instrument\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Instrument\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Instrument\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Instrument\n\n
"},{"location":"InstrumentModelEnum/","title":"Enum: InstrumentModelEnum","text":"

URI: InstrumentModelEnum

"},{"location":"InstrumentModelEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description exploris_21T None exploris_240 None exploris_480 None ltq_orbitrap_velos None orbitrap_fusion_lumos None orbitrap_eclipse_tribid None orbitrap_q_exactive None solarix_7T None solarix_12T None solarix_15T None agilent_8890A None agilent_7980A None vortex_genie_2 None novaseq None novaseq_6000 OBI:0002630 novaseq_x None hiseq None hiseq_1000 OBI:0002022 hiseq_1500 OBI:0003386 hiseq_2000 OBI:0002001 hiseq_2500 OBI:0002002 hiseq_3000 OBI:0002048 hiseq_4000 OBI:0002049 hiseq_x_ten OBI:0002129 miniseq OBI:0003114 miseq OBI:0002003 nextseq_1000 OBI:0003606 nextseq None nextseq_500 OBI:0002021 nextseq_550 OBI:0003387 gridion OBI:0002751 minion OBI:0002750 promethion OBI:0002752 rs_II OBI:0002012 sequel OBI:0002632 sequel_II OBI:0002633 revio None"},{"location":"InstrumentModelEnum/#slots","title":"Slots","text":"Name Description model"},{"location":"InstrumentModelEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InstrumentModelEnum/#schema-source","title":"Schema Source","text":""},{"location":"InstrumentModelEnum/#linkml-source","title":"LinkML Source","text":"
name: InstrumentModelEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  exploris_21T:\n    text: exploris_21T\n    aliases:\n    - Exploris 21T\n  exploris_240:\n    text: exploris_240\n    aliases:\n    - Orbitrap Exploris 240\n  exploris_480:\n    text: exploris_480\n    aliases:\n    - Orbitrap Exploris 480\n  ltq_orbitrap_velos:\n    text: ltq_orbitrap_velos\n    aliases:\n    - LTQ Orbitrap Velos\n    - LTQ Orbitrap Velos ETD\n    - Velos\n  orbitrap_fusion_lumos:\n    text: orbitrap_fusion_lumos\n    aliases:\n    - Orbitrap Fusion Lumos\n    - Fusion\n  orbitrap_eclipse_tribid:\n    text: orbitrap_eclipse_tribid\n    aliases:\n    - Orbitrap Eclipse Tribid\n    - Eclipse\n  orbitrap_q_exactive:\n    text: orbitrap_q_exactive\n    aliases:\n    - Orbitrap Q-Exactive HF\n    - Orbitrap Q-Exactive HF-X\n  solarix_7T:\n    text: solarix_7T\n    aliases:\n    - 7T Solarix\n    - 7T FT-ICR MS\n    - 7T MRMS\n  solarix_12T:\n    text: solarix_12T\n    aliases:\n    - 12T Solarix\n    - 12T FT-ICR MS\n    - 12T MRMS\n  solarix_15T:\n    text: solarix_15T\n    aliases:\n    - 15T Solarix\n    - 15T FT-ICR MS\n    - 15T MRMS\n  agilent_8890A:\n    text: agilent_8890A\n    aliases:\n    - 8890A GC-MS\n    - Agilent GC MS\n  agilent_7980A:\n    text: agilent_7980A\n    aliases:\n    - 7980A GC-MS\n    - Agilent GC MS\n  vortex_genie_2:\n    text: vortex_genie_2\n    aliases:\n    - VortexGenie2\n  novaseq:\n    text: novaseq\n    aliases:\n    - NovaSeq\n    - Illumina NovaSeq\n  novaseq_6000:\n    text: novaseq_6000\n    meaning: OBI:0002630\n    comments:\n    - Possible flowcell versions are SP, S1, S2, S4.\n    see_also:\n    - https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html\n    aliases:\n    - NovaSeq 6000\n    - Illumina NovaSeq 6000\n    structured_aliases:\n      Illumina NovaSeq S2:\n        literal_form: Illumina NovaSeq S2\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n      Illumina NovaSeq S4:\n        literal_form: Illumina NovaSeq S4\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n      Illumina NovaSeq SP:\n        literal_form: Illumina NovaSeq SP\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n  novaseq_x:\n    text: novaseq_x\n    comments:\n    - Possible flowcell versions are 1.5B, 10B, 25B. Only difference between X and\n      X Plus is 2 flowcells for X Plus versus 1 flowcell for X.\n    see_also:\n    - https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html\n    aliases:\n    - Illumina NovaSeq X\n    - Illumina NovaSeq X Plus\n  hiseq:\n    text: hiseq\n    aliases:\n    - Illumina HiSeq\n  hiseq_1000:\n    text: hiseq_1000\n    meaning: OBI:0002022\n    aliases:\n    - Illumina HiSeq 1000\n  hiseq_1500:\n    text: hiseq_1500\n    meaning: OBI:0003386\n    aliases:\n    - Illumina HiSeq 1500\n  hiseq_2000:\n    text: hiseq_2000\n    meaning: OBI:0002001\n    aliases:\n    - Illumina HiSeq 2000\n  hiseq_2500:\n    text: hiseq_2500\n    meaning: OBI:0002002\n    aliases:\n    - Illumina HiSeq 2500\n    structured_aliases:\n      Illumina HiSeq 2500-1TB:\n        literal_form: Illumina HiSeq 2500-1TB\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n      Illumina HiSeq 2500-Rapid:\n        literal_form: Illumina HiSeq 2500-Rapid\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n  hiseq_3000:\n    text: hiseq_3000\n    meaning: OBI:0002048\n    aliases:\n    - Illumina HiSeq 3000\n  hiseq_4000:\n    text: hiseq_4000\n    meaning: OBI:0002049\n    aliases:\n    - Illumina HiSeq 4000\n  hiseq_x_ten:\n    text: hiseq_x_ten\n    meaning: OBI:0002129\n    aliases:\n    - Illumina HiSeq X Ten\n  miniseq:\n    text: miniseq\n    meaning: OBI:0003114\n    aliases:\n    - Illumina MiniSeq\n  miseq:\n    text: miseq\n    meaning: OBI:0002003\n    aliases:\n    - MiSeq\n    - Illumina MiSeq\n  nextseq_1000:\n    text: nextseq_1000\n    meaning: OBI:0003606\n    aliases:\n    - Illumina NextSeq 1000\n  nextseq:\n    text: nextseq\n    aliases:\n    - NextSeq\n    - Illumina NextSeq\n    structured_aliases:\n      Illumina NextSeq-HO:\n        literal_form: Illumina NextSeq-HO\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n      Illumina NextSeq-MO:\n        literal_form: Illumina NextSeq-MO\n        predicate: NARROW_SYNONYM\n        contexts:\n        - https://gold.jgi.doe.gov/\n  nextseq_500:\n    text: nextseq_500\n    meaning: OBI:0002021\n    aliases:\n    - NextSeq 500\n    - Illumina NextSeq 500\n  nextseq_550:\n    text: nextseq_550\n    meaning: OBI:0003387\n    aliases:\n    - NextSeq 550\n    - Illumina NextSeq 550\n  gridion:\n    text: gridion\n    meaning: OBI:0002751\n    aliases:\n    - Oxford Nanopore GridION Mk1\n  minion:\n    text: minion\n    meaning: OBI:0002750\n    aliases:\n    - Oxford Nanopore MinION\n  promethion:\n    text: promethion\n    meaning: OBI:0002752\n    aliases:\n    - Oxford Nanopore PromethION\n  rs_II:\n    text: rs_II\n    meaning: OBI:0002012\n    aliases:\n    - PacBio RS II\n  sequel:\n    text: sequel\n    meaning: OBI:0002632\n    aliases:\n    - PacBio Sequel\n  sequel_II:\n    text: sequel_II\n    meaning: OBI:0002633\n    aliases:\n    - PacBio Sequel II\n  revio:\n    text: revio\n    aliases:\n    - PacBio Revio\n    - Revio\n\n
"},{"location":"InstrumentVendorEnum/","title":"Enum: InstrumentVendorEnum","text":"

URI: InstrumentVendorEnum

"},{"location":"InstrumentVendorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description waters None agilent None bruker None thermo_fisher None vwr None perkin_elmer None gilson None scientific_industries None illumina OBI:0000759 pacbio OBI:0001856 oxford_nanopore OBI:0002755 pnnl None"},{"location":"InstrumentVendorEnum/#slots","title":"Slots","text":"Name Description vendor"},{"location":"InstrumentVendorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InstrumentVendorEnum/#schema-source","title":"Schema Source","text":""},{"location":"InstrumentVendorEnum/#linkml-source","title":"LinkML Source","text":"
name: InstrumentVendorEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  waters:\n    text: waters\n    aliases:\n    - Waters Corporation\n  agilent:\n    text: agilent\n    aliases:\n    - Agilent Technologies\n  bruker:\n    text: bruker\n    aliases:\n    - Bruker Corporation\n    - Bruker Daltonics\n  thermo_fisher:\n    text: thermo_fisher\n    aliases:\n    - ThermoFisher\n    - Thermo Fisher Scientific\n  vwr:\n    text: vwr\n  perkin_elmer:\n    text: perkin_elmer\n  gilson:\n    text: gilson\n  scientific_industries:\n    text: scientific_industries\n  illumina:\n    text: illumina\n    meaning: OBI:0000759\n    aliases:\n    - Illumina\n  pacbio:\n    text: pacbio\n    meaning: OBI:0001856\n    aliases:\n    - PacBio\n    - Pacific Biosciences\n  oxford_nanopore:\n    text: oxford_nanopore\n    meaning: OBI:0002755\n    aliases:\n    - Oxford Nanopore Technologies\n  pnnl:\n    text: pnnl\n    aliases:\n    - PNNL\n\n
"},{"location":"IntWallCondEnum/","title":"Enum: IntWallCondEnum","text":"

URI: IntWallCondEnum

"},{"location":"IntWallCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"IntWallCondEnum/#slots","title":"Slots","text":"Name Description int_wall_cond The physical condition of the wall at the time of sampling; photos or video p..."},{"location":"IntWallCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IntWallCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"IntWallCondEnum/#linkml-source","title":"LinkML Source","text":"
name: int_wall_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  new:\n    text: new\n  visible wear:\n    text: visible wear\n  needs repair:\n    text: needs repair\n  damaged:\n    text: damaged\n  rupture:\n    text: rupture\n\n
"},{"location":"Integer/","title":"Type: Integer","text":"

An integer

URI: xsd:integer

"},{"location":"Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Integer/#schema-source","title":"Schema Source","text":""},{"location":"Integer/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:integer native nmdc:integer exact schema:Integer"},{"location":"Investigation/","title":"Subset: Investigation","text":"

URI: Investigation

"},{"location":"Investigation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Investigation/#schema-source","title":"Schema Source","text":""},{"location":"IonizationSourceEnum/","title":"Enum: IonizationSourceEnum","text":"

URI: IonizationSourceEnum

"},{"location":"IonizationSourceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description electrospray_ionization None matrix_assisted_laser_desorption_ionization None atmospheric_pressure_photo_ionization None atmospheric_pressure_chemical_ionization None electron_ionization None"},{"location":"IonizationSourceEnum/#slots","title":"Slots","text":"Name Description ionization_source The ionization source used to introduce processed samples into a mass spectro..."},{"location":"IonizationSourceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IonizationSourceEnum/#schema-source","title":"Schema Source","text":""},{"location":"IonizationSourceEnum/#linkml-source","title":"LinkML Source","text":"
name: IonizationSourceEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  electrospray_ionization:\n    text: electrospray_ionization\n    aliases:\n    - ESI\n  matrix_assisted_laser_desorption_ionization:\n    text: matrix_assisted_laser_desorption_ionization\n    aliases:\n    - MALDI\n  atmospheric_pressure_photo_ionization:\n    text: atmospheric_pressure_photo_ionization\n    aliases:\n    - APPI\n  atmospheric_pressure_chemical_ionization:\n    text: atmospheric_pressure_chemical_ionization\n    aliases:\n    - APCI\n  electron_ionization:\n    text: electron_ionization\n    aliases:\n    - EI\n\n
"},{"location":"JgiContTypeEnum/","title":"Enum: JgiContTypeEnum","text":"

URI: JgiContTypeEnum

"},{"location":"JgiContTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plate None tube None"},{"location":"JgiContTypeEnum/#slots","title":"Slots","text":"Name Description dna_cont_type Tube or plate (96-well) rna_cont_type Tube or plate (96-well)"},{"location":"JgiContTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"JgiContTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"JgiContTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: JgiContTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  plate:\n    text: plate\n  tube:\n    text: tube\n\n
"},{"location":"Jsonpath/","title":"Type: Jsonpath","text":"

A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.

URI: xsd:string

"},{"location":"Jsonpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Jsonpath/#schema-source","title":"Schema Source","text":""},{"location":"Jsonpath/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:jsonpath"},{"location":"Jsonpointer/","title":"Type: Jsonpointer","text":"

A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.

URI: xsd:string

"},{"location":"Jsonpointer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Jsonpointer/#schema-source","title":"Schema Source","text":""},{"location":"Jsonpointer/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:jsonpointer"},{"location":"LanguageCode/","title":"Type: LanguageCode","text":"

A language code conforming to ISO_639-1

URI: xsd:language

"},{"location":"LanguageCode/#see-also","title":"See Also","text":""},{"location":"LanguageCode/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LanguageCode/#schema-source","title":"Schema Source","text":""},{"location":"LanguageCode/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:language native nmdc:language_code"},{"location":"LibraryPreparation/","title":"Class: LibraryPreparation","text":"

URI: nmdc:LibraryPreparation

classDiagram\n  class LibraryPreparation\n  click LibraryPreparation href \"../LibraryPreparation\"\n    MaterialProcessing <|-- LibraryPreparation\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  LibraryPreparation : alternative_identifiers\n\n  LibraryPreparation : description\n\n  LibraryPreparation : end_date\n\n  LibraryPreparation : has_failure_categorization\n\n      LibraryPreparation --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  LibraryPreparation : has_input\n\n      LibraryPreparation --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  LibraryPreparation : has_output\n\n      LibraryPreparation --> \"1..*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  LibraryPreparation : id\n\n  LibraryPreparation : instrument_used\n\n      LibraryPreparation --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  LibraryPreparation : is_stranded\n\n  LibraryPreparation : library_preparation_kit\n\n  LibraryPreparation : library_type\n\n      LibraryPreparation --> \"0..1\" LibraryTypeEnum : library_type\n    click LibraryTypeEnum href \"../LibraryTypeEnum\"\n\n  LibraryPreparation : name\n\n  LibraryPreparation : nucl_acid_amp\n\n      LibraryPreparation --> \"0..1\" TextValue : nucl_acid_amp\n    click TextValue href \"../TextValue\"\n\n  LibraryPreparation : pcr_cond\n\n      LibraryPreparation --> \"0..1\" TextValue : pcr_cond\n    click TextValue href \"../TextValue\"\n\n  LibraryPreparation : pcr_cycles\n\n  LibraryPreparation : pcr_primers\n\n      LibraryPreparation --> \"0..1\" TextValue : pcr_primers\n    click TextValue href \"../TextValue\"\n\n  LibraryPreparation : processing_institution\n\n      LibraryPreparation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  LibraryPreparation : protocol_link\n\n      LibraryPreparation --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  LibraryPreparation : qc_comment\n\n  LibraryPreparation : qc_status\n\n      LibraryPreparation --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  LibraryPreparation : start_date\n\n  LibraryPreparation : stranded_orientation\n\n      LibraryPreparation --> \"0..1\" StrandedOrientationEnum : stranded_orientation\n    click StrandedOrientationEnum href \"../StrandedOrientationEnum\"\n\n  LibraryPreparation : type\n\n\n\n
"},{"location":"LibraryPreparation/#inheritance","title":"Inheritance","text":""},{"location":"LibraryPreparation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance is_stranded 0..1 Boolean Is the (RNA) library stranded or non-stranded (unstranded) direct library_preparation_kit 0..1 String direct library_type 0..1 LibraryTypeEnum direct nucl_acid_amp 0..1 TextValue A link to a literature reference, electronic resource or a standard operating... direct pcr_cond 0..1 TextValue Description of reaction conditions and components of polymerase chain reactio... direct pcr_cycles 0..1 Integer direct pcr_primers 0..1 TextValue PCR primers that were used to amplify the sequence of the targeted gene, locu... direct stranded_orientation 0..1 StrandedOrientationEnum Lists the strand orientiation for a stranded RNA library preparation direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output 1..* ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"LibraryPreparation/#aliases","title":"Aliases","text":""},{"location":"LibraryPreparation/#comments","title":"Comments","text":""},{"location":"LibraryPreparation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LibraryPreparation/#schema-source","title":"Schema Source","text":""},{"location":"LibraryPreparation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:LibraryPreparation native nmdc:LibraryPreparation close OBI:0000711"},{"location":"LibraryPreparation/#linkml-source","title":"LinkML Source","text":""},{"location":"LibraryPreparation/#direct","title":"Direct","text":"
name: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: MaterialProcessing\nslots:\n- is_stranded\n- library_preparation_kit\n- library_type\n- nucl_acid_amp\n- pcr_cond\n- pcr_cycles\n- pcr_primers\n- stranded_orientation\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  pcr_cond:\n    name: pcr_cond\n    description: Description of reaction conditions and components of polymerase chain\n      reaction performed during library preparation\nclass_uri: nmdc:LibraryPreparation\n\n
"},{"location":"LibraryPreparation/#induced","title":"Induced","text":"
name: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: MaterialProcessing\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  pcr_cond:\n    name: pcr_cond\n    description: Description of reaction conditions and components of polymerase chain\n      reaction performed during library preparation\nattributes:\n  is_stranded:\n    name: is_stranded\n    description: Is the (RNA) library stranded or non-stranded (unstranded).\n    comments:\n    - A value of true means the library is stranded, flase means non-stranded.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: is_stranded\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: boolean\n  library_preparation_kit:\n    name: library_preparation_kit\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: library_preparation_kit\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: string\n  library_type:\n    name: library_type\n    title: library type\n    examples:\n    - value: DNA\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: library_type\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: LibraryTypeEnum\n  nucl_acid_amp:\n    name: nucl_acid_amp\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: PMID, DOI or URL\n    description: A link to a literature reference, electronic resource or a standard\n      operating procedure (SOP), that describes the enzymatic amplification (PCR,\n      TMA, NASBA) of specific nucleic acids\n    title: nucleic acid amplification\n    examples:\n    - value: https://phylogenomics.me/protocols/16s-pcr-protocol/\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - nucleic acid amplification\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: '{PMID}|{DOI}|{URL}'\n    slot_uri: MIXS:0000038\n    alias: nucl_acid_amp\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: TextValue\n    multivalued: false\n  pcr_cond:\n    name: pcr_cond\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n          elongation:degrees_minutes;total cycles\n    description: Description of reaction conditions and components of polymerase chain\n      reaction performed during library preparation\n    title: pcr conditions\n    examples:\n    - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pcr conditions\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n      elongation:degrees_minutes;total cycles\n    slot_uri: MIXS:0000049\n    alias: pcr_cond\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: TextValue\n    multivalued: false\n  pcr_cycles:\n    name: pcr_cycles\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - OBI:0002475\n    rank: 1000\n    alias: pcr_cycles\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: integer\n  pcr_primers:\n    name: pcr_primers\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: 'FWD: forward primer sequence;REV:reverse primer sequence'\n    description: PCR primers that were used to amplify the sequence of the targeted\n      gene, locus or subfragment. This field should contain all the primers used for\n      a single PCR reaction if multiple forward or reverse primers are present in\n      a single PCR reaction. The primer sequence should be reported in uppercase letters\n    title: pcr primers\n    examples:\n    - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - pcr primers\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: FWD:{dna};REV:{dna}\n    slot_uri: MIXS:0000046\n    alias: pcr_primers\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: TextValue\n    multivalued: false\n  stranded_orientation:\n    name: stranded_orientation\n    description: Lists the strand orientiation for a stranded RNA library preparation.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: stranded_orientation\n    owner: LibraryPreparation\n    domain_of:\n    - LibraryPreparation\n    range: StrandedOrientationEnum\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: LibraryPreparation\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: LibraryPreparation\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: LibraryPreparation\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: LibraryPreparation\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: LibraryPreparation\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: LibraryPreparation\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: LibraryPreparation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:LibraryPreparation\n\n
"},{"location":"LibraryTypeEnum/","title":"Enum: LibraryTypeEnum","text":"

URI: LibraryTypeEnum

"},{"location":"LibraryTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None"},{"location":"LibraryTypeEnum/#slots","title":"Slots","text":"Name Description library_type"},{"location":"LibraryTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LibraryTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"LibraryTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: LibraryTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  DNA:\n    text: DNA\n  RNA:\n    text: RNA\n\n
"},{"location":"LightTypeEnum/","title":"Enum: LightTypeEnum","text":"

URI: LightTypeEnum

"},{"location":"LightTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description natural light None electric light None desk lamp None flourescent lights None none None"},{"location":"LightTypeEnum/#slots","title":"Slots","text":"Name Description light_type Application of light to achieve some practical or aesthetic effect"},{"location":"LightTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LightTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"LightTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: light_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  natural light:\n    text: natural light\n  electric light:\n    text: electric light\n  desk lamp:\n    text: desk lamp\n  flourescent lights:\n    text: flourescent lights\n  none:\n    text: none\n\n
"},{"location":"LithologyEnum/","title":"Enum: LithologyEnum","text":"

URI: LithologyEnum

"},{"location":"LithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Basement None Chalk None Chert None Coal None Conglomerate None Diatomite None Dolomite None Limestone None Sandstone None Shale None Siltstone None Volcanic None other None"},{"location":"LithologyEnum/#slots","title":"Slots","text":"Name Description lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki"},{"location":"LithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LithologyEnum/#schema-source","title":"Schema Source","text":""},{"location":"LithologyEnum/#linkml-source","title":"LinkML Source","text":"
name: lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Basement:\n    text: Basement\n  Chalk:\n    text: Chalk\n  Chert:\n    text: Chert\n  Coal:\n    text: Coal\n  Conglomerate:\n    text: Conglomerate\n  Diatomite:\n    text: Diatomite\n  Dolomite:\n    text: Dolomite\n  Limestone:\n    text: Limestone\n  Sandstone:\n    text: Sandstone\n  Shale:\n    text: Shale\n  Siltstone:\n    text: Siltstone\n  Volcanic:\n    text: Volcanic\n  other:\n    text: other\n\n
"},{"location":"MagBin/","title":"Class: MagBin","text":"

URI: nmdc:MagBin

classDiagram\n  class MagBin\n  click MagBin href \"../MagBin\"\n\n  MagBin : bin_name\n\n  MagBin : bin_quality\n\n  MagBin : completeness\n\n  MagBin : contamination\n\n  MagBin : eukaryotic_evaluation\n\n      MagBin --> \"0..1\" EukEval : eukaryotic_evaluation\n    click EukEval href \"../EukEval\"\n\n  MagBin : gene_count\n\n  MagBin : gtdbtk_class\n\n  MagBin : gtdbtk_domain\n\n  MagBin : gtdbtk_family\n\n  MagBin : gtdbtk_genus\n\n  MagBin : gtdbtk_order\n\n  MagBin : gtdbtk_phylum\n\n  MagBin : gtdbtk_species\n\n  MagBin : members_id\n\n  MagBin : num_16s\n\n  MagBin : num_23s\n\n  MagBin : num_5s\n\n  MagBin : num_t_rna\n\n  MagBin : number_of_contig\n\n  MagBin : total_bases\n\n  MagBin : type\n\n\n\n
"},{"location":"MagBin/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance bin_name 0..1 String direct bin_quality 0..1 String direct completeness 0..1 Float direct contamination 0..1 Float direct gene_count 0..1 Integer direct gtdbtk_class 0..1 String direct gtdbtk_domain 0..1 String direct gtdbtk_family 0..1 String direct gtdbtk_genus 0..1 String direct gtdbtk_order 0..1 String direct gtdbtk_phylum 0..1 String direct gtdbtk_species 0..1 String direct members_id * String direct num_16s 0..1 Integer direct num_23s 0..1 Integer direct num_5s 0..1 Integer direct num_t_rna 0..1 Integer direct number_of_contig 0..1 Integer direct total_bases 0..1 Integer direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct eukaryotic_evaluation 0..1 EukEval Contains results from evaluating if a Metagenome-Assembled Genome is of eukar... direct"},{"location":"MagBin/#usages","title":"Usages","text":"used by used in type used MagsAnalysis mags_list range MagBin"},{"location":"MagBin/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MagBin/#schema-source","title":"Schema Source","text":""},{"location":"MagBin/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MagBin native nmdc:MagBin"},{"location":"MagBin/#linkml-source","title":"LinkML Source","text":""},{"location":"MagBin/#direct","title":"Direct","text":"
name: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- bin_name\n- bin_quality\n- completeness\n- contamination\n- gene_count\n- gtdbtk_class\n- gtdbtk_domain\n- gtdbtk_family\n- gtdbtk_genus\n- gtdbtk_order\n- gtdbtk_phylum\n- gtdbtk_species\n- members_id\n- num_16s\n- num_23s\n- num_5s\n- num_t_rna\n- number_of_contig\n- total_bases\n- type\n- eukaryotic_evaluation\nclass_uri: nmdc:MagBin\n\n
"},{"location":"MagBin/#induced","title":"Induced","text":"
name: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  bin_name:\n    name: bin_name\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: bin_name\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  bin_quality:\n    name: bin_quality\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: bin_quality\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  completeness:\n    name: completeness\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: completeness\n    owner: MagBin\n    domain_of:\n    - EukEval\n    - MagBin\n    range: float\n  contamination:\n    name: contamination\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: contamination\n    owner: MagBin\n    domain_of:\n    - EukEval\n    - MagBin\n    range: float\n  gene_count:\n    name: gene_count\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gene_count\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  gtdbtk_class:\n    name: gtdbtk_class\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_class\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_domain:\n    name: gtdbtk_domain\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_domain\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_family:\n    name: gtdbtk_family\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_family\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_genus:\n    name: gtdbtk_genus\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_genus\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_order:\n    name: gtdbtk_order\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_order\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_phylum:\n    name: gtdbtk_phylum\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_phylum\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  gtdbtk_species:\n    name: gtdbtk_species\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: gtdbtk_species\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n  members_id:\n    name: members_id\n    todos:\n    - this slot needs some basic textual annotations and constraints\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: members_id\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: string\n    multivalued: true\n  num_16s:\n    name: num_16s\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: num_16s\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  num_23s:\n    name: num_23s\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: num_23s\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  num_5s:\n    name: num_5s\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: num_5s\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  num_t_rna:\n    name: num_t_rna\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: num_t_rna\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  number_of_contig:\n    name: number_of_contig\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: number_of_contig\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  total_bases:\n    name: total_bases\n    todos:\n    - this slot needs some basic textual annotations and constraints\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: total_bases\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: integer\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MagBin\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  eukaryotic_evaluation:\n    name: eukaryotic_evaluation\n    description: Contains results from evaluating if a Metagenome-Assembled Genome\n      is of eukaryotic lineage.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: eukaryotic_evaluation\n    owner: MagBin\n    domain_of:\n    - MagBin\n    range: EukEval\nclass_uri: nmdc:MagBin\n\n
"},{"location":"MagsAnalysis/","title":"Class: Metagenome-Assembled Genome analysis activity (MagsAnalysis)","text":"

A workflow execution activity that uses computational binning tools to group assembled contigs into genomes

URI: nmdc:MagsAnalysis

classDiagram\n  class MagsAnalysis\n  click MagsAnalysis href \"../MagsAnalysis\"\n    WorkflowExecution <|-- MagsAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MagsAnalysis : alternative_identifiers\n\n  MagsAnalysis : binned_contig_num\n\n  MagsAnalysis : description\n\n  MagsAnalysis : end_date\n\n  MagsAnalysis : ended_at_time\n\n  MagsAnalysis : execution_resource\n\n      MagsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MagsAnalysis : git_url\n\n  MagsAnalysis : has_failure_categorization\n\n      MagsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MagsAnalysis : has_input\n\n      MagsAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MagsAnalysis : has_output\n\n      MagsAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MagsAnalysis : id\n\n  MagsAnalysis : img_identifiers\n\n  MagsAnalysis : input_contig_num\n\n  MagsAnalysis : low_depth_contig_num\n\n  MagsAnalysis : mags_list\n\n      MagsAnalysis --> \"*\" MagBin : mags_list\n    click MagBin href \"../MagBin\"\n\n  MagsAnalysis : name\n\n  MagsAnalysis : processing_institution\n\n      MagsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MagsAnalysis : protocol_link\n\n      MagsAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MagsAnalysis : qc_comment\n\n  MagsAnalysis : qc_status\n\n      MagsAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MagsAnalysis : start_date\n\n  MagsAnalysis : started_at_time\n\n  MagsAnalysis : too_short_contig_num\n\n  MagsAnalysis : type\n\n  MagsAnalysis : unbinned_contig_num\n\n  MagsAnalysis : version\n\n  MagsAnalysis : was_informed_by\n\n      MagsAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MagsAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"MagsAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance binned_contig_num 0..1 Integer direct input_contig_num 0..1 Integer direct low_depth_contig_num 0..1 Integer direct mags_list * MagBin direct too_short_contig_num 0..1 Integer direct unbinned_contig_num 0..1 Integer direct img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MagsAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MagsAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"MagsAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MagsAnalysis native nmdc:MagsAnalysis"},{"location":"MagsAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"MagsAnalysis/#direct","title":"Direct","text":"
name: MagsAnalysis\ndescription: A workflow execution activity that uses computational binning tools to\n  group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- binned_contig_num\n- input_contig_num\n- low_depth_contig_num\n- mags_list\n- too_short_contig_num\n- unbinned_contig_num\n- img_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MagsAnalysis\n\n
"},{"location":"MagsAnalysis/#induced","title":"Induced","text":"
name: MagsAnalysis\ndescription: A workflow execution activity that uses computational binning tools to\n  group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  binned_contig_num:\n    name: binned_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: binned_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  input_contig_num:\n    name: input_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: input_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  low_depth_contig_num:\n    name: low_depth_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: low_depth_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  mags_list:\n    name: mags_list\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mags_list\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: MagBin\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  too_short_contig_num:\n    name: too_short_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: too_short_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  unbinned_contig_num:\n    name: unbinned_contig_num\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: unbinned_contig_num\n    owner: MagsAnalysis\n    domain_of:\n    - MagsAnalysis\n    range: integer\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: MagsAnalysis\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n    maximum_cardinality: 1\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MagsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MagsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MagsAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MagsAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MagsAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MagsAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MagsAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MagsAnalysis\n\n
"},{"location":"Manifest/","title":"Class: Manifest","text":"

URI: nmdc:Manifest

classDiagram\n  class Manifest\n  click Manifest href \"../Manifest\"\n    InformationObject <|-- Manifest\n      click InformationObject href \"../InformationObject\"\n\n\n\n  Manifest : alternative_identifiers\n\n  Manifest : description\n\n  Manifest : id\n\n  Manifest : manifest_category\n\n      Manifest --> \"1\" ManifestCategoryEnum : manifest_category\n    click ManifestCategoryEnum href \"../ManifestCategoryEnum\"\n\n  Manifest : name\n\n  Manifest : type\n\n\n\n
"},{"location":"Manifest/#inheritance","title":"Inheritance","text":""},{"location":"Manifest/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance manifest_category 1 ManifestCategoryEnum The type of collection that describes the data in the collection direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Manifest/#usages","title":"Usages","text":"used by used in type used Database manifest_set range Manifest DataObject in_manifest range Manifest"},{"location":"Manifest/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Manifest/#schema-source","title":"Schema Source","text":""},{"location":"Manifest/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Manifest native nmdc:Manifest"},{"location":"Manifest/#linkml-source","title":"LinkML Source","text":""},{"location":"Manifest/#direct","title":"Direct","text":"
name: Manifest\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- manifest_category\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\nclass_uri: nmdc:Manifest\n\n
"},{"location":"Manifest/#induced","title":"Induced","text":"
name: Manifest\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\nattributes:\n  manifest_category:\n    name: manifest_category\n    description: The type of collection that describes the data in the collection.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: manifest_category\n    owner: Manifest\n    domain_of:\n    - Manifest\n    range: ManifestCategoryEnum\n    required: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Manifest\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Manifest\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Manifest\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Manifest\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Manifest\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Manifest\n\n
"},{"location":"ManifestCategoryEnum/","title":"Enum: ManifestCategoryEnum","text":"

URI: ManifestCategoryEnum

"},{"location":"ManifestCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description instrument_run None A collection of data generation records from a single run of an instrument technical_replicates None A collection of data generation records that represent technical replicates o... fractions None A collection of data generation records that represent fractions of a single ..."},{"location":"ManifestCategoryEnum/#slots","title":"Slots","text":"Name Description manifest_category The type of collection that describes the data in the collection"},{"location":"ManifestCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ManifestCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ManifestCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ManifestCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  instrument_run:\n    text: instrument_run\n    description: A collection of data generation records from a single run of an instrument.\n  technical_replicates:\n    text: technical_replicates\n    description: A collection of data generation records that represent technical\n      replicates of a single sample.\n  fractions:\n    text: fractions\n    description: A collection of data generation records that represent fractions\n      of a single sample.\n\n
"},{"location":"MassAnalyzerEnum/","title":"Enum: MassAnalyzerEnum","text":"

URI: MassAnalyzerEnum

"},{"location":"MassAnalyzerEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description time_of_flight None Instrument that separates ions by m/z in a field-free region after accelerati... quadrupole None A mass spectrometer that consists of four parallel rods whose centers form th... Orbitrap None An ion trapping device that consists of an outer barrel-like electrode and a ... ion_cyclotron_resonance None A mass spectrometer based on the principle of ion cyclotron resonance in whic... ion_trap None A device for spatially confining ions using electric and magnetic fields alon..."},{"location":"MassAnalyzerEnum/#slots","title":"Slots","text":"Name Description mass_analyzers The kind of mass analyzer(s) used during the spectra collection"},{"location":"MassAnalyzerEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassAnalyzerEnum/#schema-source","title":"Schema Source","text":""},{"location":"MassAnalyzerEnum/#linkml-source","title":"LinkML Source","text":"
name: MassAnalyzerEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  time_of_flight:\n    text: time_of_flight\n    description: Instrument that separates ions by m/z in a field-free region after\n      acceleration to a fixed acceleration energy.\n    aliases:\n    - TOF\n    exact_mappings:\n    - MS:1000084\n  quadrupole:\n    text: quadrupole\n    description: A mass spectrometer that consists of four parallel rods whose centers\n      form the corners of a square and whose opposing poles are connected. The voltage\n      applied to the rods is a superposition of a static potential and a sinusoidal\n      radio frequency potential. The motion of an ion in the x and y dimensions is\n      described by the Matthieu equation whose solutions show that ions in a particular\n      m/z range can be transmitted along the z axis.\n    aliases:\n    - Quad\n    - Q\n    exact_mappings:\n    - MS:1000081\n  Orbitrap:\n    text: Orbitrap\n    description: An ion trapping device that consists of an outer barrel-like electrode\n      and a coaxial inner spindle-like electrode that form an electrostatic field\n      with quadro-logarithmic potential distribution. The frequency of harmonic oscillations\n      of the orbitally trapped ions along the axis of the electrostatic field is independent\n      of the ion velocity and is inversely proportional to the square root of m/z\n      so that the trap can be used as a mass analyzer.\n    aliases:\n    - Orbi\n    exact_mappings:\n    - MS:1000484\n  ion_cyclotron_resonance:\n    text: ion_cyclotron_resonance\n    description: A mass spectrometer based on the principle of ion cyclotron resonance\n      in which an ion in a magnetic field moves in a circular orbit at a frequency\n      characteristic of its m/z value. Ions are coherently excited to a larger radius\n      orbit using a pulse of radio frequency energy and their image charge is detected\n      on receiver plates as a time domain signal. Fourier transformation of the time\n      domain signal results in a frequency domain signal which is converted to a mass\n      spectrum based in the inverse relationship between frequency and m/z.\n    aliases:\n    - ICR\n    exact_mappings:\n    - MS:1000079\n  ion_trap:\n    text: ion_trap\n    description: A device for spatially confining ions using electric and magnetic\n      fields alone or in combination.\n    aliases:\n    - LTQ\n    - Ion Trap\n    - Paul Trap\n    exact_mappings:\n    - MS:1000264\n\n
"},{"location":"MassSpectrometry/","title":"Class: MassSpectrometry","text":"

Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.

URI: nmdc:MassSpectrometry

classDiagram\n  class MassSpectrometry\n  click MassSpectrometry href \"../MassSpectrometry\"\n    DataGeneration <|-- MassSpectrometry\n      click DataGeneration href \"../DataGeneration\"\n\n\n\n  MassSpectrometry : add_date\n\n  MassSpectrometry : alternative_identifiers\n\n  MassSpectrometry : analyte_category\n\n      MassSpectrometry --> \"1\" AnalyteCategoryEnum : analyte_category\n    click AnalyteCategoryEnum href \"../AnalyteCategoryEnum\"\n\n  MassSpectrometry : associated_studies\n\n      MassSpectrometry --> \"1..*\" Study : associated_studies\n    click Study href \"../Study\"\n\n  MassSpectrometry : description\n\n  MassSpectrometry : eluent_introduction_category\n\n      MassSpectrometry --> \"0..1\" EluentIntroductionCategoryEnum : eluent_introduction_category\n    click EluentIntroductionCategoryEnum href \"../EluentIntroductionCategoryEnum\"\n\n  MassSpectrometry : end_date\n\n  MassSpectrometry : has_calibration\n\n  MassSpectrometry : has_chromatography_configuration\n\n      MassSpectrometry --> \"0..1\" ChromatographyConfiguration : has_chromatography_configuration\n    click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n\n  MassSpectrometry : has_failure_categorization\n\n      MassSpectrometry --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MassSpectrometry : has_input\n\n      MassSpectrometry --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MassSpectrometry : has_mass_spectrometry_configuration\n\n      MassSpectrometry --> \"0..1\" MassSpectrometryConfiguration : has_mass_spectrometry_configuration\n    click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n\n  MassSpectrometry : has_output\n\n      MassSpectrometry --> \"*\" DataObject : has_output\n    click DataObject href \"../DataObject\"\n\n  MassSpectrometry : id\n\n  MassSpectrometry : instrument_used\n\n      MassSpectrometry --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  MassSpectrometry : mod_date\n\n  MassSpectrometry : name\n\n  MassSpectrometry : principal_investigator\n\n      MassSpectrometry --> \"0..1\" PersonValue : principal_investigator\n    click PersonValue href \"../PersonValue\"\n\n  MassSpectrometry : processing_institution\n\n      MassSpectrometry --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MassSpectrometry : protocol_link\n\n      MassSpectrometry --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MassSpectrometry : qc_comment\n\n  MassSpectrometry : qc_status\n\n      MassSpectrometry --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MassSpectrometry : start_date\n\n  MassSpectrometry : type\n\n\n\n
"},{"location":"MassSpectrometry/#inheritance","title":"Inheritance","text":""},{"location":"MassSpectrometry/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance eluent_introduction_category 0..1 EluentIntroductionCategoryEnum A high-level categorization for how the processed sample is introduced into a... direct has_calibration 0..1 String\u00a0or\u00a0CalibrationInformation\u00a0or\u00a0String a calibration instance associated with a process direct has_chromatography_configuration 0..1 ChromatographyConfiguration The identifier of the associated ChromatographyConfiguration, providing infor... direct has_mass_spectrometry_configuration 0..1 MassSpectrometryConfiguration The identifier of the associated MassSpectrometryConfiguration direct add_date 0..1 String The date on which the information was added to the database DataGeneration analyte_category 1 AnalyteCategoryEnum The type of analyte(s) that were measured in the data generation process and ... DataGeneration associated_studies 1..* Study The study associated with a resource DataGeneration instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing DataGeneration mod_date 0..1 String The last date on which the database information was modified DataGeneration principal_investigator 0..1 PersonValue Principal Investigator who led the study and/or generated the dataset DataGeneration has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * DataObject An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MassSpectrometry/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometry/#schema-source","title":"Schema Source","text":""},{"location":"MassSpectrometry/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MassSpectrometry native nmdc:MassSpectrometry exact CHMO:0000470"},{"location":"MassSpectrometry/#linkml-source","title":"LinkML Source","text":""},{"location":"MassSpectrometry/#direct","title":"Direct","text":"
name: MassSpectrometry\ndescription: Spectrometry where the sample is converted into gaseous ions which are\n  characterised by their mass-to-charge ratio and relative abundance.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- CHMO:0000470\nis_a: DataGeneration\nslots:\n- eluent_introduction_category\n- has_calibration\n- has_chromatography_configuration\n- has_mass_spectrometry_configuration\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_calibration:\n    name: has_calibration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_chromatography_configuration:\n    name: has_chromatography_configuration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_mass_spectrometry_configuration:\n    name: has_mass_spectrometry_configuration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MassSpectrometry\nrules:\n- preconditions:\n    slot_conditions:\n      eluent_introduction_category:\n        name: eluent_introduction_category\n        equals_string: gas_chromatography\n  postconditions:\n    slot_conditions:\n      has_calibration:\n        name: has_calibration\n        required: true\n  description: If eluent_introduction_category is gas_chromatography, then has_calibration\n    is required.\n  title: has_calibration_required_if_gc\n- preconditions:\n    slot_conditions:\n      eluent_introduction_category:\n        name: eluent_introduction_category\n        any_of:\n        - equals_string: liquid_chromatography\n        - equals_string: gas_chromatography\n  postconditions:\n    slot_conditions:\n      has_chromatography_configuration:\n        name: has_chromatography_configuration\n        required: true\n  description: If eluent_introduction_category is liquid_chromatography or gas_chromatography,\n    then has_chromatography_configuration is required.\n  title: has_chromatography_configuration_required_if_lc_or_gc\n\n
"},{"location":"MassSpectrometry/#induced","title":"Induced","text":"
name: MassSpectrometry\ndescription: Spectrometry where the sample is converted into gaseous ions which are\n  characterised by their mass-to-charge ratio and relative abundance.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- CHMO:0000470\nis_a: DataGeneration\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_calibration:\n    name: has_calibration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_chromatography_configuration:\n    name: has_chromatography_configuration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_mass_spectrometry_configuration:\n    name: has_mass_spectrometry_configuration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  eluent_introduction_category:\n    name: eluent_introduction_category\n    description: A high-level categorization for how the processed sample is introduced\n      into a mass spectrometer.\n    examples:\n    - value: liquid_chromatography\n    - value: direct_infusion_syringe\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: eluent_introduction_category\n    owner: MassSpectrometry\n    domain_of:\n    - MassSpectrometry\n    range: EluentIntroductionCategoryEnum\n  has_calibration:\n    name: has_calibration\n    description: a calibration instance associated with a process\n    notes:\n    - 'has_calibration slot will be removed from all WorkflowExecution classes but\n      remain on the MassSpectrometry class after an ingest of the appropriate set\n      has occurred.  Once this has occurred, this slot''s range can be updated to\n      CalibrationInformation and class/slot definitions can move to nmdc.yaml.   See\n      PR #29 in Berkeley schema.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_calibration\n    owner: MassSpectrometry\n    domain_of:\n    - MassSpectrometry\n    - MetabolomicsAnalysis\n    - NomAnalysis\n    range: string\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: CalibrationInformation\n    - range: string\n  has_chromatography_configuration:\n    name: has_chromatography_configuration\n    description: The identifier of the associated ChromatographyConfiguration, providing\n      information about how a sample was introduced into the mass spectrometer.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_chromatography_configuration\n    owner: MassSpectrometry\n    domain_of:\n    - MassSpectrometry\n    range: ChromatographyConfiguration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_mass_spectrometry_configuration:\n    name: has_mass_spectrometry_configuration\n    description: The identifier of the associated MassSpectrometryConfiguration.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_mass_spectrometry_configuration\n    owner: MassSpectrometry\n    domain_of:\n    - MassSpectrometry\n    range: MassSpectrometryConfiguration\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  add_date:\n    name: add_date\n    description: The date on which the information was added to the database.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: add_date\n    owner: MassSpectrometry\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  analyte_category:\n    name: analyte_category\n    description: \"The type of analyte(s) that were measured in the data generation\\\n      \\ process and analyzed\\n  in the Workflow Chain\\n\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: analyte_category\n    owner: MassSpectrometry\n    domain_of:\n    - DataGeneration\n    range: AnalyteCategoryEnum\n    required: true\n  associated_studies:\n    name: associated_studies\n    description: The study associated with a resource.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: associated_studies\n    owner: MassSpectrometry\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: Study\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: MassSpectrometry\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  mod_date:\n    name: mod_date\n    description: The last date on which the database information was modified.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mod_date\n    owner: MassSpectrometry\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  principal_investigator:\n    name: principal_investigator\n    description: Principal Investigator who led the study and/or generated the dataset.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - PI\n    rank: 1000\n    alias: principal_investigator\n    owner: MassSpectrometry\n    domain_of:\n    - Study\n    - DataGeneration\n    range: PersonValue\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: DataObject\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MassSpectrometry\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MassSpectrometry\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MassSpectrometry\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MassSpectrometry\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MassSpectrometry\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MassSpectrometry\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MassSpectrometry\nrules:\n- preconditions:\n    slot_conditions:\n      eluent_introduction_category:\n        name: eluent_introduction_category\n        equals_string: gas_chromatography\n  postconditions:\n    slot_conditions:\n      has_calibration:\n        name: has_calibration\n        required: true\n  description: If eluent_introduction_category is gas_chromatography, then has_calibration\n    is required.\n  title: has_calibration_required_if_gc\n- preconditions:\n    slot_conditions:\n      eluent_introduction_category:\n        name: eluent_introduction_category\n        any_of:\n        - equals_string: liquid_chromatography\n        - equals_string: gas_chromatography\n  postconditions:\n    slot_conditions:\n      has_chromatography_configuration:\n        name: has_chromatography_configuration\n        required: true\n  description: If eluent_introduction_category is liquid_chromatography or gas_chromatography,\n    then has_chromatography_configuration is required.\n  title: has_chromatography_configuration_required_if_lc_or_gc\n\n
"},{"location":"MassSpectrometryAcquisitionStrategyEnum/","title":"Enum: MassSpectrometryAcquisitionStrategyEnum","text":"

URI: MassSpectrometryAcquisitionStrategyEnum

"},{"location":"MassSpectrometryAcquisitionStrategyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description data_independent_acquisition None ['Data independent mass spectrometer acquisition method wherein the full mass... data_dependent_acquisition None Mass spectrometer data acquisition method wherein MSn spectra are triggered b... full_scan_only None Mass spectrometer data acquisition method wherein only MS1 data are acquired"},{"location":"MassSpectrometryAcquisitionStrategyEnum/#slots","title":"Slots","text":"Name Description mass_spectrometry_acquisition_strategy Mode of running a mass spectrometer method by which m/z ranges are selected a..."},{"location":"MassSpectrometryAcquisitionStrategyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometryAcquisitionStrategyEnum/#schema-source","title":"Schema Source","text":""},{"location":"MassSpectrometryAcquisitionStrategyEnum/#linkml-source","title":"LinkML Source","text":"
name: MassSpectrometryAcquisitionStrategyEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  data_independent_acquisition:\n    text: data_independent_acquisition\n    description: '[''Data independent mass spectrometer acquisition method wherein\n      the full mass range is fragmented. Examples of such an approach include MS^E,\n      AIF, and bbCID.'']'\n    aliases:\n    - DIA\n    - data independent acquisition from dissociation of full mass range\n    exact_mappings:\n    - MS:1003227\n  data_dependent_acquisition:\n    text: data_dependent_acquisition\n    description: Mass spectrometer data acquisition method wherein MSn spectra are\n      triggered based on the m/z of precursor ions detected in the same run.\n    aliases:\n    - -DDA\n    exact_mappings:\n    - MS:1003221\n  full_scan_only:\n    text: full_scan_only\n    description: Mass spectrometer data acquisition method wherein only MS1 data are\n      acquired.\n    aliases:\n    - MS\n\n
"},{"location":"MassSpectrometryConfiguration/","title":"Class: MassSpectrometryConfiguration","text":"

A set of parameters that define and control the actions of a mass spectrometry process.

URI: nmdc:MassSpectrometryConfiguration

classDiagram\n  class MassSpectrometryConfiguration\n  click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n    Configuration <|-- MassSpectrometryConfiguration\n      click Configuration href \"../Configuration\"\n\n\n\n  MassSpectrometryConfiguration : alternative_identifiers\n\n  MassSpectrometryConfiguration : description\n\n  MassSpectrometryConfiguration : id\n\n  MassSpectrometryConfiguration : ionization_source\n\n      MassSpectrometryConfiguration --> \"0..1\" IonizationSourceEnum : ionization_source\n    click IonizationSourceEnum href \"../IonizationSourceEnum\"\n\n  MassSpectrometryConfiguration : mass_analyzers\n\n      MassSpectrometryConfiguration --> \"*\" MassAnalyzerEnum : mass_analyzers\n    click MassAnalyzerEnum href \"../MassAnalyzerEnum\"\n\n  MassSpectrometryConfiguration : mass_spectrometry_acquisition_strategy\n\n      MassSpectrometryConfiguration --> \"0..1\" MassSpectrometryAcquisitionStrategyEnum : mass_spectrometry_acquisition_strategy\n    click MassSpectrometryAcquisitionStrategyEnum href \"../MassSpectrometryAcquisitionStrategyEnum\"\n\n  MassSpectrometryConfiguration : mass_spectrum_collection_modes\n\n      MassSpectrometryConfiguration --> \"*\" MassSpectrumCollectionModeEnum : mass_spectrum_collection_modes\n    click MassSpectrumCollectionModeEnum href \"../MassSpectrumCollectionModeEnum\"\n\n  MassSpectrometryConfiguration : name\n\n  MassSpectrometryConfiguration : polarity_mode\n\n      MassSpectrometryConfiguration --> \"0..1\" PolarityModeEnum : polarity_mode\n    click PolarityModeEnum href \"../PolarityModeEnum\"\n\n  MassSpectrometryConfiguration : resolution_categories\n\n      MassSpectrometryConfiguration --> \"*\" ResolutionCategoryEnum : resolution_categories\n    click ResolutionCategoryEnum href \"../ResolutionCategoryEnum\"\n\n  MassSpectrometryConfiguration : type\n\n\n\n
"},{"location":"MassSpectrometryConfiguration/#inheritance","title":"Inheritance","text":""},{"location":"MassSpectrometryConfiguration/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance mass_spectrometry_acquisition_strategy 0..1 MassSpectrometryAcquisitionStrategyEnum Mode of running a mass spectrometer method by which m/z ranges are selected a... direct resolution_categories * ResolutionCategoryEnum The relative resolution at which spectra were collected direct mass_analyzers * MassAnalyzerEnum The kind of mass analyzer(s) used during the spectra collection direct ionization_source 0..1 IonizationSourceEnum The ionization source used to introduce processed samples into a mass spectro... direct mass_spectrum_collection_modes * MassSpectrumCollectionModeEnum Indicates whether mass spectra were collected in full profile, reduced profil... direct polarity_mode 0..1 PolarityModeEnum the polarity of which ions are generated and detected direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 1 String A human readable label for an entity NamedThing description 1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MassSpectrometryConfiguration/#usages","title":"Usages","text":"used by used in type used MassSpectrometry has_mass_spectrometry_configuration range MassSpectrometryConfiguration"},{"location":"MassSpectrometryConfiguration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometryConfiguration/#schema-source","title":"Schema Source","text":""},{"location":"MassSpectrometryConfiguration/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MassSpectrometryConfiguration native nmdc:MassSpectrometryConfiguration"},{"location":"MassSpectrometryConfiguration/#linkml-source","title":"LinkML Source","text":""},{"location":"MassSpectrometryConfiguration/#direct","title":"Direct","text":"
name: MassSpectrometryConfiguration\ndescription: A set of parameters that define and control the actions of a mass spectrometry\n  process.\nnotes:\n- This class is intended to represent a mass spectrometry method file that controls\n  a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslots:\n- mass_spectrometry_acquisition_strategy\n- resolution_categories\n- mass_analyzers\n- ionization_source\n- mass_spectrum_collection_modes\n- polarity_mode\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MassSpectrometryConfiguration\n\n
"},{"location":"MassSpectrometryConfiguration/#induced","title":"Induced","text":"
name: MassSpectrometryConfiguration\ndescription: A set of parameters that define and control the actions of a mass spectrometry\n  process.\nnotes:\n- This class is intended to represent a mass spectrometry method file that controls\n  a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslot_usage:\n  name:\n    name: name\n    required: true\n  description:\n    name: description\n    required: true\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  mass_spectrometry_acquisition_strategy:\n    name: mass_spectrometry_acquisition_strategy\n    description: Mode of running a mass spectrometer method by which m/z ranges are\n      selected and ions possibly fragment.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - MS:1003213\n    rank: 1000\n    alias: mass_spectrometry_acquisition_strategy\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: MassSpectrometryAcquisitionStrategyEnum\n  resolution_categories:\n    name: resolution_categories\n    description: The relative resolution at which spectra were collected.\n    examples:\n    - value: '[''high'', ''low'']'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: resolution_categories\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: ResolutionCategoryEnum\n    multivalued: true\n  mass_analyzers:\n    name: mass_analyzers\n    description: The kind of mass analyzer(s) used during the spectra collection.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - MS:1000443\n    rank: 1000\n    alias: mass_analyzers\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: MassAnalyzerEnum\n    multivalued: true\n  ionization_source:\n    name: ionization_source\n    description: The ionization source used to introduce processed samples into a\n      mass spectrometer\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - MS:1000008\n    rank: 1000\n    alias: ionization_source\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: IonizationSourceEnum\n  mass_spectrum_collection_modes:\n    name: mass_spectrum_collection_modes\n    description: Indicates whether mass spectra were collected in full profile, reduced\n      profile, or centroid mode during acquisition.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mass_spectrum_collection_modes\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: MassSpectrumCollectionModeEnum\n    multivalued: true\n  polarity_mode:\n    name: polarity_mode\n    description: the polarity of which ions are generated and detected\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: polarity_mode\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MassSpectrometryConfiguration\n    range: PolarityModeEnum\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n    required: true\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n    required: true\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MassSpectrometryConfiguration\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MassSpectrometryConfiguration\n\n
"},{"location":"MassSpectrumCollectionModeEnum/","title":"Enum: MassSpectrumCollectionModeEnum","text":"

URI: MassSpectrumCollectionModeEnum

"},{"location":"MassSpectrumCollectionModeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description full_profile None reduced_profile None centroid None"},{"location":"MassSpectrumCollectionModeEnum/#slots","title":"Slots","text":"Name Description mass_spectrum_collection_modes Indicates whether mass spectra were collected in full profile, reduced profil..."},{"location":"MassSpectrumCollectionModeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrumCollectionModeEnum/#schema-source","title":"Schema Source","text":""},{"location":"MassSpectrumCollectionModeEnum/#linkml-source","title":"LinkML Source","text":"
name: MassSpectrumCollectionModeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  full_profile:\n    text: full_profile\n  reduced_profile:\n    text: reduced_profile\n  centroid:\n    text: centroid\n\n
"},{"location":"MaterialEntity/","title":"Class: Material Entity (MaterialEntity)","text":"

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:MaterialEntity

classDiagram\n  class MaterialEntity\n  click MaterialEntity href \"../MaterialEntity\"\n    NamedThing <|-- MaterialEntity\n      click NamedThing href \"../NamedThing\"\n\n\n    MaterialEntity <|-- Biosample\n      click Biosample href \"../Biosample\"\n    MaterialEntity <|-- ProcessedSample\n      click ProcessedSample href \"../ProcessedSample\"\n    MaterialEntity <|-- Site\n      click Site href \"../Site\"\n    MaterialEntity <|-- Instrument\n      click Instrument href \"../Instrument\"\n\n\n\n  MaterialEntity : alternative_identifiers\n\n  MaterialEntity : description\n\n  MaterialEntity : id\n\n  MaterialEntity : name\n\n  MaterialEntity : type\n\n\n\n
"},{"location":"MaterialEntity/#inheritance","title":"Inheritance","text":""},{"location":"MaterialEntity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MaterialEntity/#aliases","title":"Aliases","text":""},{"location":"MaterialEntity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MaterialEntity/#schema-source","title":"Schema Source","text":""},{"location":"MaterialEntity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MaterialEntity native nmdc:MaterialEntity"},{"location":"MaterialEntity/#linkml-source","title":"LinkML Source","text":""},{"location":"MaterialEntity/#direct","title":"Direct","text":"
name: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nclass_uri: nmdc:MaterialEntity\n\n
"},{"location":"MaterialEntity/#induced","title":"Induced","text":"
name: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MaterialEntity\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MaterialEntity\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MaterialEntity\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MaterialEntity\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MaterialEntity\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MaterialEntity\n\n
"},{"location":"MaterialProcessing/","title":"Class: MaterialProcessing","text":"

A process that takes one or more samples as inputs and generates one or more samples as outputs.

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:MaterialProcessing

classDiagram\n  class MaterialProcessing\n  click MaterialProcessing href \"../MaterialProcessing\"\n    PlannedProcess <|-- MaterialProcessing\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n    MaterialProcessing <|-- Pooling\n      click Pooling href \"../Pooling\"\n    MaterialProcessing <|-- Extraction\n      click Extraction href \"../Extraction\"\n    MaterialProcessing <|-- LibraryPreparation\n      click LibraryPreparation href \"../LibraryPreparation\"\n    MaterialProcessing <|-- SubSamplingProcess\n      click SubSamplingProcess href \"../SubSamplingProcess\"\n    MaterialProcessing <|-- MixingProcess\n      click MixingProcess href \"../MixingProcess\"\n    MaterialProcessing <|-- FiltrationProcess\n      click FiltrationProcess href \"../FiltrationProcess\"\n    MaterialProcessing <|-- ChromatographicSeparationProcess\n      click ChromatographicSeparationProcess href \"../ChromatographicSeparationProcess\"\n    MaterialProcessing <|-- DissolvingProcess\n      click DissolvingProcess href \"../DissolvingProcess\"\n    MaterialProcessing <|-- ChemicalConversionProcess\n      click ChemicalConversionProcess href \"../ChemicalConversionProcess\"\n\n\n\n  MaterialProcessing : alternative_identifiers\n\n  MaterialProcessing : description\n\n  MaterialProcessing : end_date\n\n  MaterialProcessing : has_failure_categorization\n\n      MaterialProcessing --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MaterialProcessing : has_input\n\n      MaterialProcessing --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MaterialProcessing : has_output\n\n      MaterialProcessing --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  MaterialProcessing : id\n\n  MaterialProcessing : instrument_used\n\n      MaterialProcessing --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  MaterialProcessing : name\n\n  MaterialProcessing : processing_institution\n\n      MaterialProcessing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MaterialProcessing : protocol_link\n\n      MaterialProcessing --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MaterialProcessing : qc_comment\n\n  MaterialProcessing : qc_status\n\n      MaterialProcessing --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MaterialProcessing : start_date\n\n  MaterialProcessing : type\n\n\n\n
"},{"location":"MaterialProcessing/#inheritance","title":"Inheritance","text":""},{"location":"MaterialProcessing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing direct has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MaterialProcessing/#usages","title":"Usages","text":"used by used in type used Database material_processing_set range MaterialProcessing"},{"location":"MaterialProcessing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MaterialProcessing/#schema-source","title":"Schema Source","text":""},{"location":"MaterialProcessing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MaterialProcessing native nmdc:MaterialProcessing broad OBI:0000094"},{"location":"MaterialProcessing/#linkml-source","title":"LinkML Source","text":""},{"location":"MaterialProcessing/#direct","title":"Direct","text":"
name: MaterialProcessing\ndescription: A process that takes one or more samples as inputs and generates one\n  or more samples as outputs.\nnotes:\n- This class is a replacement for BiosampleProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nabstract: true\nslots:\n- instrument_used\nslot_usage:\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MaterialProcessing\n\n
"},{"location":"MaterialProcessing/#induced","title":"Induced","text":"
name: MaterialProcessing\ndescription: A process that takes one or more samples as inputs and generates one\n  or more samples as outputs.\nnotes:\n- This class is a replacement for BiosampleProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: MaterialProcessing\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MaterialProcessing\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MaterialProcessing\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MaterialProcessing\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MaterialProcessing\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MaterialProcessing\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MaterialProcessing\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MaterialProcessing\n\n
"},{"location":"MechStrucEnum/","title":"Enum: MechStrucEnum","text":"

URI: MechStrucEnum

"},{"location":"MechStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description subway None coach None carriage None elevator None escalator None boat None train None car None bus None"},{"location":"MechStrucEnum/#slots","title":"Slots","text":"Name Description mech_struc mechanical structure: a moving structure"},{"location":"MechStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MechStrucEnum/#schema-source","title":"Schema Source","text":""},{"location":"MechStrucEnum/#linkml-source","title":"LinkML Source","text":"
name: mech_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  subway:\n    text: subway\n  coach:\n    text: coach\n  carriage:\n    text: carriage\n  elevator:\n    text: elevator\n  escalator:\n    text: escalator\n  boat:\n    text: boat\n  train:\n    text: train\n  car:\n    text: car\n  bus:\n    text: bus\n\n
"},{"location":"MetaboliteIdentification/","title":"Class: MetaboliteIdentification","text":"

This is used to link a metabolomics analysis workflow to a specific metabolite

URI: nmdc:MetaboliteIdentification

classDiagram\n  class MetaboliteIdentification\n  click MetaboliteIdentification href \"../MetaboliteIdentification\"\n\n  MetaboliteIdentification : alternative_identifiers\n\n  MetaboliteIdentification : highest_similarity_score\n\n  MetaboliteIdentification : metabolite_identified\n\n      MetaboliteIdentification --> \"0..1\" ChemicalEntity : metabolite_identified\n    click ChemicalEntity href \"../ChemicalEntity\"\n\n  MetaboliteIdentification : type\n\n\n\n
"},{"location":"MetaboliteIdentification/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity direct highest_similarity_score 0..1 Float direct metabolite_identified 0..1 ChemicalEntity the specific metabolite identifier direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"MetaboliteIdentification/#usages","title":"Usages","text":"used by used in type used MetabolomicsAnalysis has_metabolite_identifications range MetaboliteIdentification"},{"location":"MetaboliteIdentification/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetaboliteIdentification/#schema-source","title":"Schema Source","text":""},{"location":"MetaboliteIdentification/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetaboliteIdentification native nmdc:MetaboliteIdentification"},{"location":"MetaboliteIdentification/#linkml-source","title":"LinkML Source","text":""},{"location":"MetaboliteIdentification/#direct","title":"Direct","text":"
name: MetaboliteIdentification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- alternative_identifiers\n- highest_similarity_score\n- metabolite_identified\n- type\nclass_uri: nmdc:MetaboliteIdentification\n\n
"},{"location":"MetaboliteIdentification/#induced","title":"Induced","text":"
name: MetaboliteIdentification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetaboliteIdentification\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  highest_similarity_score:\n    name: highest_similarity_score\n    todos:\n    - Yuri to fill in description\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: highest_similarity_score\n    owner: MetaboliteIdentification\n    domain_of:\n    - MetaboliteIdentification\n    range: float\n  metabolite_identified:\n    name: metabolite_identified\n    description: the specific metabolite identifier\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: metabolite_identified\n    owner: MetaboliteIdentification\n    domain_of:\n    - MetaboliteIdentification\n    range: ChemicalEntity\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetaboliteIdentification\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetaboliteIdentification\n\n
"},{"location":"MetabolomicsAnalysis/","title":"Class: MetabolomicsAnalysis","text":"

URI: nmdc:MetabolomicsAnalysis

classDiagram\n  class MetabolomicsAnalysis\n  click MetabolomicsAnalysis href \"../MetabolomicsAnalysis\"\n    WorkflowExecution <|-- MetabolomicsAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetabolomicsAnalysis : alternative_identifiers\n\n  MetabolomicsAnalysis : description\n\n  MetabolomicsAnalysis : end_date\n\n  MetabolomicsAnalysis : ended_at_time\n\n  MetabolomicsAnalysis : execution_resource\n\n      MetabolomicsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetabolomicsAnalysis : git_url\n\n  MetabolomicsAnalysis : has_calibration\n\n  MetabolomicsAnalysis : has_failure_categorization\n\n      MetabolomicsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetabolomicsAnalysis : has_input\n\n      MetabolomicsAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetabolomicsAnalysis : has_metabolite_identifications\n\n      MetabolomicsAnalysis --> \"*\" MetaboliteIdentification : has_metabolite_identifications\n    click MetaboliteIdentification href \"../MetaboliteIdentification\"\n\n  MetabolomicsAnalysis : has_output\n\n      MetabolomicsAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetabolomicsAnalysis : id\n\n  MetabolomicsAnalysis : name\n\n  MetabolomicsAnalysis : processing_institution\n\n      MetabolomicsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetabolomicsAnalysis : protocol_link\n\n      MetabolomicsAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetabolomicsAnalysis : qc_comment\n\n  MetabolomicsAnalysis : qc_status\n\n      MetabolomicsAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetabolomicsAnalysis : start_date\n\n  MetabolomicsAnalysis : started_at_time\n\n  MetabolomicsAnalysis : type\n\n  MetabolomicsAnalysis : version\n\n  MetabolomicsAnalysis : was_informed_by\n\n      MetabolomicsAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetabolomicsAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"MetabolomicsAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_calibration 0..1 String\u00a0or\u00a0CalibrationInformation\u00a0or\u00a0String a calibration instance associated with a process direct has_metabolite_identifications * MetaboliteIdentification direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetabolomicsAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetabolomicsAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"MetabolomicsAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetabolomicsAnalysis native nmdc:MetabolomicsAnalysis"},{"location":"MetabolomicsAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"MetabolomicsAnalysis/#direct","title":"Direct","text":"
name: MetabolomicsAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- has_calibration\n- has_metabolite_identifications\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetabolomicsAnalysis\n\n
"},{"location":"MetabolomicsAnalysis/#induced","title":"Induced","text":"
name: MetabolomicsAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_calibration:\n    name: has_calibration\n    description: a calibration instance associated with a process\n    notes:\n    - 'has_calibration slot will be removed from all WorkflowExecution classes but\n      remain on the MassSpectrometry class after an ingest of the appropriate set\n      has occurred.  Once this has occurred, this slot''s range can be updated to\n      CalibrationInformation and class/slot definitions can move to nmdc.yaml.   See\n      PR #29 in Berkeley schema.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_calibration\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - MassSpectrometry\n    - MetabolomicsAnalysis\n    - NomAnalysis\n    range: string\n    any_of:\n    - range: CalibrationInformation\n    - range: string\n  has_metabolite_identifications:\n    name: has_metabolite_identifications\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_metabolite_identifications\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - MetabolomicsAnalysis\n    range: MetaboliteIdentification\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetabolomicsAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetabolomicsAnalysis\n\n
"},{"location":"Metadata_Documentation_Overview/","title":"The NMDC Metadata Standards Documentation","text":""},{"location":"Metadata_Documentation_Overview/#introduction","title":"Introduction","text":"

This documentation provides details on the National Microbiome Data Collaborative\u2019s (NMDC) approach to sample and data processing metadata. These are key features that drive the data search and discovery aspect of the NMDC data portal (https://microbiomedata.org/data/). If you are unfamiliar with these types of metadata (Figure 1), we recommend you begin with an Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask) (https://doi.org/10.25979/1607365).

Figure 1: Microbiome metadata types: Information that contextualizes sample including its geographic location and collection date, sample preparation, data processing methods, and data products produced from a biological sample (Luke et al., 2020. Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask). DOI: 10.25979/1607365).

All data integrated into the NMDC data portal must adhere to existing metadata standards for proper indexing and display, and to ensure accurate search results are returned. This documentation outlines the standards and ontologies that were included in the NMDC data schema, a framework that defines how data were defined and linked. For the 2019-2022 pilot initiative, the NMDC Metadata Standards Team (see the NMDC Team page) leveraged existing community-driven standards developed by the Genomics Standards Consortium (GSC), the Joint Genome Institute (JGI) Genomes Online Database (GOLD), and OBO Foundry\u2019s Environmental Ontology (EnvO). In collaboration with these organizations, the NMDC has created a framework for mapping these standards into an interoperable framework that can be expanded to include additional standards and ontologies in the future.

Additional information on the activities by the NMDC Metadata Standards team can be found on the NMDC website at: https://microbiomedata.org/metadata/

"},{"location":"Metadata_Documentation_Overview/#standards-and-ontologies-used-by-the-nmdc","title":"Standards and Ontologies used by the NMDC","text":""},{"location":"Metadata_Documentation_Overview/#sample-metadata","title":"Sample Metadata","text":""},{"location":"Metadata_Documentation_Overview/#gsc-minimum-information-about-any-x-sequence-mixs","title":"GSC Minimum Information about any (x) Sequence (MIxS)","text":"

The GSC has developed standards for describing genomic and metagenomic sequences, including the \u201cminimum information about a genome sequence\u201d (MIGS), the \u201cminimum information about a metagenome sequence\u201d (MIMS), and the \u201cminimum information about a marker gene sequence\u201d (MIMARKS). To complement this community-driven standard effort, the GSC has also developed a system for describing the environment from which a biological sample originates, as \u201cenvironmental packages\u201d and established a unified standard set of checklists through the minimum information about any (x) sequence (MIxS). MIxS provides a standardized data dictionary of sample descriptors (e.g., location, environment, elevation, altitude, depth, etc.) organized into different packages for 17 different sample environments.

To standardize how physical samples are described (i.e., sample metadata, Figure 1), the NMDC schema includes environmental descriptors from the GSC MIxS standards.

Explore how to create a MIxS-compliant sample metadata spreadsheet

"},{"location":"Metadata_Documentation_Overview/#genomes-online-database-gold","title":"Genomes Online Database (GOLD)","text":"

The JGI Genomes OnLine Database (GOLD, Mukherjee 2021) is an open-access repository of genome, metagenome, and metatranscriptome sequencing projects with their associated metadata. GOLD data are organized based on Study, Biosample/Organism, Sequencing Project and Analysis Project (Mukherjee 2017). Biosamples (defined as the physical material collected from an environment) are described using a five-level ecosystem classification path (Figure 2); the NMDC schema also uses this ecosystem classification to describe sample environments.

Figure 2. The GOLD five-level ecosystem classification paths (Mukherjee 2019).

Overview of the GOLD ecosystem paths

Explore how to map sample environments using the GOLD ecosystem classification

"},{"location":"Metadata_Documentation_Overview/#environmental-ontology-envo","title":"Environmental Ontology (EnvO)","text":"

The Environment Ontology (EnvO, Buttigieg 2016) is a community-led ontology that represents environmental entities such as biomes, environmental features, and environmental materials. Each EnvO term is identified using a unique resource identifier (e.g., CURIE or IRI) that resolves in a web browser. This ensures that EnvO\u2019s terms (and their definitions) are easy to find, reference, and share amongst collaborators. It also ensures that datasets described using EnvO terms can be more easily integrated and analyzed in a reproducible manner. And since the meanings of the terms are precisely defined and accessible, humans and computers can easily connect EnvO terms across datasets.

EnvO terms are the recommended values for several of the mandatory terms in the MIxS packages, often referred to as the \"MIxS triad\u201d.

Explore how to map sample environments using the EnvO ecosystem classification

Review a step-by-step example of how to assign EnvO terms to an oligotrophic lake sediment sample below.

env_broad_scale (Biome)

Using EnvO biome categories, aquatic is appropriate. However, since the EnvO is a hierarchical system, the aquatic biome has two sub-categories: freshwater and marine biomes. The freshwater biome is further divided into freshwater lake biome and freshwater river biome. Therefore, for a lake sediment sample, freshwater lake biome is the appropriate EnvO biome category.

env_local_scale (Feature)

Next, we describe the local environmental feature in the vicinity of and likely having a strong causal influence on the sample. Using the EnvO astronomical body part categories, we step through the relevant categories (see figure on the right) until we reach the EnvO term oligotrophic lake.

env_medium (Material)

Finally, since the sample is oligotrophic lake sediment, the EnvO environmental material could be assigned sediment. But because the EnvO hierarchy provides sub-categories within sediment, the environmenta material will be assigned lake sediment.

Therefore, the EnvO triad for oligotrophic lake sediment is:

Env_broad_scale: freshwater lake biome [ENVO_01000252]

Env_local_scale: oligotrophic lake [ENVO_01000774]

Env_medium: lake sediment [ENVO_00000546]

"},{"location":"Metadata_Documentation_Overview/#classifying-samples-with-gold-and-mixsenvo","title":"Classifying samples with GOLD and MIxS/EnvO","text":"

The five-level GOLD ecosystem classification path and EnvO triad each have unique advantages in describing the environmental context of a biosample. The NMDC leverages the strengths of both the GOLD ecosystem classification path and MIxS/EnvO triad. The assignment of MIxS/EnvO triad for the biosamples currently in the NMDC data portal was achieved through a manual curation process using various metadata fields of GOLD biosamples fields, such as name, description, habitat, sample collection site, identifier, ecosystem classification path, and study description. The NMDC team is currently working on exploring solutions for automated mapping between GOLD and MIxS/EnvO.

Figure 3: Mapping between the MIxS/EnvO triad and the GOLD ecosystem classification enables integration of sample environments defined with GOLD and MIxS/EnvO.

"},{"location":"Metadata_Documentation_Overview/#data-processing-metadata","title":"Data Processing Metadata","text":"

In addition, the NMDC is adopting the MIxS standards for sequence data types (e.g., sequencing method, pcr primers and conditions, etc.), and are building on previous efforts by the Proteomics Standards Initiative and Metabolomics Standards Initiative to develop standards and controlled vocabularies for mass spectrometry data types (e.g., ionization mode, mass resolution, scan rate, etc.). Additional details on the processing metadata are coming soon.

"},{"location":"Metadata_Documentation_Overview/#overview-of-the-nmdc-data-schema","title":"Overview of the NMDC Data Schema","text":"

The NMDC has developed a normalized metadata schema (available in the NMDC GitHub) for representing studies, samples, relationships between samples, and associated data objects. The schema is organized into object classes, which act as nodes. Each class has associated slots, which are fields that contain metadata that describe the object. For more in-depth information, full documentation of the NMDC schema can be found here.

For the NMDC pilot, a python toolkit for generating NMDC-compliant JavaScript Object Notation (JSON) objects was developed to create ETL (Extract-Transform-Load) software to ingest metadata from the DOE User Facilities. Read more about the data in the NMDC pilot here.

"},{"location":"MetagenomeAnnotation/","title":"Class: MetagenomeAnnotation","text":"

A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs

URI: nmdc:MetagenomeAnnotation

classDiagram\n  class MetagenomeAnnotation\n  click MetagenomeAnnotation href \"../MetagenomeAnnotation\"\n    WorkflowExecution <|-- MetagenomeAnnotation\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetagenomeAnnotation : alternative_identifiers\n\n  MetagenomeAnnotation : description\n\n  MetagenomeAnnotation : end_date\n\n  MetagenomeAnnotation : ended_at_time\n\n  MetagenomeAnnotation : execution_resource\n\n      MetagenomeAnnotation --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetagenomeAnnotation : git_url\n\n  MetagenomeAnnotation : gold_analysis_project_identifiers\n\n  MetagenomeAnnotation : has_failure_categorization\n\n      MetagenomeAnnotation --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetagenomeAnnotation : has_input\n\n      MetagenomeAnnotation --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeAnnotation : has_output\n\n      MetagenomeAnnotation --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeAnnotation : id\n\n  MetagenomeAnnotation : img_identifiers\n\n  MetagenomeAnnotation : name\n\n  MetagenomeAnnotation : processing_institution\n\n      MetagenomeAnnotation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetagenomeAnnotation : protocol_link\n\n      MetagenomeAnnotation --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetagenomeAnnotation : qc_comment\n\n  MetagenomeAnnotation : qc_status\n\n      MetagenomeAnnotation --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetagenomeAnnotation : start_date\n\n  MetagenomeAnnotation : started_at_time\n\n  MetagenomeAnnotation : type\n\n  MetagenomeAnnotation : version\n\n  MetagenomeAnnotation : was_informed_by\n\n      MetagenomeAnnotation --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetagenomeAnnotation/#inheritance","title":"Inheritance","text":""},{"location":"MetagenomeAnnotation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct gold_analysis_project_identifiers * ExternalIdentifier identifiers for corresponding analysis projects in GOLD direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetagenomeAnnotation/#usages","title":"Usages","text":"used by used in type used FunctionalAnnotationAggMember metagenome_annotation_id any_of[range] MetagenomeAnnotation FunctionalAnnotation was_generated_by range MetagenomeAnnotation"},{"location":"MetagenomeAnnotation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetagenomeAnnotation/#schema-source","title":"Schema Source","text":""},{"location":"MetagenomeAnnotation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetagenomeAnnotation native nmdc:MetagenomeAnnotation"},{"location":"MetagenomeAnnotation/#linkml-source","title":"LinkML Source","text":""},{"location":"MetagenomeAnnotation/#direct","title":"Direct","text":"
name: MetagenomeAnnotation\ndescription: A workflow execution activity that provides functional and structural\n  annotation of assembled metagenome contigs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\n- gold_analysis_project_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\nclass_uri: nmdc:MetagenomeAnnotation\n\n
"},{"location":"MetagenomeAnnotation/#induced","title":"Induced","text":"
name: MetagenomeAnnotation\ndescription: A workflow execution activity that provides functional and structural\n  annotation of assembled metagenome contigs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\nattributes:\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: MetagenomeAnnotation\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n    maximum_cardinality: 1\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    description: identifiers for corresponding analysis projects in GOLD\n    examples:\n    - value: https://bioregistry.io/gold:Ga0526289\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: analysis_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_analysis_project_identifiers\n    owner: MetagenomeAnnotation\n    domain_of:\n    - MetagenomeAnnotation\n    - MetatranscriptomeAnnotation\n    range: external_identifier\n    multivalued: true\n    pattern: ^gold:Ga[0-9]+$\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetagenomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetagenomeAnnotation\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetagenomeAnnotation\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetagenomeAnnotation\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetagenomeAnnotation\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetagenomeAnnotation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetagenomeAnnotation\n\n
"},{"location":"MetagenomeAssembly/","title":"Class: MetagenomeAssembly","text":"

A workflow execution activity that converts sequencing reads into an assembled metagenome.

URI: nmdc:MetagenomeAssembly

classDiagram\n  class MetagenomeAssembly\n  click MetagenomeAssembly href \"../MetagenomeAssembly\"\n    WorkflowExecution <|-- MetagenomeAssembly\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetagenomeAssembly : alternative_identifiers\n\n  MetagenomeAssembly : asm_score\n\n  MetagenomeAssembly : contig_bp\n\n  MetagenomeAssembly : contigs\n\n  MetagenomeAssembly : ctg_l50\n\n  MetagenomeAssembly : ctg_l90\n\n  MetagenomeAssembly : ctg_logsum\n\n  MetagenomeAssembly : ctg_max\n\n  MetagenomeAssembly : ctg_n50\n\n  MetagenomeAssembly : ctg_n90\n\n  MetagenomeAssembly : ctg_powsum\n\n  MetagenomeAssembly : description\n\n  MetagenomeAssembly : end_date\n\n  MetagenomeAssembly : ended_at_time\n\n  MetagenomeAssembly : execution_resource\n\n      MetagenomeAssembly --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetagenomeAssembly : gap_pct\n\n  MetagenomeAssembly : gc_avg\n\n  MetagenomeAssembly : gc_std\n\n  MetagenomeAssembly : git_url\n\n  MetagenomeAssembly : has_failure_categorization\n\n      MetagenomeAssembly --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetagenomeAssembly : has_input\n\n      MetagenomeAssembly --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeAssembly : has_output\n\n      MetagenomeAssembly --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeAssembly : id\n\n  MetagenomeAssembly : insdc_assembly_identifiers\n\n  MetagenomeAssembly : name\n\n  MetagenomeAssembly : num_aligned_reads\n\n  MetagenomeAssembly : num_input_reads\n\n  MetagenomeAssembly : processing_institution\n\n      MetagenomeAssembly --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetagenomeAssembly : protocol_link\n\n      MetagenomeAssembly --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetagenomeAssembly : qc_comment\n\n  MetagenomeAssembly : qc_status\n\n      MetagenomeAssembly --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetagenomeAssembly : scaf_bp\n\n  MetagenomeAssembly : scaf_l50\n\n  MetagenomeAssembly : scaf_l90\n\n  MetagenomeAssembly : scaf_l_gt50k\n\n  MetagenomeAssembly : scaf_logsum\n\n  MetagenomeAssembly : scaf_max\n\n  MetagenomeAssembly : scaf_n50\n\n  MetagenomeAssembly : scaf_n90\n\n  MetagenomeAssembly : scaf_n_gt50k\n\n  MetagenomeAssembly : scaf_pct_gt50k\n\n  MetagenomeAssembly : scaf_powsum\n\n  MetagenomeAssembly : scaffolds\n\n  MetagenomeAssembly : start_date\n\n  MetagenomeAssembly : started_at_time\n\n  MetagenomeAssembly : type\n\n  MetagenomeAssembly : version\n\n  MetagenomeAssembly : was_informed_by\n\n      MetagenomeAssembly --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetagenomeAssembly/#inheritance","title":"Inheritance","text":""},{"location":"MetagenomeAssembly/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance asm_score 0..1 Float A score for comparing metagenomic assembly quality from same sample direct scaffolds 0..1 Float Total sequence count of all scaffolds direct scaf_logsum 0..1 Float The sum of the (length*log(length)) of all scaffolds, times some constant direct scaf_powsum 0..1 Float Powersum of all scaffolds is the same as logsum except that it uses the sum o... direct scaf_max 0..1 Float Maximum scaffold length direct scaf_bp 0..1 Float Total size in bp of all scaffolds direct scaf_n50 0..1 Float Given a set of scaffolds, each with its own length, the N50 count is defined ... direct scaf_n90 0..1 Float Given a set of scaffolds, each with its own length, the N90 count is defined ... direct scaf_l50 0..1 Float Given a set of scaffolds, the L50 is defined as the sequence length of the sh... direct scaf_l90 0..1 Float The L90 statistic is less than or equal to the L50 statistic; it is the lengt... direct scaf_n_gt50k 0..1 Float Total sequence count of scaffolds greater than 50 KB direct scaf_l_gt50k 0..1 Float Total size in bp of all scaffolds greater than 50 KB direct scaf_pct_gt50k 0..1 Float Total sequence size percentage of scaffolds greater than 50 KB direct contigs 0..1 Float The sum of the (length*log(length)) of all contigs, times some constant direct contig_bp 0..1 Float Total size in bp of all contigs direct ctg_n50 0..1 Float Given a set of contigs, each with its own length, the N50 count is defined as... direct ctg_l50 0..1 Float Given a set of contigs, the L50 is defined as the sequence length of the shor... direct ctg_n90 0..1 Float Given a set of contigs, each with its own length, the N90 count is defined as... direct ctg_l90 0..1 Float The L90 statistic is less than or equal to the L50 statistic; it is the lengt... direct ctg_logsum 0..1 Float Maximum contig length direct ctg_powsum 0..1 Float Powersum of all contigs is the same as logsum except that it uses the sum of ... direct ctg_max 0..1 Float Maximum contig length direct gap_pct 0..1 Float The gap size percentage of all scaffolds direct gc_std 0..1 Float Standard deviation of GC content of all contigs direct gc_avg 0..1 Float Average of GC content of all contigs direct num_input_reads 0..1 Float The sequence count number of input reads for assembly direct num_aligned_reads 0..1 Float The sequence count number of input reads aligned to assembled contigs direct insdc_assembly_identifiers 0..1 String direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetagenomeAssembly/#comments","title":"Comments","text":""},{"location":"MetagenomeAssembly/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetagenomeAssembly/#schema-source","title":"Schema Source","text":""},{"location":"MetagenomeAssembly/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetagenomeAssembly native nmdc:MetagenomeAssembly"},{"location":"MetagenomeAssembly/#linkml-source","title":"LinkML Source","text":""},{"location":"MetagenomeAssembly/#direct","title":"Direct","text":"
name: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n  assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n  relevant to NMDC\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetagenomeAssembly\n\n
"},{"location":"MetagenomeAssembly/#induced","title":"Induced","text":"
name: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n  assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n  relevant to NMDC\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  asm_score:\n    name: asm_score\n    description: A score for comparing metagenomic assembly quality from same sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: asm_score\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaffolds:\n    name: scaffolds\n    description: Total sequence count of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaffolds\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_logsum:\n    name: scaf_logsum\n    description: The sum of the (length*log(length)) of all scaffolds, times some\n      constant.  Increase the contiguity, the score will increase\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_logsum\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_powsum:\n    name: scaf_powsum\n    description: Powersum of all scaffolds is the same as logsum except that it uses\n      the sum of (length*(length^P)) for some power P (default P=0.25).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_powsum\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_max:\n    name: scaf_max\n    description: Maximum scaffold length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_max\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_bp:\n    name: scaf_bp\n    description: Total size in bp of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_bp\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n50:\n    name: scaf_n50\n    description: Given a set of scaffolds, each with its own length, the N50 count\n      is defined as the smallest number of scaffolds whose length sum makes up half\n      of genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n50\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n90:\n    name: scaf_n90\n    description: Given a set of scaffolds, each with its own length, the N90 count\n      is defined as the smallest number of scaffolds whose length sum makes up 90%\n      of genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n90\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l50:\n    name: scaf_l50\n    description: Given a set of scaffolds, the L50 is defined as the sequence length\n      of the shortest scaffold at 50% of the total genome length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l50\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l90:\n    name: scaf_l90\n    description: The L90 statistic is less than or equal to the L50 statistic; it\n      is the length for which the collection of all scaffolds of that length or longer\n      contains at least 90% of the sum of the lengths of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l90\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n_gt50k:\n    name: scaf_n_gt50k\n    description: Total sequence count of scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n_gt50k\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l_gt50k:\n    name: scaf_l_gt50k\n    description: Total size in bp of all scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l_gt50k\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_pct_gt50k:\n    name: scaf_pct_gt50k\n    description: Total sequence size percentage of scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_pct_gt50k\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  contigs:\n    name: contigs\n    description: The sum of the (length*log(length)) of all contigs, times some constant.  Increase\n      the contiguity, the score will increase\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: contigs\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  contig_bp:\n    name: contig_bp\n    description: Total size in bp of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: contig_bp\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_n50:\n    name: ctg_n50\n    description: Given a set of contigs, each with its own length, the N50 count is\n      defined as the smallest number_of_contigs whose length sum makes up half of\n      genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_n50\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_l50:\n    name: ctg_l50\n    description: Given a set of contigs, the L50 is defined as the sequence length\n      of the shortest contig at 50% of the total genome length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_l50\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_n90:\n    name: ctg_n90\n    description: Given a set of contigs, each with its own length, the N90 count is\n      defined as the smallest number of contigs whose length sum makes up 90% of genome\n      size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_n90\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_l90:\n    name: ctg_l90\n    description: The L90 statistic is less than or equal to the L50 statistic; it\n      is the length for which the collection of all contigs of that length or longer\n      contains at least 90% of the sum of the lengths of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_l90\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_logsum:\n    name: ctg_logsum\n    description: Maximum contig length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_logsum\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_powsum:\n    name: ctg_powsum\n    description: Powersum of all contigs is the same as logsum except that it uses\n      the sum of (length*(length^P)) for some power P (default P=0.25).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_powsum\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_max:\n    name: ctg_max\n    description: Maximum contig length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_max\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gap_pct:\n    name: gap_pct\n    description: The gap size percentage of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gap_pct\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gc_std:\n    name: gc_std\n    description: Standard deviation of GC content of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gc_std\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gc_avg:\n    name: gc_avg\n    description: Average of GC content of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gc_avg\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  num_input_reads:\n    name: num_input_reads\n    description: The sequence count number of input reads for assembly.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: num_input_reads\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  num_aligned_reads:\n    name: num_aligned_reads\n    description: The sequence count number of input reads aligned to assembled contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: num_aligned_reads\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  insdc_assembly_identifiers:\n    name: insdc_assembly_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: assembly_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_assembly_identifiers\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: string\n    pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetagenomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetagenomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetagenomeAssembly\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetagenomeAssembly\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetagenomeAssembly\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetagenomeAssembly\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetagenomeAssembly\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetagenomeAssembly\n\n
"},{"location":"MetagenomeSequencing/","title":"Class: Metagenome sequencing activity (MetagenomeSequencing)","text":"

Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.

URI: nmdc:MetagenomeSequencing

classDiagram\n  class MetagenomeSequencing\n  click MetagenomeSequencing href \"../MetagenomeSequencing\"\n    WorkflowExecution <|-- MetagenomeSequencing\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetagenomeSequencing : alternative_identifiers\n\n  MetagenomeSequencing : description\n\n  MetagenomeSequencing : end_date\n\n  MetagenomeSequencing : ended_at_time\n\n  MetagenomeSequencing : execution_resource\n\n      MetagenomeSequencing --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetagenomeSequencing : git_url\n\n  MetagenomeSequencing : has_failure_categorization\n\n      MetagenomeSequencing --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetagenomeSequencing : has_input\n\n      MetagenomeSequencing --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeSequencing : has_output\n\n      MetagenomeSequencing --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetagenomeSequencing : id\n\n  MetagenomeSequencing : name\n\n  MetagenomeSequencing : processing_institution\n\n      MetagenomeSequencing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetagenomeSequencing : protocol_link\n\n      MetagenomeSequencing --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetagenomeSequencing : qc_comment\n\n  MetagenomeSequencing : qc_status\n\n      MetagenomeSequencing --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetagenomeSequencing : start_date\n\n  MetagenomeSequencing : started_at_time\n\n  MetagenomeSequencing : type\n\n  MetagenomeSequencing : version\n\n  MetagenomeSequencing : was_informed_by\n\n      MetagenomeSequencing --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetagenomeSequencing/#inheritance","title":"Inheritance","text":""},{"location":"MetagenomeSequencing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetagenomeSequencing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetagenomeSequencing/#schema-source","title":"Schema Source","text":""},{"location":"MetagenomeSequencing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetagenomeSequencing native nmdc:MetagenomeSequencing"},{"location":"MetagenomeSequencing/#linkml-source","title":"LinkML Source","text":""},{"location":"MetagenomeSequencing/#direct","title":"Direct","text":"
name: MetagenomeSequencing\ndescription: Initial sequencing activity that precedes any analysis.  This activity\n  has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetagenomeSequencing\n\n
"},{"location":"MetagenomeSequencing/#induced","title":"Induced","text":"
name: MetagenomeSequencing\ndescription: Initial sequencing activity that precedes any analysis.  This activity\n  has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetagenomeSequencing\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetagenomeSequencing\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetagenomeSequencing\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetagenomeSequencing\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetagenomeSequencing\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetagenomeSequencing\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetagenomeSequencing\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetagenomeSequencing\n\n
"},{"location":"MetaproteomicsAnalysis/","title":"Class: MetaproteomicsAnalysis","text":"

URI: nmdc:MetaproteomicsAnalysis

classDiagram\n  class MetaproteomicsAnalysis\n  click MetaproteomicsAnalysis href \"../MetaproteomicsAnalysis\"\n    WorkflowExecution <|-- MetaproteomicsAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetaproteomicsAnalysis : alternative_identifiers\n\n  MetaproteomicsAnalysis : description\n\n  MetaproteomicsAnalysis : end_date\n\n  MetaproteomicsAnalysis : ended_at_time\n\n  MetaproteomicsAnalysis : execution_resource\n\n      MetaproteomicsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetaproteomicsAnalysis : git_url\n\n  MetaproteomicsAnalysis : has_failure_categorization\n\n      MetaproteomicsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetaproteomicsAnalysis : has_input\n\n      MetaproteomicsAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetaproteomicsAnalysis : has_output\n\n      MetaproteomicsAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetaproteomicsAnalysis : has_peptide_quantifications\n\n      MetaproteomicsAnalysis --> \"*\" PeptideQuantification : has_peptide_quantifications\n    click PeptideQuantification href \"../PeptideQuantification\"\n\n  MetaproteomicsAnalysis : id\n\n  MetaproteomicsAnalysis : name\n\n  MetaproteomicsAnalysis : processing_institution\n\n      MetaproteomicsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetaproteomicsAnalysis : protocol_link\n\n      MetaproteomicsAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetaproteomicsAnalysis : qc_comment\n\n  MetaproteomicsAnalysis : qc_status\n\n      MetaproteomicsAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetaproteomicsAnalysis : start_date\n\n  MetaproteomicsAnalysis : started_at_time\n\n  MetaproteomicsAnalysis : type\n\n  MetaproteomicsAnalysis : version\n\n  MetaproteomicsAnalysis : was_informed_by\n\n      MetaproteomicsAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetaproteomicsAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"MetaproteomicsAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_peptide_quantifications * PeptideQuantification direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetaproteomicsAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetaproteomicsAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"MetaproteomicsAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetaproteomicsAnalysis native nmdc:MetaproteomicsAnalysis"},{"location":"MetaproteomicsAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"MetaproteomicsAnalysis/#direct","title":"Direct","text":"
name: MetaproteomicsAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- has_peptide_quantifications\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetaproteomicsAnalysis\n\n
"},{"location":"MetaproteomicsAnalysis/#induced","title":"Induced","text":"
name: MetaproteomicsAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_peptide_quantifications:\n    name: has_peptide_quantifications\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_peptide_quantifications\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - MetaproteomicsAnalysis\n    range: PeptideQuantification\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetaproteomicsAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetaproteomicsAnalysis\n\n
"},{"location":"MetatranscriptomeAnnotation/","title":"Class: MetatranscriptomeAnnotation","text":"

URI: nmdc:MetatranscriptomeAnnotation

classDiagram\n  class MetatranscriptomeAnnotation\n  click MetatranscriptomeAnnotation href \"../MetatranscriptomeAnnotation\"\n    WorkflowExecution <|-- MetatranscriptomeAnnotation\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetatranscriptomeAnnotation : alternative_identifiers\n\n  MetatranscriptomeAnnotation : description\n\n  MetatranscriptomeAnnotation : end_date\n\n  MetatranscriptomeAnnotation : ended_at_time\n\n  MetatranscriptomeAnnotation : execution_resource\n\n      MetatranscriptomeAnnotation --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetatranscriptomeAnnotation : git_url\n\n  MetatranscriptomeAnnotation : gold_analysis_project_identifiers\n\n  MetatranscriptomeAnnotation : has_failure_categorization\n\n      MetatranscriptomeAnnotation --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetatranscriptomeAnnotation : has_input\n\n      MetatranscriptomeAnnotation --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeAnnotation : has_output\n\n      MetatranscriptomeAnnotation --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeAnnotation : id\n\n  MetatranscriptomeAnnotation : img_identifiers\n\n  MetatranscriptomeAnnotation : name\n\n  MetatranscriptomeAnnotation : processing_institution\n\n      MetatranscriptomeAnnotation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetatranscriptomeAnnotation : protocol_link\n\n      MetatranscriptomeAnnotation --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetatranscriptomeAnnotation : qc_comment\n\n  MetatranscriptomeAnnotation : qc_status\n\n      MetatranscriptomeAnnotation --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetatranscriptomeAnnotation : start_date\n\n  MetatranscriptomeAnnotation : started_at_time\n\n  MetatranscriptomeAnnotation : type\n\n  MetatranscriptomeAnnotation : version\n\n  MetatranscriptomeAnnotation : was_informed_by\n\n      MetatranscriptomeAnnotation --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetatranscriptomeAnnotation/#inheritance","title":"Inheritance","text":""},{"location":"MetatranscriptomeAnnotation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct gold_analysis_project_identifiers * ExternalIdentifier identifiers for corresponding analysis projects in GOLD direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetatranscriptomeAnnotation/#usages","title":"Usages","text":"used by used in type used FunctionalAnnotationAggMember metagenome_annotation_id any_of[range] MetatranscriptomeAnnotation"},{"location":"MetatranscriptomeAnnotation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetatranscriptomeAnnotation/#schema-source","title":"Schema Source","text":""},{"location":"MetatranscriptomeAnnotation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetatranscriptomeAnnotation native nmdc:MetatranscriptomeAnnotation"},{"location":"MetatranscriptomeAnnotation/#linkml-source","title":"LinkML Source","text":""},{"location":"MetatranscriptomeAnnotation/#direct","title":"Direct","text":"
name: MetatranscriptomeAnnotation\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\n- gold_analysis_project_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\nclass_uri: nmdc:MetatranscriptomeAnnotation\n\n
"},{"location":"MetatranscriptomeAnnotation/#induced","title":"Induced","text":"
name: MetatranscriptomeAnnotation\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\nattributes:\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n    maximum_cardinality: 1\n  gold_analysis_project_identifiers:\n    name: gold_analysis_project_identifiers\n    description: identifiers for corresponding analysis projects in GOLD\n    examples:\n    - value: https://bioregistry.io/gold:Ga0526289\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: analysis_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_analysis_project_identifiers\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - MetagenomeAnnotation\n    - MetatranscriptomeAnnotation\n    range: external_identifier\n    multivalued: true\n    pattern: ^gold:Ga[0-9]+$\n    structured_pattern:\n      syntax: ^gold:Ga[0-9]+$\n      interpolated: true\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetatranscriptomeAnnotation\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetatranscriptomeAnnotation\n\n
"},{"location":"MetatranscriptomeAssembly/","title":"Class: MetatranscriptomeAssembly","text":"

URI: nmdc:MetatranscriptomeAssembly

classDiagram\n  class MetatranscriptomeAssembly\n  click MetatranscriptomeAssembly href \"../MetatranscriptomeAssembly\"\n    WorkflowExecution <|-- MetatranscriptomeAssembly\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetatranscriptomeAssembly : alternative_identifiers\n\n  MetatranscriptomeAssembly : asm_score\n\n  MetatranscriptomeAssembly : contig_bp\n\n  MetatranscriptomeAssembly : contigs\n\n  MetatranscriptomeAssembly : ctg_l50\n\n  MetatranscriptomeAssembly : ctg_l90\n\n  MetatranscriptomeAssembly : ctg_logsum\n\n  MetatranscriptomeAssembly : ctg_max\n\n  MetatranscriptomeAssembly : ctg_n50\n\n  MetatranscriptomeAssembly : ctg_n90\n\n  MetatranscriptomeAssembly : ctg_powsum\n\n  MetatranscriptomeAssembly : description\n\n  MetatranscriptomeAssembly : end_date\n\n  MetatranscriptomeAssembly : ended_at_time\n\n  MetatranscriptomeAssembly : execution_resource\n\n      MetatranscriptomeAssembly --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetatranscriptomeAssembly : gap_pct\n\n  MetatranscriptomeAssembly : gc_avg\n\n  MetatranscriptomeAssembly : gc_std\n\n  MetatranscriptomeAssembly : git_url\n\n  MetatranscriptomeAssembly : has_failure_categorization\n\n      MetatranscriptomeAssembly --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetatranscriptomeAssembly : has_input\n\n      MetatranscriptomeAssembly --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeAssembly : has_output\n\n      MetatranscriptomeAssembly --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeAssembly : id\n\n  MetatranscriptomeAssembly : insdc_assembly_identifiers\n\n  MetatranscriptomeAssembly : name\n\n  MetatranscriptomeAssembly : num_aligned_reads\n\n  MetatranscriptomeAssembly : num_input_reads\n\n  MetatranscriptomeAssembly : processing_institution\n\n      MetatranscriptomeAssembly --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetatranscriptomeAssembly : protocol_link\n\n      MetatranscriptomeAssembly --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetatranscriptomeAssembly : qc_comment\n\n  MetatranscriptomeAssembly : qc_status\n\n      MetatranscriptomeAssembly --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetatranscriptomeAssembly : scaf_bp\n\n  MetatranscriptomeAssembly : scaf_l50\n\n  MetatranscriptomeAssembly : scaf_l90\n\n  MetatranscriptomeAssembly : scaf_l_gt50k\n\n  MetatranscriptomeAssembly : scaf_logsum\n\n  MetatranscriptomeAssembly : scaf_max\n\n  MetatranscriptomeAssembly : scaf_n50\n\n  MetatranscriptomeAssembly : scaf_n90\n\n  MetatranscriptomeAssembly : scaf_n_gt50k\n\n  MetatranscriptomeAssembly : scaf_pct_gt50k\n\n  MetatranscriptomeAssembly : scaf_powsum\n\n  MetatranscriptomeAssembly : scaffolds\n\n  MetatranscriptomeAssembly : start_date\n\n  MetatranscriptomeAssembly : started_at_time\n\n  MetatranscriptomeAssembly : type\n\n  MetatranscriptomeAssembly : version\n\n  MetatranscriptomeAssembly : was_informed_by\n\n      MetatranscriptomeAssembly --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetatranscriptomeAssembly/#inheritance","title":"Inheritance","text":""},{"location":"MetatranscriptomeAssembly/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance asm_score 0..1 Float A score for comparing metagenomic assembly quality from same sample direct scaffolds 0..1 Float Total sequence count of all scaffolds direct scaf_logsum 0..1 Float The sum of the (length*log(length)) of all scaffolds, times some constant direct scaf_powsum 0..1 Float Powersum of all scaffolds is the same as logsum except that it uses the sum o... direct scaf_max 0..1 Float Maximum scaffold length direct scaf_bp 0..1 Float Total size in bp of all scaffolds direct scaf_n50 0..1 Float Given a set of scaffolds, each with its own length, the N50 count is defined ... direct scaf_n90 0..1 Float Given a set of scaffolds, each with its own length, the N90 count is defined ... direct scaf_l50 0..1 Float Given a set of scaffolds, the L50 is defined as the sequence length of the sh... direct scaf_l90 0..1 Float The L90 statistic is less than or equal to the L50 statistic; it is the lengt... direct scaf_n_gt50k 0..1 Float Total sequence count of scaffolds greater than 50 KB direct scaf_l_gt50k 0..1 Float Total size in bp of all scaffolds greater than 50 KB direct scaf_pct_gt50k 0..1 Float Total sequence size percentage of scaffolds greater than 50 KB direct contigs 0..1 Float The sum of the (length*log(length)) of all contigs, times some constant direct contig_bp 0..1 Float Total size in bp of all contigs direct ctg_n50 0..1 Float Given a set of contigs, each with its own length, the N50 count is defined as... direct ctg_l50 0..1 Float Given a set of contigs, the L50 is defined as the sequence length of the shor... direct ctg_n90 0..1 Float Given a set of contigs, each with its own length, the N90 count is defined as... direct ctg_l90 0..1 Float The L90 statistic is less than or equal to the L50 statistic; it is the lengt... direct ctg_logsum 0..1 Float Maximum contig length direct ctg_powsum 0..1 Float Powersum of all contigs is the same as logsum except that it uses the sum of ... direct ctg_max 0..1 Float Maximum contig length direct gap_pct 0..1 Float The gap size percentage of all scaffolds direct gc_std 0..1 Float Standard deviation of GC content of all contigs direct gc_avg 0..1 Float Average of GC content of all contigs direct num_input_reads 0..1 Float The sequence count number of input reads for assembly direct num_aligned_reads 0..1 Float The sequence count number of input reads aligned to assembled contigs direct insdc_assembly_identifiers 0..1 String direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetatranscriptomeAssembly/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetatranscriptomeAssembly/#schema-source","title":"Schema Source","text":""},{"location":"MetatranscriptomeAssembly/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetatranscriptomeAssembly native nmdc:MetatranscriptomeAssembly"},{"location":"MetatranscriptomeAssembly/#linkml-source","title":"LinkML Source","text":""},{"location":"MetatranscriptomeAssembly/#direct","title":"Direct","text":"
name: MetatranscriptomeAssembly\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetatranscriptomeAssembly\n\n
"},{"location":"MetatranscriptomeAssembly/#induced","title":"Induced","text":"
name: MetatranscriptomeAssembly\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  asm_score:\n    name: asm_score\n    description: A score for comparing metagenomic assembly quality from same sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: asm_score\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaffolds:\n    name: scaffolds\n    description: Total sequence count of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaffolds\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_logsum:\n    name: scaf_logsum\n    description: The sum of the (length*log(length)) of all scaffolds, times some\n      constant.  Increase the contiguity, the score will increase\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_logsum\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_powsum:\n    name: scaf_powsum\n    description: Powersum of all scaffolds is the same as logsum except that it uses\n      the sum of (length*(length^P)) for some power P (default P=0.25).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_powsum\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_max:\n    name: scaf_max\n    description: Maximum scaffold length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_max\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_bp:\n    name: scaf_bp\n    description: Total size in bp of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_bp\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n50:\n    name: scaf_n50\n    description: Given a set of scaffolds, each with its own length, the N50 count\n      is defined as the smallest number of scaffolds whose length sum makes up half\n      of genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n50\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n90:\n    name: scaf_n90\n    description: Given a set of scaffolds, each with its own length, the N90 count\n      is defined as the smallest number of scaffolds whose length sum makes up 90%\n      of genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n90\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l50:\n    name: scaf_l50\n    description: Given a set of scaffolds, the L50 is defined as the sequence length\n      of the shortest scaffold at 50% of the total genome length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l50\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l90:\n    name: scaf_l90\n    description: The L90 statistic is less than or equal to the L50 statistic; it\n      is the length for which the collection of all scaffolds of that length or longer\n      contains at least 90% of the sum of the lengths of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l90\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_n_gt50k:\n    name: scaf_n_gt50k\n    description: Total sequence count of scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_n_gt50k\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_l_gt50k:\n    name: scaf_l_gt50k\n    description: Total size in bp of all scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_l_gt50k\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  scaf_pct_gt50k:\n    name: scaf_pct_gt50k\n    description: Total sequence size percentage of scaffolds greater than 50 KB.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: scaf_pct_gt50k\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  contigs:\n    name: contigs\n    description: The sum of the (length*log(length)) of all contigs, times some constant.  Increase\n      the contiguity, the score will increase\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: contigs\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  contig_bp:\n    name: contig_bp\n    description: Total size in bp of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: contig_bp\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_n50:\n    name: ctg_n50\n    description: Given a set of contigs, each with its own length, the N50 count is\n      defined as the smallest number_of_contigs whose length sum makes up half of\n      genome size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_n50\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_l50:\n    name: ctg_l50\n    description: Given a set of contigs, the L50 is defined as the sequence length\n      of the shortest contig at 50% of the total genome length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_l50\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_n90:\n    name: ctg_n90\n    description: Given a set of contigs, each with its own length, the N90 count is\n      defined as the smallest number of contigs whose length sum makes up 90% of genome\n      size.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_n90\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_l90:\n    name: ctg_l90\n    description: The L90 statistic is less than or equal to the L50 statistic; it\n      is the length for which the collection of all contigs of that length or longer\n      contains at least 90% of the sum of the lengths of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_l90\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_logsum:\n    name: ctg_logsum\n    description: Maximum contig length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_logsum\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_powsum:\n    name: ctg_powsum\n    description: Powersum of all contigs is the same as logsum except that it uses\n      the sum of (length*(length^P)) for some power P (default P=0.25).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_powsum\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  ctg_max:\n    name: ctg_max\n    description: Maximum contig length.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: ctg_max\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gap_pct:\n    name: gap_pct\n    description: The gap size percentage of all scaffolds.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gap_pct\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gc_std:\n    name: gc_std\n    description: Standard deviation of GC content of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gc_std\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  gc_avg:\n    name: gc_avg\n    description: Average of GC content of all contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: gc_avg\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  num_input_reads:\n    name: num_input_reads\n    description: The sequence count number of input reads for assembly.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: num_input_reads\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  num_aligned_reads:\n    name: num_aligned_reads\n    description: The sequence count number of input reads aligned to assembled contigs.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: metagenome_assembly_parameter\n    alias: num_aligned_reads\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: float\n  insdc_assembly_identifiers:\n    name: insdc_assembly_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: assembly_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_assembly_identifiers\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetagenomeAssembly\n    - MetatranscriptomeAssembly\n    range: string\n    pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetatranscriptomeAssembly\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetatranscriptomeAssembly\n\n
"},{"location":"MetatranscriptomeExpressionAnalysis/","title":"Class: MetatranscriptomeExpressionAnalysis","text":"

A workflow process that provides expression values and read counts for gene features predicted on the contigs.

URI: nmdc:MetatranscriptomeExpressionAnalysis

classDiagram\n  class MetatranscriptomeExpressionAnalysis\n  click MetatranscriptomeExpressionAnalysis href \"../MetatranscriptomeExpressionAnalysis\"\n    WorkflowExecution <|-- MetatranscriptomeExpressionAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  MetatranscriptomeExpressionAnalysis : alternative_identifiers\n\n  MetatranscriptomeExpressionAnalysis : description\n\n  MetatranscriptomeExpressionAnalysis : end_date\n\n  MetatranscriptomeExpressionAnalysis : ended_at_time\n\n  MetatranscriptomeExpressionAnalysis : execution_resource\n\n      MetatranscriptomeExpressionAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  MetatranscriptomeExpressionAnalysis : git_url\n\n  MetatranscriptomeExpressionAnalysis : has_failure_categorization\n\n      MetatranscriptomeExpressionAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MetatranscriptomeExpressionAnalysis : has_input\n\n      MetatranscriptomeExpressionAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeExpressionAnalysis : has_output\n\n      MetatranscriptomeExpressionAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  MetatranscriptomeExpressionAnalysis : id\n\n  MetatranscriptomeExpressionAnalysis : img_identifiers\n\n  MetatranscriptomeExpressionAnalysis : name\n\n  MetatranscriptomeExpressionAnalysis : processing_institution\n\n      MetatranscriptomeExpressionAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MetatranscriptomeExpressionAnalysis : protocol_link\n\n      MetatranscriptomeExpressionAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MetatranscriptomeExpressionAnalysis : qc_comment\n\n  MetatranscriptomeExpressionAnalysis : qc_status\n\n      MetatranscriptomeExpressionAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MetatranscriptomeExpressionAnalysis : start_date\n\n  MetatranscriptomeExpressionAnalysis : started_at_time\n\n  MetatranscriptomeExpressionAnalysis : type\n\n  MetatranscriptomeExpressionAnalysis : version\n\n  MetatranscriptomeExpressionAnalysis : was_informed_by\n\n      MetatranscriptomeExpressionAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"MetatranscriptomeExpressionAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"MetatranscriptomeExpressionAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance img_identifiers * ExternalIdentifier A list of identifiers that relate the biosample to records in the IMG databas... direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MetatranscriptomeExpressionAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetatranscriptomeExpressionAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"MetatranscriptomeExpressionAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MetatranscriptomeExpressionAnalysis native nmdc:MetatranscriptomeExpressionAnalysis"},{"location":"MetatranscriptomeExpressionAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"MetatranscriptomeExpressionAnalysis/#direct","title":"Direct","text":"
name: MetatranscriptomeExpressionAnalysis\ndescription: A workflow process that provides expression values and read counts for\n  gene features predicted on the contigs.\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MetatranscriptomeExpressionAnalysis\n\n
"},{"location":"MetatranscriptomeExpressionAnalysis/#induced","title":"Induced","text":"
name: MetatranscriptomeExpressionAnalysis\ndescription: A workflow process that provides expression values and read counts for\n  gene features predicted on the contigs.\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  img_identifiers:\n    name: img_identifiers\n    maximum_cardinality: 1\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  img_identifiers:\n    name: img_identifiers\n    description: A list of identifiers that relate the biosample to records in the\n      IMG database.\n    title: IMG Identifiers\n    todos:\n    - add is_a or mixin modeling, like other external_database_identifiers\n    - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n      else?\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    alias: img_identifiers\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - MetagenomeAnnotation\n    - Biosample\n    - MetatranscriptomeAnnotation\n    - MetatranscriptomeExpressionAnalysis\n    - MagsAnalysis\n    range: external_identifier\n    multivalued: true\n    pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n    maximum_cardinality: 1\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MetatranscriptomeExpressionAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MetatranscriptomeExpressionAnalysis\n\n
"},{"location":"MixingProcess/","title":"Class: MixingProcess","text":"

The combining of components, particles or layers into a more homogeneous state.

__

URI: nmdc:MixingProcess

classDiagram\n  class MixingProcess\n  click MixingProcess href \"../MixingProcess\"\n    MaterialProcessing <|-- MixingProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  MixingProcess : alternative_identifiers\n\n  MixingProcess : description\n\n  MixingProcess : duration\n\n      MixingProcess --> \"0..1\" QuantityValue : duration\n    click QuantityValue href \"../QuantityValue\"\n\n  MixingProcess : end_date\n\n  MixingProcess : has_failure_categorization\n\n      MixingProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  MixingProcess : has_input\n\n      MixingProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  MixingProcess : has_output\n\n      MixingProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  MixingProcess : id\n\n  MixingProcess : instrument_used\n\n      MixingProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  MixingProcess : name\n\n  MixingProcess : processing_institution\n\n      MixingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  MixingProcess : protocol_link\n\n      MixingProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  MixingProcess : qc_comment\n\n  MixingProcess : qc_status\n\n      MixingProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  MixingProcess : start_date\n\n  MixingProcess : type\n\n\n\n
"},{"location":"MixingProcess/#inheritance","title":"Inheritance","text":""},{"location":"MixingProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance duration 0..1 QuantityValue The elapsed time of an activity direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample The mixed sample PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"MixingProcess/#comments","title":"Comments","text":""},{"location":"MixingProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixingProcess/#schema-source","title":"Schema Source","text":""},{"location":"MixingProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MixingProcess native nmdc:MixingProcess"},{"location":"MixingProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"MixingProcess/#direct","title":"Direct","text":"
name: MixingProcess\ndescription: 'The combining of components, particles or layers into a more homogeneous\n  state.\n\n  '\ncomments:\n- The mixing may be achieved manually or mechanically by shifting the material with\n  stirrers or pumps or by revolving or shaking the container.\n- The process must not permit segregation of particles of different size or properties.\n- Homogeneity may be considered to have been achieved in a practical sense when the\n  sampling error of the processed portion is negligible compared to the total error\n  of the measurement system.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nis_a: MaterialProcessing\nslots:\n- duration\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The mixed sample.\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:MixingProcess\n\n
"},{"location":"MixingProcess/#induced","title":"Induced","text":"
name: MixingProcess\ndescription: 'The combining of components, particles or layers into a more homogeneous\n  state.\n\n  '\ncomments:\n- The mixing may be achieved manually or mechanically by shifting the material with\n  stirrers or pumps or by revolving or shaking the container.\n- The process must not permit segregation of particles of different size or properties.\n- Homogeneity may be considered to have been achieved in a practical sense when the\n  sampling error of the processed portion is negligible compared to the total error\n  of the measurement system.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The mixed sample.\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  duration:\n    name: duration\n    description: The elapsed time of an activity.\n    examples:\n    - value: JsonObj(has_numeric_value=2, has_unit='hours')\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: duration\n    owner: MixingProcess\n    domain_of:\n    - MixingProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: QuantityValue\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: MixingProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The mixed sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: MixingProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MixingProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: MixingProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: MixingProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: MixingProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MixingProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:MixingProcess\n\n
"},{"location":"MixsEnvironmentalTriad/","title":"Subset: MixsEnvironmentalTriad","text":"

URI: MixsEnvironmentalTriad

"},{"location":"MixsEnvironmentalTriad/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixsEnvironmentalTriad/#schema-source","title":"Schema Source","text":""},{"location":"MixsExtension/","title":"Subset: MixsExtension","text":"

URI: MixsExtension

"},{"location":"MixsExtension/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixsExtension/#schema-source","title":"Schema Source","text":""},{"location":"MixsExtension/#slots-in-subset","title":"Slots in subset","text":"Slot Description env_package MIxS extension for reporting of measurements and observations obtained from o..."},{"location":"MobilePhaseSegment/","title":"Class: MobilePhaseSegment","text":"

A fluid mixture of substances that flow though a chromatographic stationary phase.

URI: nmdc:MobilePhaseSegment

classDiagram\n  class MobilePhaseSegment\n  click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n  MobilePhaseSegment : duration\n\n      MobilePhaseSegment --> \"0..1\" QuantityValue : duration\n    click QuantityValue href \"../QuantityValue\"\n\n  MobilePhaseSegment : substances_used\n\n      MobilePhaseSegment --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  MobilePhaseSegment : type\n\n  MobilePhaseSegment : volume\n\n      MobilePhaseSegment --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"MobilePhaseSegment/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance duration 0..1 QuantityValue The elapsed time of an activity direct substances_used * PortionOfSubstance The substances that are combined to enable a ChemicalConversionProcess direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct volume 0..1 QuantityValue The volume of a substance direct"},{"location":"MobilePhaseSegment/#usages","title":"Usages","text":"used by used in type used ChromatographyConfiguration ordered_mobile_phases range MobilePhaseSegment ChromatographicSeparationProcess ordered_mobile_phases range MobilePhaseSegment"},{"location":"MobilePhaseSegment/#comments","title":"Comments","text":""},{"location":"MobilePhaseSegment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MobilePhaseSegment/#schema-source","title":"Schema Source","text":""},{"location":"MobilePhaseSegment/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:MobilePhaseSegment native nmdc:MobilePhaseSegment"},{"location":"MobilePhaseSegment/#linkml-source","title":"LinkML Source","text":""},{"location":"MobilePhaseSegment/#direct","title":"Direct","text":"
name: MobilePhaseSegment\ndescription: A fluid mixture of substances that flow though a chromatographic stationary\n  phase.\ncomments:\n- Can be assembled into a list to account for a gradient.\n- Works best for separations that can be accounted for by a series of essentially\n  linear changes in the mobile phase composition.\n- For gradients, each segment should declare it's duration.\n- For step-wise separations that might be implemented with a syringe and a cartridge,\n  it will probably be more important to assert volumes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- duration\n- substances_used\n- type\n- volume\nclass_uri: nmdc:MobilePhaseSegment\n\n
"},{"location":"MobilePhaseSegment/#induced","title":"Induced","text":"
name: MobilePhaseSegment\ndescription: A fluid mixture of substances that flow though a chromatographic stationary\n  phase.\ncomments:\n- Can be assembled into a list to account for a gradient.\n- Works best for separations that can be accounted for by a series of essentially\n  linear changes in the mobile phase composition.\n- For gradients, each segment should declare it's duration.\n- For step-wise separations that might be implemented with a syringe and a cartridge,\n  it will probably be more important to assert volumes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  duration:\n    name: duration\n    description: The elapsed time of an activity.\n    examples:\n    - value: JsonObj(has_numeric_value=2, has_unit='hours')\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: duration\n    owner: MobilePhaseSegment\n    domain_of:\n    - MixingProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: QuantityValue\n  substances_used:\n    name: substances_used\n    description: The substances that are combined to enable a ChemicalConversionProcess.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: MobilePhaseSegment\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: MobilePhaseSegment\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  volume:\n    name: volume\n    description: The volume of a substance.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: MobilePhaseSegment\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\nclass_uri: nmdc:MobilePhaseSegment\n\n
"},{"location":"NMDC/","title":"NMDC","text":"

Schema for National Microbiome Data Collaborative (NMDC). This schema is organized into multiple modules, such as:

URI: https://w3id.org/nmdc/nmdc

"},{"location":"NamedThing/","title":"Class: NamedThing","text":"

a databased entity or concept/class

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:NamedThing

classDiagram\n  class NamedThing\n  click NamedThing href \"../NamedThing\"\n    NamedThing <|-- GeneProduct\n      click GeneProduct href \"../GeneProduct\"\n    NamedThing <|-- OntologyClass\n      click OntologyClass href \"../OntologyClass\"\n    NamedThing <|-- MaterialEntity\n      click MaterialEntity href \"../MaterialEntity\"\n    NamedThing <|-- PlannedProcess\n      click PlannedProcess href \"../PlannedProcess\"\n    NamedThing <|-- Study\n      click Study href \"../Study\"\n    NamedThing <|-- InformationObject\n      click InformationObject href \"../InformationObject\"\n\n\n\n  NamedThing : alternative_identifiers\n\n  NamedThing : description\n\n  NamedThing : id\n\n  NamedThing : name\n\n  NamedThing : type\n\n\n\n
"},{"location":"NamedThing/#inheritance","title":"Inheritance","text":""},{"location":"NamedThing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing direct name 0..1 String A human readable label for an entity direct description 0..1 String a human-readable description of a thing direct alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"NamedThing/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_input range NamedThing MassSpectrometry has_input range NamedThing Pooling has_input range NamedThing Extraction has_input range NamedThing LibraryPreparation has_input range NamedThing ProtocolExecution has_input range NamedThing ProtocolExecution has_output range NamedThing SubSamplingProcess has_input range NamedThing MixingProcess has_input range NamedThing FiltrationProcess has_input range NamedThing StorageProcess has_input range NamedThing StorageProcess has_output range NamedThing ChromatographicSeparationProcess has_input range NamedThing DissolvingProcess has_input range NamedThing ChemicalConversionProcess has_input range NamedThing MetagenomeAnnotation has_input range NamedThing MetagenomeAnnotation has_output range NamedThing MaterialProcessing has_input range NamedThing PlannedProcess has_input range NamedThing PlannedProcess has_output range NamedThing DataGeneration has_input range NamedThing WorkflowExecution has_input range NamedThing WorkflowExecution has_output range NamedThing MetagenomeAssembly has_input range NamedThing MetagenomeAssembly has_output range NamedThing MetatranscriptomeAssembly has_input range NamedThing MetatranscriptomeAssembly has_output range NamedThing MetatranscriptomeAnnotation has_input range NamedThing MetatranscriptomeAnnotation has_output range NamedThing MetatranscriptomeExpressionAnalysis has_input range NamedThing MetatranscriptomeExpressionAnalysis has_output range NamedThing MagsAnalysis has_input range NamedThing MagsAnalysis has_output range NamedThing MetagenomeSequencing has_input range NamedThing MetagenomeSequencing has_output range NamedThing ReadQcAnalysis has_input range NamedThing ReadQcAnalysis has_output range NamedThing ReadBasedTaxonomyAnalysis has_input range NamedThing ReadBasedTaxonomyAnalysis has_output range NamedThing MetabolomicsAnalysis has_input range NamedThing MetabolomicsAnalysis has_output range NamedThing MetaproteomicsAnalysis has_input range NamedThing MetaproteomicsAnalysis has_output range NamedThing NomAnalysis has_input range NamedThing NomAnalysis has_output range NamedThing"},{"location":"NamedThing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NamedThing/#schema-source","title":"Schema Source","text":""},{"location":"NamedThing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:NamedThing native nmdc:NamedThing"},{"location":"NamedThing/#linkml-source","title":"LinkML Source","text":""},{"location":"NamedThing/#direct","title":"Direct","text":"
name: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- id\n- name\n- description\n- alternative_identifiers\n- type\nclass_uri: nmdc:NamedThing\n\n
"},{"location":"NamedThing/#induced","title":"Induced","text":"
name: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NamedThing\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: NamedThing\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: NamedThing\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: NamedThing\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: NamedThing\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:NamedThing\n\n
"},{"location":"Ncname/","title":"Type: Ncname","text":"

Prefix part of CURIE

URI: xsd:string

"},{"location":"Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Ncname/#schema-source","title":"Schema Source","text":""},{"location":"Ncname/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:ncname"},{"location":"Nodeidentifier/","title":"Type: Nodeidentifier","text":"

A URI, CURIE or BNODE that represents a node in a model.

URI: shex:nonLiteral

"},{"location":"Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"location":"Nodeidentifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self shex:nonLiteral native nmdc:nodeidentifier"},{"location":"NomAnalysis/","title":"Class: NomAnalysis","text":"

URI: nmdc:NomAnalysis

classDiagram\n  class NomAnalysis\n  click NomAnalysis href \"../NomAnalysis\"\n    WorkflowExecution <|-- NomAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  NomAnalysis : alternative_identifiers\n\n  NomAnalysis : description\n\n  NomAnalysis : end_date\n\n  NomAnalysis : ended_at_time\n\n  NomAnalysis : execution_resource\n\n      NomAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  NomAnalysis : git_url\n\n  NomAnalysis : has_calibration\n\n  NomAnalysis : has_failure_categorization\n\n      NomAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  NomAnalysis : has_input\n\n      NomAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  NomAnalysis : has_output\n\n      NomAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  NomAnalysis : id\n\n  NomAnalysis : name\n\n  NomAnalysis : processing_institution\n\n      NomAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  NomAnalysis : protocol_link\n\n      NomAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  NomAnalysis : qc_comment\n\n  NomAnalysis : qc_status\n\n      NomAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  NomAnalysis : start_date\n\n  NomAnalysis : started_at_time\n\n  NomAnalysis : type\n\n  NomAnalysis : version\n\n  NomAnalysis : was_informed_by\n\n      NomAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"NomAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"NomAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_calibration 0..1 String\u00a0or\u00a0CalibrationInformation\u00a0or\u00a0String a calibration instance associated with a process direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"NomAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NomAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"NomAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:NomAnalysis native nmdc:NomAnalysis"},{"location":"NomAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"NomAnalysis/#direct","title":"Direct","text":"
name: NomAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- has_calibration\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:NomAnalysis\n\n
"},{"location":"NomAnalysis/#induced","title":"Induced","text":"
name: NomAnalysis\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_calibration:\n    name: has_calibration\n    description: a calibration instance associated with a process\n    notes:\n    - 'has_calibration slot will be removed from all WorkflowExecution classes but\n      remain on the MassSpectrometry class after an ingest of the appropriate set\n      has occurred.  Once this has occurred, this slot''s range can be updated to\n      CalibrationInformation and class/slot definitions can move to nmdc.yaml.   See\n      PR #29 in Berkeley schema.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_calibration\n    owner: NomAnalysis\n    domain_of:\n    - MassSpectrometry\n    - MetabolomicsAnalysis\n    - NomAnalysis\n    range: string\n    any_of:\n    - range: CalibrationInformation\n    - range: string\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: NomAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: NomAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NomAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: NomAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: NomAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: NomAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: NomAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:NomAnalysis\n\n
"},{"location":"NucleicAcidSequenceSource/","title":"Subset: NucleicAcidSequenceSource","text":"

URI: NucleicAcidSequenceSource

"},{"location":"NucleicAcidSequenceSource/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NucleicAcidSequenceSource/#schema-source","title":"Schema Source","text":""},{"location":"NucleotideSequencing/","title":"Class: NucleotideSequencing","text":"

A DataGeneration in which the sequence of DNA or RNA molecules is generated.

URI: nmdc:NucleotideSequencing

classDiagram\n  class NucleotideSequencing\n  click NucleotideSequencing href \"../NucleotideSequencing\"\n    DataGeneration <|-- NucleotideSequencing\n      click DataGeneration href \"../DataGeneration\"\n\n\n\n  NucleotideSequencing : add_date\n\n  NucleotideSequencing : alternative_identifiers\n\n  NucleotideSequencing : analyte_category\n\n      NucleotideSequencing --> \"1\" AnalyteCategoryEnum : analyte_category\n    click AnalyteCategoryEnum href \"../AnalyteCategoryEnum\"\n\n  NucleotideSequencing : associated_studies\n\n      NucleotideSequencing --> \"1..*\" Study : associated_studies\n    click Study href \"../Study\"\n\n  NucleotideSequencing : description\n\n  NucleotideSequencing : end_date\n\n  NucleotideSequencing : gold_sequencing_project_identifiers\n\n  NucleotideSequencing : has_failure_categorization\n\n      NucleotideSequencing --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  NucleotideSequencing : has_input\n\n      NucleotideSequencing --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  NucleotideSequencing : has_output\n\n      NucleotideSequencing --> \"*\" DataObject : has_output\n    click DataObject href \"../DataObject\"\n\n  NucleotideSequencing : id\n\n  NucleotideSequencing : insdc_bioproject_identifiers\n\n  NucleotideSequencing : insdc_experiment_identifiers\n\n  NucleotideSequencing : instrument_used\n\n      NucleotideSequencing --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  NucleotideSequencing : mod_date\n\n  NucleotideSequencing : name\n\n  NucleotideSequencing : ncbi_project_name\n\n  NucleotideSequencing : principal_investigator\n\n      NucleotideSequencing --> \"0..1\" PersonValue : principal_investigator\n    click PersonValue href \"../PersonValue\"\n\n  NucleotideSequencing : processing_institution\n\n      NucleotideSequencing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  NucleotideSequencing : protocol_link\n\n      NucleotideSequencing --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  NucleotideSequencing : qc_comment\n\n  NucleotideSequencing : qc_status\n\n      NucleotideSequencing --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  NucleotideSequencing : start_date\n\n  NucleotideSequencing : target_gene\n\n      NucleotideSequencing --> \"0..1\" TextValue : target_gene\n    click TextValue href \"../TextValue\"\n\n  NucleotideSequencing : target_subfragment\n\n      NucleotideSequencing --> \"0..1\" TextValue : target_subfragment\n    click TextValue href \"../TextValue\"\n\n  NucleotideSequencing : type\n\n\n\n
"},{"location":"NucleotideSequencing/#inheritance","title":"Inheritance","text":""},{"location":"NucleotideSequencing/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance gold_sequencing_project_identifiers * ExternalIdentifier identifiers for corresponding sequencing project in GOLD direct insdc_bioproject_identifiers * ExternalIdentifier identifiers for corresponding project in INSDC Bioproject direct insdc_experiment_identifiers * ExternalIdentifier direct ncbi_project_name 0..1 String direct target_gene 0..1 TextValue Targeted gene or locus name for marker gene studies direct target_subfragment 0..1 TextValue Name of subfragment of a gene or locus direct add_date 0..1 String The date on which the information was added to the database DataGeneration analyte_category 1 AnalyteCategoryEnum The type of analyte(s) that were measured in the data generation process and ... DataGeneration associated_studies 1..* Study The study associated with a resource DataGeneration instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing DataGeneration mod_date 0..1 String The last date on which the database information was modified DataGeneration principal_investigator 0..1 PersonValue Principal Investigator who led the study and/or generated the dataset DataGeneration has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * DataObject An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"NucleotideSequencing/#comments","title":"Comments","text":""},{"location":"NucleotideSequencing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NucleotideSequencing/#schema-source","title":"Schema Source","text":""},{"location":"NucleotideSequencing/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:NucleotideSequencing native nmdc:NucleotideSequencing"},{"location":"NucleotideSequencing/#linkml-source","title":"LinkML Source","text":""},{"location":"NucleotideSequencing/#direct","title":"Direct","text":"
name: NucleotideSequencing\ndescription: A DataGeneration in which the sequence of DNA or RNA molecules is generated.\ncomments:\n- For example data generated from an Illumina or Pacific Biosciences instrument.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: DataGeneration\nslots:\n- gold_sequencing_project_identifiers\n- insdc_bioproject_identifiers\n- insdc_experiment_identifiers\n- ncbi_project_name\n- target_gene\n- target_subfragment\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:NucleotideSequencing\n\n
"},{"location":"NucleotideSequencing/#induced","title":"Induced","text":"
name: NucleotideSequencing\ndescription: A DataGeneration in which the sequence of DNA or RNA molecules is generated.\ncomments:\n- For example data generated from an Illumina or Pacific Biosciences instrument.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: DataGeneration\nslot_usage:\n  id:\n    name: id\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  gold_sequencing_project_identifiers:\n    name: gold_sequencing_project_identifiers\n    description: identifiers for corresponding sequencing project in GOLD\n    examples:\n    - value: https://bioregistry.io/gold:Gp0108335\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: omics_processing_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_sequencing_project_identifiers\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    range: external_identifier\n    multivalued: true\n    pattern: ^gold:Gp[0-9]+$\n  insdc_bioproject_identifiers:\n    name: insdc_bioproject_identifiers\n    description: identifiers for corresponding project in INSDC Bioproject\n    comments:\n    - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n      one to one\n    examples:\n    - value: https://bioregistry.io/bioproject:PRJNA366857\n      description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2\n        metatranscriptome\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ncbi.nlm.nih.gov/bioproject/\n    - https://www.ddbj.nig.ac.jp/bioproject/index-e.html\n    aliases:\n    - NCBI bioproject identifiers\n    - DDBJ bioproject identifiers\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_bioproject_identifiers\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n  insdc_experiment_identifiers:\n    name: insdc_experiment_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: external_database_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_experiment_identifiers\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    - DataObject\n    range: external_identifier\n    multivalued: true\n    pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n  ncbi_project_name:\n    name: ncbi_project_name\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: ncbi_project_name\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    range: string\n  target_gene:\n    name: target_gene\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gene name\n    description: Targeted gene or locus name for marker gene studies\n    title: target gene\n    examples:\n    - value: 16S rRNA, 18S rRNA, nif, amoA, rpo\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - target gene\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000044\n    alias: target_gene\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    range: TextValue\n    multivalued: false\n  target_subfragment:\n    name: target_subfragment\n    annotations:\n      expected_value:\n        tag: expected_value\n        value: gene fragment name\n    description: Name of subfragment of a gene or locus. Important to e.g. identify\n      special regions on marker genes like V6 on 16S rRNA\n    title: target subfragment\n    examples:\n    - value: V6, V9, ITS\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - target subfragment\n    rank: 1000\n    is_a: sequencing field\n    string_serialization: '{text}'\n    slot_uri: MIXS:0000045\n    alias: target_subfragment\n    owner: NucleotideSequencing\n    domain_of:\n    - NucleotideSequencing\n    range: TextValue\n    multivalued: false\n  add_date:\n    name: add_date\n    description: The date on which the information was added to the database.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: add_date\n    owner: NucleotideSequencing\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  analyte_category:\n    name: analyte_category\n    description: \"The type of analyte(s) that were measured in the data generation\\\n      \\ process and analyzed\\n  in the Workflow Chain\\n\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: analyte_category\n    owner: NucleotideSequencing\n    domain_of:\n    - DataGeneration\n    range: AnalyteCategoryEnum\n    required: true\n  associated_studies:\n    name: associated_studies\n    description: The study associated with a resource.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: associated_studies\n    owner: NucleotideSequencing\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: Study\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: NucleotideSequencing\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  mod_date:\n    name: mod_date\n    description: The last date on which the database information was modified.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: mod_date\n    owner: NucleotideSequencing\n    domain_of:\n    - Biosample\n    - DataGeneration\n    range: string\n  principal_investigator:\n    name: principal_investigator\n    description: Principal Investigator who led the study and/or generated the dataset.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - PI\n    rank: 1000\n    alias: principal_investigator\n    owner: NucleotideSequencing\n    domain_of:\n    - Study\n    - DataGeneration\n    range: PersonValue\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: DataObject\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: NucleotideSequencing\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: NucleotideSequencing\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: NucleotideSequencing\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: NucleotideSequencing\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: NucleotideSequencing\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: NucleotideSequencing\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:NucleotideSequencing\n\n
"},{"location":"Objectidentifier/","title":"Type: Objectidentifier","text":"

A URI or CURIE that represents an object in the model.

URI: shex:iri

"},{"location":"Objectidentifier/#comments","title":"Comments","text":""},{"location":"Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Objectidentifier/#schema-source","title":"Schema Source","text":""},{"location":"Objectidentifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self shex:iri native nmdc:objectidentifier"},{"location":"OccupDocumentEnum/","title":"Enum: OccupDocumentEnum","text":"

URI: OccupDocumentEnum

"},{"location":"OccupDocumentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description automated count None estimate None manual count None videos None"},{"location":"OccupDocumentEnum/#slots","title":"Slots","text":"Name Description occup_document The type of documentation of occupancy"},{"location":"OccupDocumentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OccupDocumentEnum/#schema-source","title":"Schema Source","text":""},{"location":"OccupDocumentEnum/#linkml-source","title":"LinkML Source","text":"
name: occup_document_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  automated count:\n    text: automated count\n  estimate:\n    text: estimate\n  manual count:\n    text: manual count\n  videos:\n    text: videos\n\n
"},{"location":"OntologyClass/","title":"Class: OntologyClass","text":"

URI: nmdc:OntologyClass

classDiagram\n  class OntologyClass\n  click OntologyClass href \"../OntologyClass\"\n    NamedThing <|-- OntologyClass\n      click NamedThing href \"../NamedThing\"\n\n\n    OntologyClass <|-- EnvironmentalMaterialTerm\n      click EnvironmentalMaterialTerm href \"../EnvironmentalMaterialTerm\"\n    OntologyClass <|-- ChemicalEntity\n      click ChemicalEntity href \"../ChemicalEntity\"\n    OntologyClass <|-- FunctionalAnnotationTerm\n      click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n  OntologyClass : alternative_identifiers\n\n  OntologyClass : description\n\n  OntologyClass : id\n\n  OntologyClass : name\n\n  OntologyClass : type\n\n\n\n
"},{"location":"OntologyClass/#inheritance","title":"Inheritance","text":""},{"location":"OntologyClass/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"OntologyClass/#usages","title":"Usages","text":"used by used in type used ControlledTermValue term range OntologyClass ControlledIdentifiedTermValue term range OntologyClass"},{"location":"OntologyClass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OntologyClass/#schema-source","title":"Schema Source","text":""},{"location":"OntologyClass/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:OntologyClass native nmdc:OntologyClass"},{"location":"OntologyClass/#linkml-source","title":"LinkML Source","text":""},{"location":"OntologyClass/#direct","title":"Direct","text":"
name: OntologyClass\nnotes:\n- The identifiers for terms from external ontologies can't have their ids constrained\n  to the nmdc namespace\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n  id:\n    name: id\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nclass_uri: nmdc:OntologyClass\n\n
"},{"location":"OntologyClass/#induced","title":"Induced","text":"
name: OntologyClass\nnotes:\n- The identifiers for terms from external ontologies can't have their ids constrained\n  to the nmdc namespace\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n  id:\n    name: id\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: OntologyClass\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: OntologyClass\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: OntologyClass\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: OntologyClass\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: OntologyClass\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:OntologyClass\n\n
"},{"location":"OrganismCountEnum/","title":"Enum: OrganismCountEnum","text":"

URI: OrganismCountEnum

"},{"location":"OrganismCountEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ATP None MPN None other None"},{"location":"OrganismCountEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OrganismCountEnum/#schema-source","title":"Schema Source","text":""},{"location":"OrganismCountEnum/#linkml-source","title":"LinkML Source","text":"
name: organism_count_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  ATP:\n    text: ATP\n  MPN:\n    text: MPN\n  other:\n    text: other\n\n
"},{"location":"OrthologyGroup/","title":"Class: OrthologyGroup","text":"

A set of genes or gene products in which all members are orthologous

URI: nmdc:OrthologyGroup

classDiagram\n  class OrthologyGroup\n  click OrthologyGroup href \"../OrthologyGroup\"\n    FunctionalAnnotationTerm <|-- OrthologyGroup\n      click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n  OrthologyGroup : alternative_identifiers\n\n  OrthologyGroup : description\n\n  OrthologyGroup : id\n\n  OrthologyGroup : name\n\n  OrthologyGroup : type\n\n\n\n
"},{"location":"OrthologyGroup/#inheritance","title":"Inheritance","text":""},{"location":"OrthologyGroup/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"OrthologyGroup/#todos","title":"TODOs","text":""},{"location":"OrthologyGroup/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OrthologyGroup/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"OrthologyGroup/#schema-source","title":"Schema Source","text":""},{"location":"OrthologyGroup/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:OrthologyGroup native nmdc:OrthologyGroup exact biolink:GeneFamily"},{"location":"OrthologyGroup/#linkml-source","title":"LinkML Source","text":""},{"location":"OrthologyGroup/#direct","title":"Direct","text":"
name: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\ntodos:\n- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable\n  in the Data Portal?\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nclass_uri: nmdc:OrthologyGroup\n\n
"},{"location":"OrthologyGroup/#induced","title":"Induced","text":"
name: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\ntodos:\n- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable\n  in the Data Portal?\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: OrthologyGroup\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: OrthologyGroup\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: OrthologyGroup\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: OrthologyGroup\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: OrthologyGroup\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:OrthologyGroup\n\n
"},{"location":"OxyStatSampEnum/","title":"Enum: OxyStatSampEnum","text":"

URI: OxyStatSampEnum

"},{"location":"OxyStatSampEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aerobic None anaerobic None other None"},{"location":"OxyStatSampEnum/#slots","title":"Slots","text":"Name Description oxy_stat_samp Oxygenation status of sample"},{"location":"OxyStatSampEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OxyStatSampEnum/#schema-source","title":"Schema Source","text":""},{"location":"OxyStatSampEnum/#linkml-source","title":"LinkML Source","text":"
name: oxy_stat_samp_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  aerobic:\n    text: aerobic\n  anaerobic:\n    text: anaerobic\n  other:\n    text: other\n\n
"},{"location":"Package/","title":"Subset: Package","text":"

A MIxS package. These can be combined with checklists

URI: Package

"},{"location":"Package/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Package/#schema-source","title":"Schema Source","text":""},{"location":"Pathway/","title":"Class: Pathway (DEPRECATED)

A pathway is a sequence of steps/reactions carried out by an organism or community of organisms

URI: nmdc:Pathway

classDiagram\n  class Pathway\n  click Pathway href \"../Pathway\"\n    FunctionalAnnotationTerm <|-- Pathway\n      click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n  Pathway : alternative_identifiers\n\n  Pathway : description\n\n  Pathway : id\n\n  Pathway : name\n\n  Pathway : type\n\n\n\n
","text":""},{"location":"Pathway/#inheritance","title":"Inheritance","text":""},{"location":"Pathway/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Pathway/#aliases","title":"Aliases","text":""},{"location":"Pathway/#todos","title":"TODOs","text":""},{"location":"Pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Pathway/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"Pathway/#schema-source","title":"Schema Source","text":""},{"location":"Pathway/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Pathway native nmdc:Pathway exact biolink:Pathway"},{"location":"Pathway/#linkml-source","title":"LinkML Source","text":""},{"location":"Pathway/#direct","title":"Direct","text":"
name: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n  or community of organisms\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\ntodos:\n- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable\n  part_of a Pathway\n- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in\n  the Data Portal?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nclass_uri: nmdc:Pathway\n\n
"},{"location":"Pathway/#induced","title":"Induced","text":"
name: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n  or community of organisms\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\ntodos:\n- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable\n  part_of a Pathway\n- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in\n  the Data Portal?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Pathway\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Pathway\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Pathway\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Pathway\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Pathway\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Pathway\n\n
"},{"location":"PeptideQuantification/","title":"Class: PeptideQuantification","text":"

This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information

URI: nmdc:PeptideQuantification

classDiagram\n  class PeptideQuantification\n  click PeptideQuantification href \"../PeptideQuantification\"\n\n  PeptideQuantification : all_proteins\n\n      PeptideQuantification --> \"*\" GeneProduct : all_proteins\n    click GeneProduct href \"../GeneProduct\"\n\n  PeptideQuantification : best_protein\n\n      PeptideQuantification --> \"0..1\" GeneProduct : best_protein\n    click GeneProduct href \"../GeneProduct\"\n\n  PeptideQuantification : min_q_value\n\n  PeptideQuantification : peptide_sequence\n\n  PeptideQuantification : peptide_spectral_count\n\n  PeptideQuantification : peptide_sum_masic_abundance\n\n  PeptideQuantification : type\n\n\n\n
"},{"location":"PeptideQuantification/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance type 1 Uriorcurie the class_uri of the class that has been instantiated direct all_proteins * GeneProduct the list of protein identifiers that are associated with the peptide sequence direct best_protein 0..1 GeneProduct the specific protein identifier most correctly associated with the peptide se... direct min_q_value 0..1 Float smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... direct peptide_sequence 0..1 String direct peptide_spectral_count 0..1 Integer sum of filter passing MS2 spectra associated with the peptide sequence within... direct peptide_sum_masic_abundance 0..1 Integer combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... direct"},{"location":"PeptideQuantification/#usages","title":"Usages","text":"used by used in type used MetaproteomicsAnalysis has_peptide_quantifications range PeptideQuantification"},{"location":"PeptideQuantification/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PeptideQuantification/#schema-source","title":"Schema Source","text":""},{"location":"PeptideQuantification/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:PeptideQuantification native nmdc:PeptideQuantification"},{"location":"PeptideQuantification/#linkml-source","title":"LinkML Source","text":""},{"location":"PeptideQuantification/#direct","title":"Direct","text":"
name: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n  peptide sequence and related information\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- type\n- all_proteins\n- best_protein\n- min_q_value\n- peptide_sequence\n- peptide_spectral_count\n- peptide_sum_masic_abundance\nclass_uri: nmdc:PeptideQuantification\n\n
"},{"location":"PeptideQuantification/#induced","title":"Induced","text":"
name: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n  peptide sequence and related information\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: PeptideQuantification\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  all_proteins:\n    name: all_proteins\n    description: the list of protein identifiers that are associated with the peptide\n      sequence\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: all_proteins\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    - ProteinQuantification\n    range: GeneProduct\n    multivalued: true\n  best_protein:\n    name: best_protein\n    description: the specific protein identifier most correctly associated with the\n      peptide sequence\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: best_protein\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    - ProteinQuantification\n    range: GeneProduct\n  min_q_value:\n    name: min_q_value\n    description: smallest Q-Value associated with the peptide sequence as provided\n      by MSGFPlus tool\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - OBI:0001442\n    rank: 1000\n    alias: min_q_value\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    range: float\n  peptide_sequence:\n    name: peptide_sequence\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: peptide_sequence\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    range: string\n  peptide_spectral_count:\n    name: peptide_spectral_count\n    description: sum of filter passing MS2 spectra associated with the peptide sequence\n      within a given LC-MS/MS data file\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: peptide_spectral_count\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    range: integer\n  peptide_sum_masic_abundance:\n    name: peptide_sum_masic_abundance\n    description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n      associated with the peptide sequence from a given LC-MS/MS data file using the\n      MASIC tool\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: peptide_sum_masic_abundance\n    owner: PeptideQuantification\n    domain_of:\n    - PeptideQuantification\n    range: integer\nclass_uri: nmdc:PeptideQuantification\n\n
"},{"location":"PersonValue/","title":"Class: PersonValue","text":"

An attribute value representing a person

URI: nmdc:PersonValue

classDiagram\n  class PersonValue\n  click PersonValue href \"../PersonValue\"\n    AttributeValue <|-- PersonValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  PersonValue : email\n\n  PersonValue : has_raw_value\n\n  PersonValue : name\n\n  PersonValue : orcid\n\n  PersonValue : profile_image_url\n\n  PersonValue : type\n\n  PersonValue : websites\n\n\n\n
"},{"location":"PersonValue/#inheritance","title":"Inheritance","text":""},{"location":"PersonValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance email 0..1 String An email address for an entity such as a person direct name 0..1 String The full name of the Investigator direct orcid 0..1 String The ORCID of a person direct profile_image_url 0..1 String A url that points to an image of a person direct websites * String A list of websites that are associated with the entity direct has_raw_value 0..1 String The full name of the Investigator in format FIRST LAST AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"PersonValue/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing principal_investigator range PersonValue MassSpectrometry principal_investigator range PersonValue CreditAssociation applies_to_person range PersonValue Study principal_investigator range PersonValue DataGeneration principal_investigator range PersonValue"},{"location":"PersonValue/#todos","title":"TODOs","text":""},{"location":"PersonValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PersonValue/#schema-source","title":"Schema Source","text":""},{"location":"PersonValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:PersonValue native nmdc:PersonValue"},{"location":"PersonValue/#linkml-source","title":"LinkML Source","text":""},{"location":"PersonValue/#direct","title":"Direct","text":"
name: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- email\n- name\n- orcid\n- profile_image_url\n- websites\nslot_usage:\n  orcid:\n    name: orcid\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Open Researcher and Contributor ID for this person. See https://orcid.org\n  email:\n    name: email\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Email address for this person.\n  has_raw_value:\n    name: has_raw_value\n    description: The full name of the Investigator in format FIRST LAST.\n    notes:\n    - May eventually be deprecated in favor of \"name\".\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: First name, middle initial, and last name of this person.\n    description: The full name of the Investigator. It should follow the format FIRST\n      [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\nclass_uri: nmdc:PersonValue\n\n
"},{"location":"PersonValue/#induced","title":"Induced","text":"
name: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslot_usage:\n  orcid:\n    name: orcid\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Open Researcher and Contributor ID for this person. See https://orcid.org\n  email:\n    name: email\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Email address for this person.\n  has_raw_value:\n    name: has_raw_value\n    description: The full name of the Investigator in format FIRST LAST.\n    notes:\n    - May eventually be deprecated in favor of \"name\".\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: First name, middle initial, and last name of this person.\n    description: The full name of the Investigator. It should follow the format FIRST\n      [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\nattributes:\n  email:\n    name: email\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Email address for this person.\n    description: An email address for an entity such as a person. This should be the\n      primary email address used.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: schema:email\n    alias: email\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    range: string\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: First name, middle initial, and last name of this person.\n    description: The full name of the Investigator. It should follow the format FIRST\n      [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  orcid:\n    name: orcid\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Open Researcher and Contributor ID for this person. See https://orcid.org\n    description: The ORCID of a person.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: orcid\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    range: string\n  profile_image_url:\n    name: profile_image_url\n    description: A url that points to an image of a person.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: profile_image_url\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    range: string\n  websites:\n    name: websites\n    description: A list of websites that are associated with the entity.\n    comments:\n    - DOIs should not be included as websites. Instead, use the associated_dois slot.\n    - A consortium's homepage website should be included in the homepage_website slot,\n      not in websites.\n    - consortium is a convenience term for a Study whose study_category value is consortium\n    - the website slot and its subproperties are virtually identical to the url slot,\n      except that they are multivalued and url is single-valued.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:url\n    rank: 1000\n    alias: websites\n    owner: PersonValue\n    domain_of:\n    - PersonValue\n    - Study\n    range: string\n    multivalued: true\n    pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n  has_raw_value:\n    name: has_raw_value\n    description: The full name of the Investigator in format FIRST LAST.\n    notes:\n    - May eventually be deprecated in favor of \"name\".\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: PersonValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: PersonValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:PersonValue\n\n
"},{"location":"PlannedProcess/","title":"Class: Planned Process (PlannedProcess)","text":"

Note

This is an abstract class and should not be instantiated directly.

URI: OBI:0000011

classDiagram\n  class PlannedProcess\n  click PlannedProcess href \"../PlannedProcess\"\n    NamedThing <|-- PlannedProcess\n      click NamedThing href \"../NamedThing\"\n\n\n    PlannedProcess <|-- CollectingBiosamplesFromSite\n      click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n    PlannedProcess <|-- ProtocolExecution\n      click ProtocolExecution href \"../ProtocolExecution\"\n    PlannedProcess <|-- StorageProcess\n      click StorageProcess href \"../StorageProcess\"\n    PlannedProcess <|-- MaterialProcessing\n      click MaterialProcessing href \"../MaterialProcessing\"\n    PlannedProcess <|-- DataGeneration\n      click DataGeneration href \"../DataGeneration\"\n    PlannedProcess <|-- WorkflowExecution\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  PlannedProcess : alternative_identifiers\n\n  PlannedProcess : description\n\n  PlannedProcess : end_date\n\n  PlannedProcess : has_failure_categorization\n\n      PlannedProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  PlannedProcess : has_input\n\n      PlannedProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  PlannedProcess : has_output\n\n      PlannedProcess --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  PlannedProcess : id\n\n  PlannedProcess : name\n\n  PlannedProcess : processing_institution\n\n      PlannedProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  PlannedProcess : protocol_link\n\n      PlannedProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  PlannedProcess : qc_comment\n\n  PlannedProcess : qc_status\n\n      PlannedProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  PlannedProcess : start_date\n\n  PlannedProcess : type\n\n\n\n
"},{"location":"PlannedProcess/#inheritance","title":"Inheritance","text":""},{"location":"PlannedProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_input * NamedThing An input to a process direct has_output * NamedThing An output from a process direct processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample direct protocol_link 0..1 Protocol direct start_date 0..1 String The date on which any process or activity was started direct end_date 0..1 String The date on which any process or activity was ended direct qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... direct qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output direct has_failure_categorization * FailureCategorization direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"PlannedProcess/#usages","title":"Usages","text":"used by used in type used ProtocolExecution has_process_parts range PlannedProcess"},{"location":"PlannedProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlannedProcess/#schema-source","title":"Schema Source","text":""},{"location":"PlannedProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self OBI:0000011 native nmdc:PlannedProcess"},{"location":"PlannedProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"PlannedProcess/#direct","title":"Direct","text":"
name: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nslots:\n- has_input\n- has_output\n- processing_institution\n- protocol_link\n- start_date\n- end_date\n- qc_status\n- qc_comment\n- has_failure_categorization\nclass_uri: OBI:0000011\n\n
"},{"location":"PlannedProcess/#induced","title":"Induced","text":"
name: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nattributes:\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: PlannedProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: PlannedProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: PlannedProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: PlannedProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: PlannedProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: PlannedProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: OBI:0000011\n\n
"},{"location":"PlantGrowthMedEnum/","title":"Enum: PlantGrowthMedEnum","text":"

URI: PlantGrowthMedEnum

"},{"location":"PlantGrowthMedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description other artificial liquid medium None other artificial solid medium None peat moss None perlite None pumice None sand None soil None vermiculite None water None"},{"location":"PlantGrowthMedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantGrowthMedEnum/#schema-source","title":"Schema Source","text":""},{"location":"PlantGrowthMedEnum/#linkml-source","title":"LinkML Source","text":"
name: plant_growth_med_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  other artificial liquid medium:\n    text: other artificial liquid medium\n  other artificial solid medium:\n    text: other artificial solid medium\n  peat moss:\n    text: peat moss\n  perlite:\n    text: perlite\n  pumice:\n    text: pumice\n  sand:\n    text: sand\n  soil:\n    text: soil\n  vermiculite:\n    text: vermiculite\n  water:\n    text: water\n\n
"},{"location":"PlantSexEnum/","title":"Enum: PlantSexEnum","text":"

URI: PlantSexEnum

"},{"location":"PlantSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Androdioecious None Androecious None Androgynous None Androgynomonoecious None Andromonoecious None Bisexual None Dichogamous None Diclinous None Dioecious None Gynodioecious None Gynoecious None Gynomonoecious None Hermaphroditic None Imperfect None Monoclinous None Monoecious None Perfect None Polygamodioecious None Polygamomonoecious None Polygamous None Protandrous None Protogynous None Subandroecious None Subdioecious None Subgynoecious None Synoecious None Trimonoecious None Trioecious None Unisexual None"},{"location":"PlantSexEnum/#slots","title":"Slots","text":"Name Description plant_sex Sex of the reproductive parts on the whole plant, e"},{"location":"PlantSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantSexEnum/#schema-source","title":"Schema Source","text":""},{"location":"PlantSexEnum/#linkml-source","title":"LinkML Source","text":"
name: plant_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Androdioecious:\n    text: Androdioecious\n  Androecious:\n    text: Androecious\n  Androgynous:\n    text: Androgynous\n  Androgynomonoecious:\n    text: Androgynomonoecious\n  Andromonoecious:\n    text: Andromonoecious\n  Bisexual:\n    text: Bisexual\n  Dichogamous:\n    text: Dichogamous\n  Diclinous:\n    text: Diclinous\n  Dioecious:\n    text: Dioecious\n  Gynodioecious:\n    text: Gynodioecious\n  Gynoecious:\n    text: Gynoecious\n  Gynomonoecious:\n    text: Gynomonoecious\n  Hermaphroditic:\n    text: Hermaphroditic\n  Imperfect:\n    text: Imperfect\n  Monoclinous:\n    text: Monoclinous\n  Monoecious:\n    text: Monoecious\n  Perfect:\n    text: Perfect\n  Polygamodioecious:\n    text: Polygamodioecious\n  Polygamomonoecious:\n    text: Polygamomonoecious\n  Polygamous:\n    text: Polygamous\n  Protandrous:\n    text: Protandrous\n  Protogynous:\n    text: Protogynous\n  Subandroecious:\n    text: Subandroecious\n  Subdioecious:\n    text: Subdioecious\n  Subgynoecious:\n    text: Subgynoecious\n  Synoecious:\n    text: Synoecious\n  Trimonoecious:\n    text: Trimonoecious\n  Trioecious:\n    text: Trioecious\n  Unisexual:\n    text: Unisexual\n\n
"},{"location":"PolarityModeEnum/","title":"Enum: PolarityModeEnum","text":"

URI: PolarityModeEnum

"},{"location":"PolarityModeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description positive None negative None"},{"location":"PolarityModeEnum/#slots","title":"Slots","text":"Name Description polarity_mode the polarity of which ions are generated and detected"},{"location":"PolarityModeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PolarityModeEnum/#schema-source","title":"Schema Source","text":""},{"location":"PolarityModeEnum/#linkml-source","title":"LinkML Source","text":"
name: PolarityModeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  positive:\n    text: positive\n  negative:\n    text: negative\n\n
"},{"location":"Pooling/","title":"Class: Pooling","text":"

physical combination of several instances of like material.

URI: nmdc:Pooling

classDiagram\n  class Pooling\n  click Pooling href \"../Pooling\"\n    MaterialProcessing <|-- Pooling\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  Pooling : alternative_identifiers\n\n  Pooling : description\n\n  Pooling : end_date\n\n  Pooling : has_failure_categorization\n\n      Pooling --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  Pooling : has_input\n\n      Pooling --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  Pooling : has_output\n\n      Pooling --> \"1..*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  Pooling : id\n\n  Pooling : instrument_used\n\n      Pooling --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  Pooling : name\n\n  Pooling : processing_institution\n\n      Pooling --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  Pooling : protocol_link\n\n      Pooling --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  Pooling : qc_comment\n\n  Pooling : qc_status\n\n      Pooling --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  Pooling : start_date\n\n  Pooling : type\n\n\n\n
"},{"location":"Pooling/#inheritance","title":"Inheritance","text":""},{"location":"Pooling/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input 1..* NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output 1..* ProcessedSample An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Pooling/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Pooling/#schema-source","title":"Schema Source","text":""},{"location":"Pooling/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Pooling native nmdc:Pooling exact OBI:0600016"},{"location":"Pooling/#linkml-source","title":"LinkML Source","text":""},{"location":"Pooling/#direct","title":"Direct","text":"
name: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: MaterialProcessing\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 2\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 1\n    maximum_cardinality: 1\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:Pooling\n\n
"},{"location":"Pooling/#induced","title":"Induced","text":"
name: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: MaterialProcessing\nslot_usage:\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 2\n  has_output:\n    name: has_output\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 1\n    maximum_cardinality: 1\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: Pooling\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 2\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    minimum_cardinality: 1\n    maximum_cardinality: 1\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: Pooling\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Pooling\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Pooling\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Pooling\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Pooling\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Pooling\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Pooling\n\n
"},{"location":"PortionOfSubstance/","title":"Class: Portion of a Substance (PortionOfSubstance)","text":"

A portion of any matter of defined composition that has discrete existence, whose origin may be biological, mineral or chemical.

URI: nmdc:PortionOfSubstance

classDiagram\n  class PortionOfSubstance\n  click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  PortionOfSubstance : final_concentration\n\n      PortionOfSubstance --> \"0..1\" QuantityValue : final_concentration\n    click QuantityValue href \"../QuantityValue\"\n\n  PortionOfSubstance : known_as\n\n      PortionOfSubstance --> \"0..1\" ChemicalEntity : known_as\n    click ChemicalEntity href \"../ChemicalEntity\"\n\n  PortionOfSubstance : mass\n\n      PortionOfSubstance --> \"0..1\" QuantityValue : mass\n    click QuantityValue href \"../QuantityValue\"\n\n  PortionOfSubstance : sample_state_information\n\n      PortionOfSubstance --> \"0..1\" SampleStateEnum : sample_state_information\n    click SampleStateEnum href \"../SampleStateEnum\"\n\n  PortionOfSubstance : source_concentration\n\n      PortionOfSubstance --> \"0..1\" QuantityValue : source_concentration\n    click QuantityValue href \"../QuantityValue\"\n\n  PortionOfSubstance : substance_role\n\n      PortionOfSubstance --> \"0..1\" SubstanceRoleEnum : substance_role\n    click SubstanceRoleEnum href \"../SubstanceRoleEnum\"\n\n  PortionOfSubstance : type\n\n  PortionOfSubstance : volume\n\n      PortionOfSubstance --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"PortionOfSubstance/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance final_concentration 0..1 QuantityValue When solutions A (containing substance X) and B are combined together, this s... direct known_as 0..1 ChemicalEntity direct mass 0..1 QuantityValue A physical quality that inheres in a bearer by virtue of the proportion of th... direct sample_state_information 0..1 SampleStateEnum The chemical phase of a pure sample, or the state of a mixed sample direct source_concentration 0..1 QuantityValue When solutions A (containing substance X) and B are combined together, this s... direct substance_role 0..1 SubstanceRoleEnum The role of a substance in a process direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct volume 0..1 QuantityValue The volume of a substance direct"},{"location":"PortionOfSubstance/#usages","title":"Usages","text":"used by used in type used Extraction substances_used range PortionOfSubstance StorageProcess substances_used range PortionOfSubstance DissolvingProcess substances_used range PortionOfSubstance ChemicalConversionProcess substances_used range PortionOfSubstance MobilePhaseSegment substances_used range PortionOfSubstance"},{"location":"PortionOfSubstance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PortionOfSubstance/#schema-source","title":"Schema Source","text":""},{"location":"PortionOfSubstance/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:PortionOfSubstance native nmdc:PortionOfSubstance undefined schema:Substance"},{"location":"PortionOfSubstance/#linkml-source","title":"LinkML Source","text":""},{"location":"PortionOfSubstance/#direct","title":"Direct","text":"
name: PortionOfSubstance\ndescription: A portion of any matter of defined composition that has discrete existence,\n  whose origin may be biological, mineral or chemical.\ntitle: Portion of a Substance\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:Substance\nslots:\n- final_concentration\n- known_as\n- mass\n- sample_state_information\n- source_concentration\n- substance_role\n- type\n- volume\nclass_uri: nmdc:PortionOfSubstance\n\n
"},{"location":"PortionOfSubstance/#induced","title":"Induced","text":"
name: PortionOfSubstance\ndescription: A portion of any matter of defined composition that has discrete existence,\n  whose origin may be biological, mineral or chemical.\ntitle: Portion of a Substance\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:Substance\nattributes:\n  final_concentration:\n    name: final_concentration\n    description: When solutions A (containing substance X) and B are combined together,\n      this slot captures the concentration of X in the combination\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: concentration\n    alias: final_concentration\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: QuantityValue\n  known_as:\n    name: known_as\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: known_as\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: ChemicalEntity\n  mass:\n    name: mass\n    description: A physical quality that inheres in a bearer by virtue of the proportion\n      of the bearer's amount of matter.\n    title: mass\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - PATO:0000125\n    rank: 1000\n    alias: mass\n    owner: PortionOfSubstance\n    domain_of:\n    - SubSamplingProcess\n    - PortionOfSubstance\n    range: QuantityValue\n  sample_state_information:\n    name: sample_state_information\n    description: The chemical phase of a pure sample, or the state of a mixed sample\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: sample_state_information\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: SampleStateEnum\n  source_concentration:\n    name: source_concentration\n    description: When solutions A (containing substance X) and B are combined together,\n      this slot captures the concentration of X in solution A\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: concentration\n    alias: source_concentration\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: QuantityValue\n  substance_role:\n    name: substance_role\n    description: The role of a substance in a process\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substance_role\n    owner: PortionOfSubstance\n    domain_of:\n    - PortionOfSubstance\n    range: SubstanceRoleEnum\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: PortionOfSubstance\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\n  volume:\n    name: volume\n    description: The volume of a substance.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: PortionOfSubstance\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\nclass_uri: nmdc:PortionOfSubstance\n\n
"},{"location":"ProcessedSample/","title":"Class: Processed Sample (ProcessedSample)","text":"

URI: nmdc:ProcessedSample

classDiagram\n  class ProcessedSample\n  click ProcessedSample href \"../ProcessedSample\"\n    MaterialEntity <|-- ProcessedSample\n      click MaterialEntity href \"../MaterialEntity\"\n\n\n\n  ProcessedSample : alternative_identifiers\n\n  ProcessedSample : biomaterial_purity\n\n      ProcessedSample --> \"0..1\" QuantityValue : biomaterial_purity\n    click QuantityValue href \"../QuantityValue\"\n\n  ProcessedSample : description\n\n  ProcessedSample : dna_absorb1\n\n  ProcessedSample : dna_concentration\n\n  ProcessedSample : external_database_identifiers\n\n  ProcessedSample : id\n\n  ProcessedSample : name\n\n  ProcessedSample : type\n\n\n\n
"},{"location":"ProcessedSample/#inheritance","title":"Inheritance","text":""},{"location":"ProcessedSample/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance biomaterial_purity 0..1 QuantityValue direct dna_absorb1 0..1 recommended Float 260/280 measurement of DNA sample purity direct dna_concentration 0..1 recommended Float direct external_database_identifiers * ExternalIdentifier Link to corresponding identifier in external database direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ProcessedSample/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing has_input any_of[range] ProcessedSample MassSpectrometry has_input any_of[range] ProcessedSample Database processed_sample_set range ProcessedSample Pooling has_input any_of[range] ProcessedSample Pooling has_output range ProcessedSample Extraction has_input any_of[range] ProcessedSample Extraction has_output range ProcessedSample LibraryPreparation has_input any_of[range] ProcessedSample LibraryPreparation has_output range ProcessedSample SubSamplingProcess has_input any_of[range] ProcessedSample SubSamplingProcess has_output range ProcessedSample MixingProcess has_input any_of[range] ProcessedSample MixingProcess has_output range ProcessedSample FiltrationProcess has_input any_of[range] ProcessedSample FiltrationProcess has_output range ProcessedSample ChromatographicSeparationProcess has_input any_of[range] ProcessedSample ChromatographicSeparationProcess has_output range ProcessedSample DissolvingProcess has_input any_of[range] ProcessedSample DissolvingProcess has_output range ProcessedSample ChemicalConversionProcess has_input any_of[range] ProcessedSample ChemicalConversionProcess has_output range ProcessedSample MaterialProcessing has_input any_of[range] ProcessedSample MaterialProcessing has_output range ProcessedSample DataGeneration has_input any_of[range] ProcessedSample"},{"location":"ProcessedSample/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProcessedSample/#schema-source","title":"Schema Source","text":""},{"location":"ProcessedSample/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ProcessedSample native nmdc:ProcessedSample"},{"location":"ProcessedSample/#linkml-source","title":"LinkML Source","text":""},{"location":"ProcessedSample/#direct","title":"Direct","text":"
name: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslots:\n- biomaterial_purity\n- dna_absorb1\n- dna_concentration\n- external_database_identifiers\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ProcessedSample\n\n
"},{"location":"ProcessedSample/#induced","title":"Induced","text":"
name: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  biomaterial_purity:\n    name: biomaterial_purity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: biomaterial_purity\n    owner: ProcessedSample\n    domain_of:\n    - ProcessedSample\n    range: QuantityValue\n  dna_absorb1:\n    name: dna_absorb1\n    description: 260/280 measurement of DNA sample purity\n    title: DNA absorbance 260/280\n    comments:\n    - Recommended value is between 1 and 3.\n    examples:\n    - value: '2.02'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 7\n    is_a: biomaterial_purity\n    alias: dna_absorb1\n    owner: ProcessedSample\n    domain_of:\n    - Biosample\n    - ProcessedSample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n  dna_concentration:\n    name: dna_concentration\n    title: DNA concentration in ng/ul\n    comments:\n    - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n      a fluorometric method. Acceptable values are 0-2000.\n    examples:\n    - value: '100'\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:nucleic_acid_concentration\n    rank: 5\n    alias: dna_concentration\n    owner: ProcessedSample\n    domain_of:\n    - Biosample\n    - ProcessedSample\n    slot_group: JGI-Metagenomics\n    range: float\n    recommended: true\n    minimum_value: 0\n    maximum_value: 2000\n  external_database_identifiers:\n    name: external_database_identifiers\n    description: Link to corresponding identifier in external database\n    notes:\n    - had tried ranges of external identifier and string\n    comments:\n    - The value of this field is always a registered CURIE\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - skos:closeMatch\n    rank: 1000\n    is_a: alternative_identifiers\n    abstract: true\n    alias: external_database_identifiers\n    owner: ProcessedSample\n    domain_of:\n    - ProcessedSample\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ProcessedSample\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ProcessedSample\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ProcessedSample\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ProcessedSample\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ProcessedSample\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ProcessedSample\n\n
"},{"location":"ProcessingInstitutionEnum/","title":"Enum: ProcessingInstitutionEnum","text":"

URI: ProcessingInstitutionEnum

"},{"location":"ProcessingInstitutionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UCSD https://ror.org/0168r3w48 JGI https://ror.org/04xm1d337 EMSL https://ror.org/04rc0xn13 Battelle https://ror.org/01h5tnr73 ANL https://ror.org/05gvnxz63 UCD_Genome_Center https://genomecenter.ucdavis.edu/ Azenta https://www.azenta.com/"},{"location":"ProcessingInstitutionEnum/#slots","title":"Slots","text":"Name Description processing_institution The organization that processed the sample"},{"location":"ProcessingInstitutionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProcessingInstitutionEnum/#schema-source","title":"Schema Source","text":""},{"location":"ProcessingInstitutionEnum/#linkml-source","title":"LinkML Source","text":"
name: ProcessingInstitutionEnum\nnotes:\n- use ROR meanings like https://ror.org/0168r3w48 for UCSD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  UCSD:\n    text: UCSD\n    meaning: https://ror.org/0168r3w48\n    title: University of California, San Diego\n  JGI:\n    text: JGI\n    meaning: https://ror.org/04xm1d337\n    title: Joint Genome Institute\n  EMSL:\n    text: EMSL\n    meaning: https://ror.org/04rc0xn13\n    title: Environmental Molecular Sciences Laboratory\n    aliases:\n    - Environmental Molecular Science Laboratory\n    - Environmental Molecular Sciences Lab\n  Battelle:\n    text: Battelle\n    meaning: https://ror.org/01h5tnr73\n    title: Battelle Memorial Institute\n  ANL:\n    text: ANL\n    meaning: https://ror.org/05gvnxz63\n    title: Argonne National Laboratory\n  UCD_Genome_Center:\n    text: UCD_Genome_Center\n    meaning: https://genomecenter.ucdavis.edu/\n    title: University of California, Davis Genome Center\n  Azenta:\n    text: Azenta\n    meaning: https://www.azenta.com/\n    title: Azenta Life Sciences\n\n
"},{"location":"ProfilePositionEnum/","title":"Enum: ProfilePositionEnum","text":"

URI: ProfilePositionEnum

"},{"location":"ProfilePositionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description summit None shoulder None backslope None footslope None toeslope None"},{"location":"ProfilePositionEnum/#slots","title":"Slots","text":"Name Description profile_position Cross-sectional position in the hillslope where sample was collected"},{"location":"ProfilePositionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProfilePositionEnum/#schema-source","title":"Schema Source","text":""},{"location":"ProfilePositionEnum/#linkml-source","title":"LinkML Source","text":"
name: profile_position_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  summit:\n    text: summit\n  shoulder:\n    text: shoulder\n  backslope:\n    text: backslope\n  footslope:\n    text: footslope\n  toeslope:\n    text: toeslope\n\n
"},{"location":"Proteases/","title":"Subset: Proteases","text":"

URI: Proteases

"},{"location":"Proteases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Proteases/#schema-source","title":"Schema Source","text":""},{"location":"ProteinQuantification/","title":"Class: ProteinQuantification","text":"

This is used to link a metaproteomics analysis workflow to a specific protein

URI: nmdc:ProteinQuantification

classDiagram\n  class ProteinQuantification\n  click ProteinQuantification href \"../ProteinQuantification\"\n\n  ProteinQuantification : all_proteins\n\n      ProteinQuantification --> \"*\" GeneProduct : all_proteins\n    click GeneProduct href \"../GeneProduct\"\n\n  ProteinQuantification : best_protein\n\n      ProteinQuantification --> \"0..1\" GeneProduct : best_protein\n    click GeneProduct href \"../GeneProduct\"\n\n  ProteinQuantification : peptide_sequence_count\n\n  ProteinQuantification : protein_spectral_count\n\n  ProteinQuantification : protein_sum_masic_abundance\n\n  ProteinQuantification : type\n\n\n\n
"},{"location":"ProteinQuantification/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance all_proteins * GeneProduct the grouped list of protein identifiers associated with the peptide sequences... direct best_protein 0..1 GeneProduct the specific protein identifier most correctly grouped to its associated pept... direct peptide_sequence_count 0..1 Integer count of peptide sequences grouped to the best_protein direct protein_spectral_count 0..1 Integer sum of filter passing MS2 spectra associated with the best protein within a g... direct protein_sum_masic_abundance 0..1 Integer combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"ProteinQuantification/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProteinQuantification/#schema-source","title":"Schema Source","text":""},{"location":"ProteinQuantification/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ProteinQuantification native nmdc:ProteinQuantification"},{"location":"ProteinQuantification/#linkml-source","title":"LinkML Source","text":""},{"location":"ProteinQuantification/#direct","title":"Direct","text":"
name: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n  protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- all_proteins\n- best_protein\n- peptide_sequence_count\n- protein_spectral_count\n- protein_sum_masic_abundance\n- type\nslot_usage:\n  best_protein:\n    name: best_protein\n    description: the specific protein identifier most correctly grouped to its associated\n      peptide sequences\n  all_proteins:\n    name: all_proteins\n    description: the grouped list of protein identifiers associated with the peptide\n      sequences that were grouped to a best protein\nclass_uri: nmdc:ProteinQuantification\n\n
"},{"location":"ProteinQuantification/#induced","title":"Induced","text":"
name: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n  protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n  best_protein:\n    name: best_protein\n    description: the specific protein identifier most correctly grouped to its associated\n      peptide sequences\n  all_proteins:\n    name: all_proteins\n    description: the grouped list of protein identifiers associated with the peptide\n      sequences that were grouped to a best protein\nattributes:\n  all_proteins:\n    name: all_proteins\n    description: the grouped list of protein identifiers associated with the peptide\n      sequences that were grouped to a best protein\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: all_proteins\n    owner: ProteinQuantification\n    domain_of:\n    - PeptideQuantification\n    - ProteinQuantification\n    range: GeneProduct\n    multivalued: true\n  best_protein:\n    name: best_protein\n    description: the specific protein identifier most correctly grouped to its associated\n      peptide sequences\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: best_protein\n    owner: ProteinQuantification\n    domain_of:\n    - PeptideQuantification\n    - ProteinQuantification\n    range: GeneProduct\n  peptide_sequence_count:\n    name: peptide_sequence_count\n    description: count of peptide sequences grouped to the best_protein\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: peptide_sequence_count\n    owner: ProteinQuantification\n    domain_of:\n    - ProteinQuantification\n    range: integer\n  protein_spectral_count:\n    name: protein_spectral_count\n    description: sum of filter passing MS2 spectra associated with the best protein\n      within a given LC-MS/MS data file\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protein_spectral_count\n    owner: ProteinQuantification\n    domain_of:\n    - ProteinQuantification\n    range: integer\n  protein_sum_masic_abundance:\n    name: protein_sum_masic_abundance\n    description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n      associated with the best protein from a given LC-MS/MS data file using the MASIC\n      tool\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protein_sum_masic_abundance\n    owner: ProteinQuantification\n    domain_of:\n    - ProteinQuantification\n    range: integer\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ProteinQuantification\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ProteinQuantification\n\n
"},{"location":"Protocol/","title":"Class: Protocol","text":"

URI: nmdc:Protocol

classDiagram\n  class Protocol\n  click Protocol href \"../Protocol\"\n\n  Protocol : name\n\n  Protocol : type\n\n  Protocol : url\n\n\n\n
"},{"location":"Protocol/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance url 0..1 String direct name 0..1 String A human readable label for an entity direct type 1 Uriorcurie the class_uri of the class that has been instantiated direct"},{"location":"Protocol/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing protocol_link range Protocol MassSpectrometry protocol_link range Protocol Pooling protocol_link range Protocol Extraction protocol_link range Protocol LibraryPreparation protocol_link range Protocol CollectingBiosamplesFromSite protocol_link range Protocol ProtocolExecution protocol_link range Protocol SubSamplingProcess protocol_link range Protocol MixingProcess protocol_link range Protocol FiltrationProcess protocol_link range Protocol StorageProcess protocol_link range Protocol ChromatographicSeparationProcess protocol_link range Protocol DissolvingProcess protocol_link range Protocol ChemicalConversionProcess protocol_link range Protocol MetagenomeAnnotation protocol_link range Protocol MaterialProcessing protocol_link range Protocol PlannedProcess protocol_link range Protocol Study protocol_link range Protocol DataGeneration protocol_link range Protocol WorkflowExecution protocol_link range Protocol MetagenomeAssembly protocol_link range Protocol MetatranscriptomeAssembly protocol_link range Protocol MetatranscriptomeAnnotation protocol_link range Protocol MetatranscriptomeExpressionAnalysis protocol_link range Protocol MagsAnalysis protocol_link range Protocol MetagenomeSequencing protocol_link range Protocol ReadQcAnalysis protocol_link range Protocol ReadBasedTaxonomyAnalysis protocol_link range Protocol MetabolomicsAnalysis protocol_link range Protocol MetaproteomicsAnalysis protocol_link range Protocol NomAnalysis protocol_link range Protocol"},{"location":"Protocol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Protocol/#schema-source","title":"Schema Source","text":""},{"location":"Protocol/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Protocol native nmdc:Protocol"},{"location":"Protocol/#linkml-source","title":"LinkML Source","text":""},{"location":"Protocol/#direct","title":"Direct","text":"
name: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- url\n- name\n- type\nclass_uri: nmdc:Protocol\n\n
"},{"location":"Protocol/#induced","title":"Induced","text":"
name: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n  url:\n    name: url\n    notes:\n    - See issue 207 - this clashes with the mixs field\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: url\n    owner: Protocol\n    domain_of:\n    - ImageValue\n    - Protocol\n    - DataObject\n    range: string\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Protocol\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Protocol\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Protocol\n\n
"},{"location":"ProtocolCategoryEnum/","title":"Enum: ProtocolCategoryEnum","text":"

The possible protocols that may be followed for an assay.

URI: ProtocolCategoryEnum

"},{"location":"ProtocolCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mplex None derivatization None filter_clean_up None organic_matter_extraction None solid_phase_extraction None phosphorus_extraction None ph_measurement None respiration_measurement None texture_measurement None dna_extraction None phenol_chloroform_extraction None"},{"location":"ProtocolCategoryEnum/#slots","title":"Slots","text":"Name Description protocol_execution_category"},{"location":"ProtocolCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProtocolCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ProtocolCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ProtocolCategoryEnum\ndescription: The possible protocols that may be followed for an assay.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  mplex:\n    text: mplex\n  derivatization:\n    text: derivatization\n  filter_clean_up:\n    text: filter_clean_up\n  organic_matter_extraction:\n    text: organic_matter_extraction\n  solid_phase_extraction:\n    text: solid_phase_extraction\n  phosphorus_extraction:\n    text: phosphorus_extraction\n  ph_measurement:\n    text: ph_measurement\n  respiration_measurement:\n    text: respiration_measurement\n  texture_measurement:\n    text: texture_measurement\n  dna_extraction:\n    text: dna_extraction\n  phenol_chloroform_extraction:\n    text: phenol_chloroform_extraction\n\n
"},{"location":"ProtocolExecution/","title":"Class: ProtocolExecution","text":"

A PlannedProces that has PlannedProcess parts. Can be used to represent the case of someone following a Protocol.

URI: nmdc:ProtocolExecution

classDiagram\n  class ProtocolExecution\n  click ProtocolExecution href \"../ProtocolExecution\"\n    PlannedProcess <|-- ProtocolExecution\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n\n  ProtocolExecution : alternative_identifiers\n\n  ProtocolExecution : description\n\n  ProtocolExecution : end_date\n\n  ProtocolExecution : has_failure_categorization\n\n      ProtocolExecution --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ProtocolExecution : has_input\n\n      ProtocolExecution --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ProtocolExecution : has_output\n\n      ProtocolExecution --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  ProtocolExecution : has_process_parts\n\n      ProtocolExecution --> \"1..*\" PlannedProcess : has_process_parts\n    click PlannedProcess href \"../PlannedProcess\"\n\n  ProtocolExecution : id\n\n  ProtocolExecution : name\n\n  ProtocolExecution : processing_institution\n\n      ProtocolExecution --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ProtocolExecution : protocol_execution_category\n\n      ProtocolExecution --> \"1\" ProtocolCategoryEnum : protocol_execution_category\n    click ProtocolCategoryEnum href \"../ProtocolCategoryEnum\"\n\n  ProtocolExecution : protocol_link\n\n      ProtocolExecution --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ProtocolExecution : qc_comment\n\n  ProtocolExecution : qc_status\n\n      ProtocolExecution --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ProtocolExecution : start_date\n\n  ProtocolExecution : type\n\n\n\n
"},{"location":"ProtocolExecution/#inheritance","title":"Inheritance","text":""},{"location":"ProtocolExecution/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_process_parts 1..* PlannedProcess The MaterialProcessing steps that are discrete parts of the ProtocolExecution direct protocol_execution_category 1 ProtocolCategoryEnum direct has_input * NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ProtocolExecution/#usages","title":"Usages","text":"used by used in type used Database protocol_execution_set range ProtocolExecution"},{"location":"ProtocolExecution/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProtocolExecution/#schema-source","title":"Schema Source","text":""},{"location":"ProtocolExecution/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ProtocolExecution native nmdc:ProtocolExecution"},{"location":"ProtocolExecution/#linkml-source","title":"LinkML Source","text":""},{"location":"ProtocolExecution/#direct","title":"Direct","text":"
name: ProtocolExecution\ndescription: A PlannedProces that has PlannedProcess parts. Can be used to represent\n  the case of someone following a Protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: PlannedProcess\nslots:\n- has_process_parts\n- protocol_execution_category\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_process_parts:\n    name: has_process_parts\n    description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ProtocolExecution\n\n
"},{"location":"ProtocolExecution/#induced","title":"Induced","text":"
name: ProtocolExecution\ndescription: A PlannedProces that has PlannedProcess parts. Can be used to represent\n  the case of someone following a Protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: PlannedProcess\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_process_parts:\n    name: has_process_parts\n    description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  has_process_parts:\n    name: has_process_parts\n    description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    list_elements_ordered: true\n    alias: has_process_parts\n    owner: ProtocolExecution\n    domain_of:\n    - ProtocolExecution\n    range: PlannedProcess\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  protocol_execution_category:\n    name: protocol_execution_category\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_execution_category\n    owner: ProtocolExecution\n    domain_of:\n    - ProtocolExecution\n    range: ProtocolCategoryEnum\n    required: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ProtocolExecution\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ProtocolExecution\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ProtocolExecution\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ProtocolExecution\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ProtocolExecution\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ProtocolExecution\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ProtocolExecution\n\n
"},{"location":"QuadPosEnum/","title":"Enum: QuadPosEnum","text":"

URI: QuadPosEnum

"},{"location":"QuadPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description North side None West side None South side None East side None"},{"location":"QuadPosEnum/#slots","title":"Slots","text":"Name Description quad_pos The quadrant position of the sampling room within the building"},{"location":"QuadPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"QuadPosEnum/#schema-source","title":"Schema Source","text":""},{"location":"QuadPosEnum/#linkml-source","title":"LinkML Source","text":"
name: quad_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  North side:\n    text: North side\n  West side:\n    text: West side\n  South side:\n    text: South side\n  East side:\n    text: East side\n\n
"},{"location":"QuantityValue/","title":"Class: QuantityValue","text":"

A simple quantity, e.g. 2cm

URI: nmdc:QuantityValue

classDiagram\n  class QuantityValue\n  click QuantityValue href \"../QuantityValue\"\n    AttributeValue <|-- QuantityValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  QuantityValue : has_maximum_numeric_value\n\n  QuantityValue : has_minimum_numeric_value\n\n  QuantityValue : has_numeric_value\n\n  QuantityValue : has_raw_value\n\n  QuantityValue : has_unit\n\n  QuantityValue : type\n\n\n\n
"},{"location":"QuantityValue/#inheritance","title":"Inheritance","text":""},{"location":"QuantityValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_maximum_numeric_value 0..1 Decimal The maximum value part, expressed as number, of the quantity value when the v... direct has_minimum_numeric_value 0..1 Decimal The minimum value part, expressed as number, of the quantity value when the v... direct has_numeric_value 0..1 Decimal The number part of the quantity direct has_unit 0..1 Unit The unit of the quantity direct has_raw_value 0..1 String Unnormalized atomic string representation, should in syntax {number} {unit} AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"QuantityValue/#usages","title":"Usages","text":"used by used in type used ChromatographyConfiguration temperature range QuantityValue Extraction input_mass range QuantityValue Extraction volume range QuantityValue SubSamplingProcess container_size range QuantityValue SubSamplingProcess temperature range QuantityValue SubSamplingProcess volume range QuantityValue SubSamplingProcess mass range QuantityValue MixingProcess duration range QuantityValue FiltrationProcess container_size range QuantityValue FiltrationProcess filter_pore_size range QuantityValue FiltrationProcess volume range QuantityValue StorageProcess temperature range QuantityValue ChromatographicSeparationProcess temperature range QuantityValue DissolvingProcess duration range QuantityValue DissolvingProcess temperature range QuantityValue ChemicalConversionProcess duration range QuantityValue ChemicalConversionProcess temperature range QuantityValue ChemicalConversionProcess substances_volume range QuantityValue Biosample abs_air_humidity range QuantityValue Biosample air_temp range QuantityValue Biosample al_sat range QuantityValue Biosample alkalinity range QuantityValue Biosample alkyl_diethers range QuantityValue Biosample alt range QuantityValue Biosample aminopept_act range QuantityValue Biosample ammonium range QuantityValue Biosample ammonium_nitrogen range QuantityValue Biosample amount_light range QuantityValue Biosample annual_precpt range QuantityValue Biosample annual_temp range QuantityValue Biosample api range QuantityValue Biosample avg_dew_point range QuantityValue Biosample avg_temp range QuantityValue Biosample bac_prod range QuantityValue Biosample bac_resp range QuantityValue Biosample bacteria_carb_prod range QuantityValue Biosample barometric_press range QuantityValue Biosample benzene range QuantityValue Biosample biochem_oxygen_dem range QuantityValue Biosample bishomohopanol range QuantityValue Biosample blood_press_diast range QuantityValue Biosample blood_press_syst range QuantityValue Biosample bromide range QuantityValue Biosample built_struc_age range QuantityValue Biosample calcium range QuantityValue Biosample carb_dioxide range QuantityValue Biosample carb_monoxide range QuantityValue Biosample carb_nitro_ratio range QuantityValue Biosample ceil_area range QuantityValue Biosample ceil_thermal_mass range QuantityValue Biosample chem_oxygen_dem range QuantityValue Biosample chloride range QuantityValue Biosample chlorophyll range QuantityValue Biosample conduc range QuantityValue Biosample density range QuantityValue Biosample depth range QuantityValue Biosample dew_point range QuantityValue Biosample diss_carb_dioxide range QuantityValue Biosample diss_hydrogen range QuantityValue Biosample diss_inorg_carb range QuantityValue Biosample diss_inorg_nitro range QuantityValue Biosample diss_inorg_phosp range QuantityValue Biosample diss_iron range QuantityValue Biosample diss_org_carb range QuantityValue Biosample diss_org_nitro range QuantityValue Biosample diss_oxygen range QuantityValue Biosample diss_oxygen_fluid range QuantityValue Biosample door_size range QuantityValue Biosample down_par range QuantityValue Biosample efficiency_percent range QuantityValue Biosample ethylbenzene range QuantityValue Biosample exp_duct range QuantityValue Biosample exp_pipe range QuantityValue Biosample floor_age range QuantityValue Biosample floor_area range QuantityValue Biosample floor_thermal_mass range QuantityValue Biosample fluor range QuantityValue Biosample freq_clean range QuantityValue Biosample freq_cook range QuantityValue Biosample glucosidase_act range QuantityValue Biosample hcr_fw_salinity range QuantityValue Biosample height_carper_fiber range QuantityValue Biosample host_age range QuantityValue Biosample host_body_temp range QuantityValue Biosample host_dry_mass range QuantityValue Biosample host_height range QuantityValue Biosample host_length range QuantityValue Biosample host_tot_mass range QuantityValue Biosample host_wet_mass range QuantityValue Biosample humidity range QuantityValue Biosample indust_eff_percent range QuantityValue Biosample inside_lux range QuantityValue Biosample iwf range QuantityValue Biosample lbc_thirty range QuantityValue Biosample lbceq range QuantityValue Biosample light_intensity range QuantityValue Biosample magnesium range QuantityValue Biosample manganese range QuantityValue Biosample max_occup range QuantityValue Biosample mean_frict_vel range QuantityValue Biosample mean_peak_frict_vel range QuantityValue Biosample methane range QuantityValue Biosample microbial_biomass range QuantityValue Biosample nitrate range QuantityValue Biosample nitrate_nitrogen range QuantityValue Biosample nitrite range QuantityValue Biosample nitrite_nitrogen range QuantityValue Biosample nitro range QuantityValue Biosample number_pets range QuantityValue Biosample number_plants range QuantityValue Biosample number_resident range QuantityValue Biosample occup_density_samp range QuantityValue Biosample occup_samp range QuantityValue Biosample org_carb range QuantityValue Biosample org_matter range QuantityValue Biosample org_nitro range QuantityValue Biosample organism_count range QuantityValue Biosample owc_tvdss range QuantityValue Biosample oxygen range QuantityValue Biosample part_org_carb range QuantityValue Biosample part_org_nitro range QuantityValue Biosample petroleum_hydrocarb range QuantityValue Biosample phosphate range QuantityValue Biosample photon_flux range QuantityValue Biosample potassium range QuantityValue Biosample pour_point range QuantityValue Biosample pressure range QuantityValue Biosample primary_prod range QuantityValue Biosample prod_rate range QuantityValue Biosample redox_potential range QuantityValue Biosample rel_air_humidity range QuantityValue Biosample rel_humidity_out range QuantityValue Biosample room_air_exch_rate range QuantityValue Biosample room_occup range QuantityValue Biosample root_med_ph range QuantityValue Biosample salinity range QuantityValue Biosample samp_md range QuantityValue Biosample samp_size range QuantityValue Biosample samp_store_temp range QuantityValue Biosample season_precpt range QuantityValue Biosample season_temp range QuantityValue Biosample silicate range QuantityValue Biosample size_frac_low range QuantityValue Biosample size_frac_up range QuantityValue Biosample slope_aspect range QuantityValue Biosample slope_gradient range QuantityValue Biosample sludge_retent_time range QuantityValue Biosample sodium range QuantityValue Biosample soil_text_measure range QuantityValue Biosample solar_irradiance range QuantityValue Biosample soluble_react_phosp range QuantityValue Biosample specific_humidity range QuantityValue Biosample sulfate range QuantityValue Biosample sulfate_fw range QuantityValue Biosample sulfide range QuantityValue Biosample surf_humidity range QuantityValue Biosample surf_moisture range QuantityValue Biosample surf_temp range QuantityValue Biosample suspend_part_matter range QuantityValue Biosample tan range QuantityValue Biosample temp range QuantityValue Biosample temp_out range QuantityValue Biosample toluene range QuantityValue Biosample tot_carb range QuantityValue Biosample tot_depth_water_col range QuantityValue Biosample tot_diss_nitro range QuantityValue Biosample tot_inorg_nitro range QuantityValue Biosample tot_iron range QuantityValue Biosample tot_nitro range QuantityValue Biosample tot_nitro_content range QuantityValue Biosample tot_org_carb range QuantityValue Biosample tot_part_carb range QuantityValue Biosample tot_phosp range QuantityValue Biosample tot_phosphate range QuantityValue Biosample tot_sulfur range QuantityValue Biosample turbidity range QuantityValue Biosample tvdss_of_hcr_press range QuantityValue Biosample tvdss_of_hcr_temp range QuantityValue Biosample ventilation_rate range QuantityValue Biosample vfa range QuantityValue Biosample vfa_fw range QuantityValue Biosample wall_area range QuantityValue Biosample wall_height range QuantityValue Biosample wall_thermal_mass range QuantityValue Biosample water_current range QuantityValue Biosample water_cut range QuantityValue Biosample water_feat_size range QuantityValue Biosample water_prod_rate range QuantityValue Biosample wind_speed range QuantityValue Biosample xylene range QuantityValue Biosample zinc range QuantityValue Biosample subsurface_depth range QuantityValue Biosample bulk_elect_conductivity range QuantityValue MobilePhaseSegment duration range QuantityValue MobilePhaseSegment volume range QuantityValue PortionOfSubstance final_concentration range QuantityValue PortionOfSubstance mass range QuantityValue PortionOfSubstance source_concentration range QuantityValue PortionOfSubstance volume range QuantityValue ProcessedSample biomaterial_purity range QuantityValue"},{"location":"QuantityValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"QuantityValue/#schema-source","title":"Schema Source","text":""},{"location":"QuantityValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:QuantityValue native nmdc:QuantityValue undefined schema:QuantityValue"},{"location":"QuantityValue/#linkml-source","title":"LinkML Source","text":""},{"location":"QuantityValue/#direct","title":"Direct","text":"
name: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslots:\n- has_maximum_numeric_value\n- has_minimum_numeric_value\n- has_numeric_value\n- has_unit\nslot_usage:\n  has_raw_value:\n    name: has_raw_value\n    description: Unnormalized atomic string representation, should in syntax {number}\n      {unit}\n  has_unit:\n    name: has_unit\n    description: The unit of the quantity\n  has_numeric_value:\n    name: has_numeric_value\n    description: The number part of the quantity\nclass_uri: nmdc:QuantityValue\n\n
"},{"location":"QuantityValue/#induced","title":"Induced","text":"
name: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslot_usage:\n  has_raw_value:\n    name: has_raw_value\n    description: Unnormalized atomic string representation, should in syntax {number}\n      {unit}\n  has_unit:\n    name: has_unit\n    description: The unit of the quantity\n  has_numeric_value:\n    name: has_numeric_value\n    description: The number part of the quantity\nattributes:\n  has_maximum_numeric_value:\n    name: has_maximum_numeric_value\n    description: The maximum value part, expressed as number, of the quantity value\n      when the value covers a range.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: has_numeric_value\n    alias: has_maximum_numeric_value\n    owner: QuantityValue\n    domain_of:\n    - QuantityValue\n    range: decimal\n  has_minimum_numeric_value:\n    name: has_minimum_numeric_value\n    description: The minimum value part, expressed as number, of the quantity value\n      when the value covers a range.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: has_numeric_value\n    alias: has_minimum_numeric_value\n    owner: QuantityValue\n    domain_of:\n    - QuantityValue\n    range: decimal\n  has_numeric_value:\n    name: has_numeric_value\n    description: The number part of the quantity\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - qud:quantityValue\n    - schema:value\n    rank: 1000\n    alias: has_numeric_value\n    owner: QuantityValue\n    domain_of:\n    - QuantityValue\n    range: decimal\n  has_unit:\n    name: has_unit\n    description: The unit of the quantity\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - scale\n    mappings:\n    - qud:unit\n    - schema:unitCode\n    rank: 1000\n    alias: has_unit\n    owner: QuantityValue\n    domain_of:\n    - QuantityValue\n    range: unit\n  has_raw_value:\n    name: has_raw_value\n    description: Unnormalized atomic string representation, should in syntax {number}\n      {unit}\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: QuantityValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: QuantityValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:QuantityValue\n\n
"},{"location":"RNASampleFormatEnum/","title":"Enum: RNASampleFormatEnum","text":"

URI: RNASampleFormatEnum

"},{"location":"RNASampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"RNASampleFormatEnum/#slots","title":"Slots","text":"Name Description rna_sample_format Solution in which the RNA sample has been suspended"},{"location":"RNASampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RNASampleFormatEnum/#schema-source","title":"Schema Source","text":""},{"location":"RNASampleFormatEnum/#linkml-source","title":"LinkML Source","text":"
name: RNASampleFormatEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  10 mM Tris-HCl:\n    text: 10 mM Tris-HCl\n  DNAStable:\n    text: DNAStable\n  Ethanol:\n    text: Ethanol\n  Low EDTA TE:\n    text: Low EDTA TE\n  MDA reaction buffer:\n    text: MDA reaction buffer\n  PBS:\n    text: PBS\n  Pellet:\n    text: Pellet\n  RNAStable:\n    text: RNAStable\n  TE:\n    text: TE\n  Water:\n    text: Water\n  Gentegra-DNA:\n    text: Gentegra-DNA\n  Gentegra-RNA:\n    text: Gentegra-RNA\n\n
"},{"location":"ReadBasedTaxonomyAnalysis/","title":"Class: Read based analysis activity (ReadBasedTaxonomyAnalysis)","text":"

A workflow execution activity that performs taxonomy classification using sequencing reads

URI: nmdc:ReadBasedTaxonomyAnalysis

classDiagram\n  class ReadBasedTaxonomyAnalysis\n  click ReadBasedTaxonomyAnalysis href \"../ReadBasedTaxonomyAnalysis\"\n    WorkflowExecution <|-- ReadBasedTaxonomyAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  ReadBasedTaxonomyAnalysis : alternative_identifiers\n\n  ReadBasedTaxonomyAnalysis : description\n\n  ReadBasedTaxonomyAnalysis : end_date\n\n  ReadBasedTaxonomyAnalysis : ended_at_time\n\n  ReadBasedTaxonomyAnalysis : execution_resource\n\n      ReadBasedTaxonomyAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  ReadBasedTaxonomyAnalysis : git_url\n\n  ReadBasedTaxonomyAnalysis : has_failure_categorization\n\n      ReadBasedTaxonomyAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ReadBasedTaxonomyAnalysis : has_input\n\n      ReadBasedTaxonomyAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ReadBasedTaxonomyAnalysis : has_output\n\n      ReadBasedTaxonomyAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  ReadBasedTaxonomyAnalysis : id\n\n  ReadBasedTaxonomyAnalysis : name\n\n  ReadBasedTaxonomyAnalysis : processing_institution\n\n      ReadBasedTaxonomyAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ReadBasedTaxonomyAnalysis : protocol_link\n\n      ReadBasedTaxonomyAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ReadBasedTaxonomyAnalysis : qc_comment\n\n  ReadBasedTaxonomyAnalysis : qc_status\n\n      ReadBasedTaxonomyAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ReadBasedTaxonomyAnalysis : start_date\n\n  ReadBasedTaxonomyAnalysis : started_at_time\n\n  ReadBasedTaxonomyAnalysis : type\n\n  ReadBasedTaxonomyAnalysis : version\n\n  ReadBasedTaxonomyAnalysis : was_informed_by\n\n      ReadBasedTaxonomyAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"ReadBasedTaxonomyAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"ReadBasedTaxonomyAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ReadBasedTaxonomyAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ReadBasedTaxonomyAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"ReadBasedTaxonomyAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ReadBasedTaxonomyAnalysis native nmdc:ReadBasedTaxonomyAnalysis"},{"location":"ReadBasedTaxonomyAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"ReadBasedTaxonomyAnalysis/#direct","title":"Direct","text":"
name: ReadBasedTaxonomyAnalysis\ndescription: A workflow execution activity that performs taxonomy classification using\n  sequencing reads\ntitle: Read based analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ReadBasedTaxonomyAnalysis\n\n
"},{"location":"ReadBasedTaxonomyAnalysis/#induced","title":"Induced","text":"
name: ReadBasedTaxonomyAnalysis\ndescription: A workflow execution activity that performs taxonomy classification using\n  sequencing reads\ntitle: Read based analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ReadBasedTaxonomyAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ReadBasedTaxonomyAnalysis\n\n
"},{"location":"ReadQcAnalysis/","title":"Class: Read quality control analysis activity (ReadQcAnalysis)","text":"

A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal

URI: nmdc:ReadQcAnalysis

classDiagram\n  class ReadQcAnalysis\n  click ReadQcAnalysis href \"../ReadQcAnalysis\"\n    WorkflowExecution <|-- ReadQcAnalysis\n      click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n  ReadQcAnalysis : alternative_identifiers\n\n  ReadQcAnalysis : description\n\n  ReadQcAnalysis : end_date\n\n  ReadQcAnalysis : ended_at_time\n\n  ReadQcAnalysis : execution_resource\n\n      ReadQcAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n    click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n  ReadQcAnalysis : git_url\n\n  ReadQcAnalysis : has_failure_categorization\n\n      ReadQcAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  ReadQcAnalysis : has_input\n\n      ReadQcAnalysis --> \"1..*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  ReadQcAnalysis : has_output\n\n      ReadQcAnalysis --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  ReadQcAnalysis : id\n\n  ReadQcAnalysis : input_base_count\n\n  ReadQcAnalysis : input_read_bases\n\n  ReadQcAnalysis : input_read_count\n\n  ReadQcAnalysis : name\n\n  ReadQcAnalysis : output_base_count\n\n  ReadQcAnalysis : output_read_bases\n\n  ReadQcAnalysis : output_read_count\n\n  ReadQcAnalysis : processing_institution\n\n      ReadQcAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  ReadQcAnalysis : protocol_link\n\n      ReadQcAnalysis --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  ReadQcAnalysis : qc_comment\n\n  ReadQcAnalysis : qc_status\n\n      ReadQcAnalysis --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  ReadQcAnalysis : start_date\n\n  ReadQcAnalysis : started_at_time\n\n  ReadQcAnalysis : type\n\n  ReadQcAnalysis : version\n\n  ReadQcAnalysis : was_informed_by\n\n      ReadQcAnalysis --> \"1\" DataGeneration : was_informed_by\n    click DataGeneration href \"../DataGeneration\"\n\n\n\n
"},{"location":"ReadQcAnalysis/#inheritance","title":"Inheritance","text":""},{"location":"ReadQcAnalysis/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance input_base_count 0..1 Float The nucleotide base count number of input reads for QC analysis direct input_read_bases 0..1 Float TODO direct input_read_count 0..1 Float The sequence count number of input reads for QC analysis direct output_base_count 0..1 Float After QC analysis nucleotide base count number direct output_read_bases 0..1 Float TODO direct output_read_count 0..1 Float After QC analysis sequence count number direct ended_at_time 0..1 String WorkflowExecution execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed WorkflowExecution git_url 1 String The url that points to the exact github location of a workflow WorkflowExecution started_at_time 1 String WorkflowExecution version 0..1 String WorkflowExecution was_informed_by 1 DataGeneration WorkflowExecution has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"ReadQcAnalysis/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ReadQcAnalysis/#schema-source","title":"Schema Source","text":""},{"location":"ReadQcAnalysis/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:ReadQcAnalysis native nmdc:ReadQcAnalysis"},{"location":"ReadQcAnalysis/#linkml-source","title":"LinkML Source","text":""},{"location":"ReadQcAnalysis/#direct","title":"Direct","text":"
name: ReadQcAnalysis\ndescription: A workflow execution activity that performs quality control on raw Illumina\n  reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n  spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- input_base_count\n- input_read_bases\n- input_read_count\n- output_base_count\n- output_read_bases\n- output_read_count\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:ReadQcAnalysis\n\n
"},{"location":"ReadQcAnalysis/#induced","title":"Induced","text":"
name: ReadQcAnalysis\ndescription: A workflow execution activity that performs quality control on raw Illumina\n  reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n  spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  was_informed_by:\n    name: was_informed_by\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  input_base_count:\n    name: input_base_count\n    description: The nucleotide base count number of input reads for QC analysis.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: read_qc_analysis_statistic\n    alias: input_base_count\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  input_read_bases:\n    name: input_read_bases\n    description: 'TODO      '\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: input_read_bases\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  input_read_count:\n    name: input_read_count\n    description: The sequence count number of input reads for QC analysis.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: read_qc_analysis_statistic\n    alias: input_read_count\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  output_base_count:\n    name: output_base_count\n    description: After QC analysis nucleotide base count number.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: read_qc_analysis_statistic\n    alias: output_base_count\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  output_read_bases:\n    name: output_read_bases\n    description: TODO\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: output_read_bases\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  output_read_count:\n    name: output_read_count\n    description: After QC analysis sequence count number.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: read_qc_analysis_statistic\n    alias: output_read_count\n    owner: ReadQcAnalysis\n    domain_of:\n    - ReadQcAnalysis\n    range: float\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: ReadQcAnalysis\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: ReadQcAnalysis\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ReadQcAnalysis\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: ReadQcAnalysis\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: ReadQcAnalysis\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: ReadQcAnalysis\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: ReadQcAnalysis\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:ReadQcAnalysis\n\n
"},{"location":"RelSampLocEnum/","title":"Enum: RelSampLocEnum","text":"

URI: RelSampLocEnum

"},{"location":"RelSampLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description edge of car None center of car None under a seat None"},{"location":"RelSampLocEnum/#slots","title":"Slots","text":"Name Description rel_samp_loc The sampling location within the train car"},{"location":"RelSampLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RelSampLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"RelSampLocEnum/#linkml-source","title":"LinkML Source","text":"
name: rel_samp_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  edge of car:\n    text: edge of car\n  center of car:\n    text: center of car\n  under a seat:\n    text: under a seat\n\n
"},{"location":"ResolutionCategoryEnum/","title":"Enum: ResolutionCategoryEnum","text":"

URI: ResolutionCategoryEnum

"},{"location":"ResolutionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description high None higher than unit resolution low None at unit resolution"},{"location":"ResolutionCategoryEnum/#slots","title":"Slots","text":"Name Description resolution_categories The relative resolution at which spectra were collected"},{"location":"ResolutionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ResolutionCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"ResolutionCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: ResolutionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  high:\n    text: high\n    description: higher than unit resolution\n  low:\n    text: low\n    description: at unit resolution\n\n
"},{"location":"RoomCondtEnum/","title":"Enum: RoomCondtEnum","text":"

URI: RoomCondtEnum

"},{"location":"RoomCondtEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None visible signs of mold/mildew None"},{"location":"RoomCondtEnum/#slots","title":"Slots","text":"Name Description room_condt The condition of the room at the time of sampling"},{"location":"RoomCondtEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomCondtEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomCondtEnum/#linkml-source","title":"LinkML Source","text":"
name: room_condt_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  new:\n    text: new\n  visible wear:\n    text: visible wear\n  needs repair:\n    text: needs repair\n  damaged:\n    text: damaged\n  rupture:\n    text: rupture\n  visible signs of mold/mildew:\n    text: visible signs of mold/mildew\n\n
"},{"location":"RoomConnectedEnum/","title":"Enum: RoomConnectedEnum","text":"

URI: RoomConnectedEnum

"},{"location":"RoomConnectedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None office None stairwell None"},{"location":"RoomConnectedEnum/#slots","title":"Slots","text":"Name Description room_connected List of rooms connected to the sampling room by a doorway"},{"location":"RoomConnectedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomConnectedEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomConnectedEnum/#linkml-source","title":"LinkML Source","text":"
name: room_connected_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  attic:\n    text: attic\n  bathroom:\n    text: bathroom\n  closet:\n    text: closet\n  conference room:\n    text: conference room\n  elevator:\n    text: elevator\n  examining room:\n    text: examining room\n  hallway:\n    text: hallway\n  kitchen:\n    text: kitchen\n  mail room:\n    text: mail room\n  office:\n    text: office\n  stairwell:\n    text: stairwell\n\n
"},{"location":"RoomLocEnum/","title":"Enum: RoomLocEnum","text":"

URI: RoomLocEnum

"},{"location":"RoomLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description corner room None interior room None exterior wall None"},{"location":"RoomLocEnum/#slots","title":"Slots","text":"Name Description room_loc The position of the room within the building"},{"location":"RoomLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomLocEnum/#linkml-source","title":"LinkML Source","text":"
name: room_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  corner room:\n    text: corner room\n  interior room:\n    text: interior room\n  exterior wall:\n    text: exterior wall\n\n
"},{"location":"RoomSampPosEnum/","title":"Enum: RoomSampPosEnum","text":"

URI: RoomSampPosEnum

"},{"location":"RoomSampPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north corner None south corner None west corner None east corner None northeast corner None northwest corner None southeast corner None southwest corner None center None"},{"location":"RoomSampPosEnum/#slots","title":"Slots","text":"Name Description room_samp_pos The horizontal sampling position in the room relative to architectural elemen..."},{"location":"RoomSampPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomSampPosEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomSampPosEnum/#linkml-source","title":"LinkML Source","text":"
name: room_samp_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north corner:\n    text: north corner\n  south corner:\n    text: south corner\n  west corner:\n    text: west corner\n  east corner:\n    text: east corner\n  northeast corner:\n    text: northeast corner\n  northwest corner:\n    text: northwest corner\n  southeast corner:\n    text: southeast corner\n  southwest corner:\n    text: southwest corner\n  center:\n    text: center\n\n
"},{"location":"RoomTypeEnum/","title":"Enum: RoomTypeEnum","text":"

URI: RoomTypeEnum

"},{"location":"RoomTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None private office None open office None stairwell None ,restroom None lobby None vestibule None mechanical or electrical room None data center None laboratory_wet None laboratory_dry None gymnasium None natatorium None auditorium None lockers None cafe None warehouse None"},{"location":"RoomTypeEnum/#slots","title":"Slots","text":"Name Description room_type The main purpose or activity of the sampling room"},{"location":"RoomTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"RoomTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: room_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  attic:\n    text: attic\n  bathroom:\n    text: bathroom\n  closet:\n    text: closet\n  conference room:\n    text: conference room\n  elevator:\n    text: elevator\n  examining room:\n    text: examining room\n  hallway:\n    text: hallway\n  kitchen:\n    text: kitchen\n  mail room:\n    text: mail room\n  private office:\n    text: private office\n  open office:\n    text: open office\n  stairwell:\n    text: stairwell\n  ',restroom':\n    text: ',restroom'\n  lobby:\n    text: lobby\n  vestibule:\n    text: vestibule\n  mechanical or electrical room:\n    text: mechanical or electrical room\n  data center:\n    text: data center\n  laboratory_wet:\n    text: laboratory_wet\n  laboratory_dry:\n    text: laboratory_dry\n  gymnasium:\n    text: gymnasium\n  natatorium:\n    text: natatorium\n  auditorium:\n    text: auditorium\n  lockers:\n    text: lockers\n  cafe:\n    text: cafe\n  warehouse:\n    text: warehouse\n\n
"},{"location":"SampCaptStatusEnum/","title":"Enum: SampCaptStatusEnum","text":"

URI: SampCaptStatusEnum

"},{"location":"SampCaptStatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description active surveillance in response to an outbreak None active surveillance not initiated by an outbreak None farm sample None market sample None other None"},{"location":"SampCaptStatusEnum/#slots","title":"Slots","text":"Name Description samp_capt_status Reason for the sample"},{"location":"SampCaptStatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCaptStatusEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampCaptStatusEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_capt_status_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  active surveillance in response to an outbreak:\n    text: active surveillance in response to an outbreak\n  active surveillance not initiated by an outbreak:\n    text: active surveillance not initiated by an outbreak\n  farm sample:\n    text: farm sample\n  market sample:\n    text: market sample\n  other:\n    text: other\n\n
"},{"location":"SampCollectPointEnum/","title":"Enum: SampCollectPointEnum","text":"

URI: SampCollectPointEnum

"},{"location":"SampCollectPointEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description well None test well None drilling rig None wellhead None separator None storage tank None other None"},{"location":"SampCollectPointEnum/#slots","title":"Slots","text":"Name Description samp_collect_point Sampling point on the asset were sample was collected (e"},{"location":"SampCollectPointEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCollectPointEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampCollectPointEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_collect_point_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  well:\n    text: well\n  test well:\n    text: test well\n  drilling rig:\n    text: drilling rig\n  wellhead:\n    text: wellhead\n  separator:\n    text: separator\n  storage tank:\n    text: storage tank\n  other:\n    text: other\n\n
"},{"location":"SampDisStageEnum/","title":"Enum: SampDisStageEnum","text":"

URI: SampDisStageEnum

"},{"location":"SampDisStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dissemination None growth and reproduction None infection None inoculation None penetration None other None"},{"location":"SampDisStageEnum/#slots","title":"Slots","text":"Name Description samp_dis_stage Stage of the disease at the time of sample collection, e"},{"location":"SampDisStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampDisStageEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampDisStageEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_dis_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  dissemination:\n    text: dissemination\n  growth and reproduction:\n    text: growth and reproduction\n  infection:\n    text: infection\n  inoculation:\n    text: inoculation\n  penetration:\n    text: penetration\n  other:\n    text: other\n\n
"},{"location":"SampFloorEnum/","title":"Enum: SampFloorEnum","text":"

URI: SampFloorEnum

"},{"location":"SampFloorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 1st floor None 2nd floor None basement None lobby None"},{"location":"SampFloorEnum/#slots","title":"Slots","text":"Name Description samp_floor The floor of the building, where the sampling room is located"},{"location":"SampFloorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampFloorEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampFloorEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_floor_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  1st floor:\n    text: 1st floor\n  2nd floor:\n    text: 2nd floor\n  basement:\n    text: basement\n  lobby:\n    text: lobby\n\n
"},{"location":"SampMdEnum/","title":"Enum: SampMdEnum","text":"

URI: SampMdEnum

"},{"location":"SampMdEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DF None RT None KB None MSL None other None"},{"location":"SampMdEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampMdEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampMdEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_md_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  DF:\n    text: DF\n  RT:\n    text: RT\n  KB:\n    text: KB\n  MSL:\n    text: MSL\n  other:\n    text: other\n\n
"},{"location":"SampSubtypeEnum/","title":"Enum: SampSubtypeEnum","text":"

URI: SampSubtypeEnum

"},{"location":"SampSubtypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description oil phase None water phase None biofilm None not applicable None other None"},{"location":"SampSubtypeEnum/#slots","title":"Slots","text":"Name Description samp_subtype Name of sample sub-type"},{"location":"SampSubtypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampSubtypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampSubtypeEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_subtype_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  oil phase:\n    text: oil phase\n  water phase:\n    text: water phase\n  biofilm:\n    text: biofilm\n  not applicable:\n    text: not applicable\n  other:\n    text: other\n\n
"},{"location":"SampWeatherEnum/","title":"Enum: SampWeatherEnum","text":"

URI: SampWeatherEnum

"},{"location":"SampWeatherEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clear sky None cloudy None foggy None hail None rain None snow None sleet None sunny None windy None"},{"location":"SampWeatherEnum/#slots","title":"Slots","text":"Name Description samp_weather The weather on the sampling day"},{"location":"SampWeatherEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampWeatherEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampWeatherEnum/#linkml-source","title":"LinkML Source","text":"
name: samp_weather_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  clear sky:\n    text: clear sky\n  cloudy:\n    text: cloudy\n  foggy:\n    text: foggy\n  hail:\n    text: hail\n  rain:\n    text: rain\n  snow:\n    text: snow\n  sleet:\n    text: sleet\n  sunny:\n    text: sunny\n  windy:\n    text: windy\n\n
"},{"location":"SamplePortionEnum/","title":"Enum: SamplePortionEnum","text":"

URI: SamplePortionEnum

"},{"location":"SamplePortionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description supernatant None pellet None organic_layer None aqueous_layer None non_polar_layer None"},{"location":"SamplePortionEnum/#slots","title":"Slots","text":"Name Description sampled_portion The portion of the sample that is taken for downstream activity"},{"location":"SamplePortionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SamplePortionEnum/#schema-source","title":"Schema Source","text":""},{"location":"SamplePortionEnum/#linkml-source","title":"LinkML Source","text":"
name: SamplePortionEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  supernatant:\n    text: supernatant\n    aliases:\n    - top_layer\n  pellet:\n    text: pellet\n    aliases:\n    - bottom_layer\n  organic_layer:\n    text: organic_layer\n  aqueous_layer:\n    text: aqueous_layer\n  non_polar_layer:\n    text: non_polar_layer\n\n
"},{"location":"SampleStateEnum/","title":"Enum: SampleStateEnum","text":"

URI: SampleStateEnum

"},{"location":"SampleStateEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description solid None liquid None gas None"},{"location":"SampleStateEnum/#slots","title":"Slots","text":"Name Description sample_state_information The chemical phase of a pure sample, or the state of a mixed sample"},{"location":"SampleStateEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleStateEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampleStateEnum/#linkml-source","title":"LinkML Source","text":"
name: SampleStateEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  solid:\n    text: solid\n  liquid:\n    text: liquid\n  gas:\n    text: gas\n\n
"},{"location":"SampleSubset/","title":"Subset: SampleSubset","text":"

Subset consisting of entities linked to the processing of samples. Currently, this subset consists of study, omics process, and biosample.

URI: SampleSubset

"},{"location":"SampleSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleSubset/#schema-source","title":"Schema Source","text":""},{"location":"SampleSubset/#classes-in-subset","title":"Classes in subset","text":"Class Description Biosample Biological source material which can be characterized by an experiment DataGeneration The methods and processes used to generate omics data from a biosample or org... Study A study summarizes the overall goal of a research initiative and outlines the..."},{"location":"SampleTypeEnum/","title":"Enum: SampleTypeEnum","text":"

URI: SampleTypeEnum

"},{"location":"SampleTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description soil None soil - water extract None plant associated None sediment None water None"},{"location":"SampleTypeEnum/#slots","title":"Slots","text":"Name Description sample_type Type of sample being submitted"},{"location":"SampleTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SampleTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: SampleTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  soil:\n    text: soil\n  soil - water extract:\n    text: soil - water extract\n  plant associated:\n    text: plant associated\n  sediment:\n    text: sediment\n  water:\n    text: water\n\n
"},{"location":"SeasonUseEnum/","title":"Enum: SeasonUseEnum","text":"

URI: SeasonUseEnum

"},{"location":"SeasonUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Spring None Summer None Fall None Winter None"},{"location":"SeasonUseEnum/#slots","title":"Slots","text":"Name Description season_use The seasons the space is occupied"},{"location":"SeasonUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeasonUseEnum/#schema-source","title":"Schema Source","text":""},{"location":"SeasonUseEnum/#linkml-source","title":"LinkML Source","text":"
name: season_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Spring:\n    text: Spring\n  Summer:\n    text: Summer\n  Fall:\n    text: Fall\n  Winter:\n    text: Winter\n\n
"},{"location":"SedimentTypeEnum/","title":"Enum: SedimentTypeEnum","text":"

URI: SedimentTypeEnum

"},{"location":"SedimentTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description biogenous None cosmogenous None hydrogenous None lithogenous None"},{"location":"SedimentTypeEnum/#slots","title":"Slots","text":"Name Description sediment_type Information about the sediment type based on major constituents"},{"location":"SedimentTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SedimentTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SedimentTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: sediment_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  biogenous:\n    text: biogenous\n  cosmogenous:\n    text: cosmogenous\n  hydrogenous:\n    text: hydrogenous\n  lithogenous:\n    text: lithogenous\n\n
"},{"location":"SeparationMethodEnum/","title":"Enum: SeparationMethodEnum","text":"

The tool/substance used to separate or filter a solution or mixture.

URI: SeparationMethodEnum

"},{"location":"SeparationMethodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ptfe_96_well_filter_plate None syringe None"},{"location":"SeparationMethodEnum/#slots","title":"Slots","text":"Name Description separation_method The method that was used to separate a substance from a solution or mixture"},{"location":"SeparationMethodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeparationMethodEnum/#schema-source","title":"Schema Source","text":""},{"location":"SeparationMethodEnum/#linkml-source","title":"LinkML Source","text":"
name: SeparationMethodEnum\ndescription: The tool/substance used to separate or filter a solution or mixture.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\npermissible_values:\n  ptfe_96_well_filter_plate:\n    text: ptfe_96_well_filter_plate\n  syringe:\n    text: syringe\n\n
"},{"location":"Sequencing/","title":"Subset: Sequencing","text":"

URI: Sequencing

"},{"location":"Sequencing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Sequencing/#schema-source","title":"Schema Source","text":""},{"location":"ShadingDeviceCondEnum/","title":"Enum: ShadingDeviceCondEnum","text":"

URI: ShadingDeviceCondEnum

"},{"location":"ShadingDeviceCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"ShadingDeviceCondEnum/#slots","title":"Slots","text":"Name Description shading_device_cond The physical condition of the shading device at the time of sampling"},{"location":"ShadingDeviceCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"ShadingDeviceCondEnum/#linkml-source","title":"LinkML Source","text":"
name: shading_device_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  damaged:\n    text: damaged\n  needs repair:\n    text: needs repair\n  new:\n    text: new\n  rupture:\n    text: rupture\n  visible wear:\n    text: visible wear\n\n
"},{"location":"ShadingDeviceTypeEnum/","title":"Enum: ShadingDeviceTypeEnum","text":"

URI: ShadingDeviceTypeEnum

"},{"location":"ShadingDeviceTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bahama shutters None exterior roll blind None gambrel awning None hood awning None porchroller awning None sarasota shutters None slatted aluminum None solid aluminum awning None sun screen None tree None trellis None venetian awning None"},{"location":"ShadingDeviceTypeEnum/#slots","title":"Slots","text":"Name Description shading_device_type The type of shading device"},{"location":"ShadingDeviceTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"ShadingDeviceTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: shading_device_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  bahama shutters:\n    text: bahama shutters\n  exterior roll blind:\n    text: exterior roll blind\n  gambrel awning:\n    text: gambrel awning\n  hood awning:\n    text: hood awning\n  porchroller awning:\n    text: porchroller awning\n  sarasota shutters:\n    text: sarasota shutters\n  slatted aluminum:\n    text: slatted aluminum\n  solid aluminum awning:\n    text: solid aluminum awning\n  sun screen:\n    text: sun screen\n  tree:\n    text: tree\n  trellis:\n    text: trellis\n  venetian awning:\n    text: venetian awning\n\n
"},{"location":"Site/","title":"Class: Site (Site)","text":"

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:Site

classDiagram\n  class Site\n  click Site href \"../Site\"\n    MaterialEntity <|-- Site\n      click MaterialEntity href \"../MaterialEntity\"\n\n\n    Site <|-- FieldResearchSite\n      click FieldResearchSite href \"../FieldResearchSite\"\n\n\n\n  Site : alternative_identifiers\n\n  Site : description\n\n  Site : id\n\n  Site : name\n\n  Site : type\n\n\n\n
"},{"location":"Site/#inheritance","title":"Inheritance","text":""},{"location":"Site/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Site/#usages","title":"Usages","text":"used by used in type used CollectingBiosamplesFromSite has_input range Site"},{"location":"Site/#comments","title":"Comments","text":""},{"location":"Site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Site/#schema-source","title":"Schema Source","text":""},{"location":"Site/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Site native nmdc:Site"},{"location":"Site/#linkml-source","title":"LinkML Source","text":""},{"location":"Site/#direct","title":"Direct","text":"
name: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nclass_uri: nmdc:Site\n\n
"},{"location":"Site/#induced","title":"Induced","text":"
name: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nattributes:\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Site\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Site\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Site\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Site\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Site\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Site\n\n
"},{"location":"SoilHorizonEnum/","title":"Enum: SoilHorizonEnum","text":"

URI: SoilHorizonEnum

"},{"location":"SoilHorizonEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description O horizon None A horizon None E horizon None B horizon None C horizon None R layer None Permafrost None M horizon None"},{"location":"SoilHorizonEnum/#slots","title":"Slots","text":"Name Description soil_horizon Specific layer in the land area which measures parallel to the soil surface a..."},{"location":"SoilHorizonEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SoilHorizonEnum/#schema-source","title":"Schema Source","text":""},{"location":"SoilHorizonEnum/#linkml-source","title":"LinkML Source","text":"
name: soil_horizon_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  O horizon:\n    text: O horizon\n  A horizon:\n    text: A horizon\n  E horizon:\n    text: E horizon\n  B horizon:\n    text: B horizon\n  C horizon:\n    text: C horizon\n  R layer:\n    text: R layer\n  Permafrost:\n    text: Permafrost\n  M horizon:\n    text: M horizon\n\n
"},{"location":"Sparqlpath/","title":"Type: Sparqlpath","text":"

A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.

URI: xsd:string

"},{"location":"Sparqlpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Sparqlpath/#schema-source","title":"Schema Source","text":""},{"location":"Sparqlpath/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:sparqlpath"},{"location":"SpecificEnum/","title":"Enum: SpecificEnum","text":"

URI: SpecificEnum

"},{"location":"SpecificEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None photos None"},{"location":"SpecificEnum/#slots","title":"Slots","text":"Name Description specific The building specifications"},{"location":"SpecificEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SpecificEnum/#schema-source","title":"Schema Source","text":""},{"location":"SpecificEnum/#linkml-source","title":"LinkML Source","text":"
name: specific_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  operation:\n    text: operation\n  as built:\n    text: as built\n  construction:\n    text: construction\n  bid:\n    text: bid\n  design:\n    text: design\n  photos:\n    text: photos\n\n
"},{"location":"SrDepEnvEnum/","title":"Enum: SrDepEnvEnum","text":"

URI: SrDepEnvEnum

"},{"location":"SrDepEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Lacustine None Fluvioldeltaic None Fluviomarine None Marine None other None"},{"location":"SrDepEnvEnum/#slots","title":"Slots","text":"Name Description sr_dep_env Source rock depositional environment (https://en"},{"location":"SrDepEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrDepEnvEnum/#schema-source","title":"Schema Source","text":""},{"location":"SrDepEnvEnum/#linkml-source","title":"LinkML Source","text":"
name: sr_dep_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Lacustine:\n    text: Lacustine\n  Fluvioldeltaic:\n    text: Fluvioldeltaic\n  Fluviomarine:\n    text: Fluviomarine\n  Marine:\n    text: Marine\n  other:\n    text: other\n\n
"},{"location":"SrGeolAgeEnum/","title":"Enum: SrGeolAgeEnum","text":"

URI: SrGeolAgeEnum

"},{"location":"SrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"SrGeolAgeEnum/#slots","title":"Slots","text":"Name Description sr_geol_age Geological age of source rock (Additional info: https://en"},{"location":"SrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrGeolAgeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SrGeolAgeEnum/#linkml-source","title":"LinkML Source","text":"
name: sr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Archean:\n    text: Archean\n  Cambrian:\n    text: Cambrian\n  Carboniferous:\n    text: Carboniferous\n  Cenozoic:\n    text: Cenozoic\n  Cretaceous:\n    text: Cretaceous\n  Devonian:\n    text: Devonian\n  Jurassic:\n    text: Jurassic\n  Mesozoic:\n    text: Mesozoic\n  Neogene:\n    text: Neogene\n  Ordovician:\n    text: Ordovician\n  Paleogene:\n    text: Paleogene\n  Paleozoic:\n    text: Paleozoic\n  Permian:\n    text: Permian\n  Precambrian:\n    text: Precambrian\n  Proterozoic:\n    text: Proterozoic\n  Silurian:\n    text: Silurian\n  Triassic:\n    text: Triassic\n  other:\n    text: other\n\n
"},{"location":"SrKerogTypeEnum/","title":"Enum: SrKerogTypeEnum","text":"

URI: SrKerogTypeEnum

"},{"location":"SrKerogTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Type I None Type II None Type III None Type IV None other None"},{"location":"SrKerogTypeEnum/#slots","title":"Slots","text":"Name Description sr_kerog_type Origin of kerogen"},{"location":"SrKerogTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrKerogTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SrKerogTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: sr_kerog_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Type I:\n    text: Type I\n  Type II:\n    text: Type II\n  Type III:\n    text: Type III\n  Type IV:\n    text: Type IV\n  other:\n    text: other\n\n
"},{"location":"SrLithologyEnum/","title":"Enum: SrLithologyEnum","text":"

URI: SrLithologyEnum

"},{"location":"SrLithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Clastic None Carbonate None Coal None Biosilicieous None other None"},{"location":"SrLithologyEnum/#slots","title":"Slots","text":"Name Description sr_lithology Lithology of source rock (https://en"},{"location":"SrLithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrLithologyEnum/#schema-source","title":"Schema Source","text":""},{"location":"SrLithologyEnum/#linkml-source","title":"LinkML Source","text":"
name: sr_lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Clastic:\n    text: Clastic\n  Carbonate:\n    text: Carbonate\n  Coal:\n    text: Coal\n  Biosilicieous:\n    text: Biosilicieous\n  other:\n    text: other\n\n
"},{"location":"StationaryPhaseEnum/","title":"Enum: StationaryPhaseEnum","text":"

The type of stationary phase used in a chromatography process.

URI: StationaryPhaseEnum

"},{"location":"StationaryPhaseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description BEH-HILIC None C18 None C8 None C4 None C2 None C1 None C30 None C60 None CNT None CN None Diol None HILIC None NH2 None Phenyl None Polysiloxane None PS-DVB None SAX None SCX None Silica None WCX None WAX None ZIC-HILIC None ZIC-pHILIC None ZIC-cHILIC None"},{"location":"StationaryPhaseEnum/#slots","title":"Slots","text":"Name Description stationary_phase The material the stationary phase is comprised of used in chromatography"},{"location":"StationaryPhaseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StationaryPhaseEnum/#schema-source","title":"Schema Source","text":""},{"location":"StationaryPhaseEnum/#linkml-source","title":"LinkML Source","text":"
name: StationaryPhaseEnum\ndescription: The type of stationary phase used in a chromatography process.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-4504-1039\nrank: 1000\npermissible_values:\n  BEH-HILIC:\n    text: BEH-HILIC\n  C18:\n    text: C18\n  C8:\n    text: C8\n  C4:\n    text: C4\n  C2:\n    text: C2\n  C1:\n    text: C1\n  C30:\n    text: C30\n  C60:\n    text: C60\n  CNT:\n    text: CNT\n  CN:\n    text: CN\n  Diol:\n    text: Diol\n  HILIC:\n    text: HILIC\n  NH2:\n    text: NH2\n  Phenyl:\n    text: Phenyl\n  Polysiloxane:\n    text: Polysiloxane\n  PS-DVB:\n    text: PS-DVB\n  SAX:\n    text: SAX\n  SCX:\n    text: SCX\n  Silica:\n    text: Silica\n  WCX:\n    text: WCX\n  WAX:\n    text: WAX\n  ZIC-HILIC:\n    text: ZIC-HILIC\n  ZIC-pHILIC:\n    text: ZIC-pHILIC\n  ZIC-cHILIC:\n    text: ZIC-cHILIC\n\n
"},{"location":"StatusEnum/","title":"Enum: StatusEnum","text":"

URI: StatusEnum

"},{"location":"StatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description pass None fail None"},{"location":"StatusEnum/#slots","title":"Slots","text":"Name Description qc_status Stores information about the result of a process (ie the process of sequencin..."},{"location":"StatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StatusEnum/#schema-source","title":"Schema Source","text":""},{"location":"StatusEnum/#linkml-source","title":"LinkML Source","text":"
name: StatusEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  pass:\n    text: pass\n  fail:\n    text: fail\n\n
"},{"location":"StorageProcess/","title":"Class: StorageProcess","text":"

A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment.

URI: nmdc:StorageProcess

classDiagram\n  class StorageProcess\n  click StorageProcess href \"../StorageProcess\"\n    PlannedProcess <|-- StorageProcess\n      click PlannedProcess href \"../PlannedProcess\"\n\n\n\n  StorageProcess : alternative_identifiers\n\n  StorageProcess : contained_in\n\n      StorageProcess --> \"0..1\" ContainerCategoryEnum : contained_in\n    click ContainerCategoryEnum href \"../ContainerCategoryEnum\"\n\n  StorageProcess : description\n\n  StorageProcess : end_date\n\n  StorageProcess : has_failure_categorization\n\n      StorageProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  StorageProcess : has_input\n\n      StorageProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  StorageProcess : has_output\n\n      StorageProcess --> \"*\" NamedThing : has_output\n    click NamedThing href \"../NamedThing\"\n\n  StorageProcess : id\n\n  StorageProcess : name\n\n  StorageProcess : processing_institution\n\n      StorageProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  StorageProcess : protocol_link\n\n      StorageProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  StorageProcess : qc_comment\n\n  StorageProcess : qc_status\n\n      StorageProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  StorageProcess : start_date\n\n  StorageProcess : substances_used\n\n      StorageProcess --> \"*\" PortionOfSubstance : substances_used\n    click PortionOfSubstance href \"../PortionOfSubstance\"\n\n  StorageProcess : temperature\n\n      StorageProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  StorageProcess : type\n\n\n\n
"},{"location":"StorageProcess/#inheritance","title":"Inheritance","text":""},{"location":"StorageProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance substances_used * PortionOfSubstance The substance(s) that a processed sample is stored in direct contained_in 0..1 ContainerCategoryEnum A type of container direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct has_input * NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"StorageProcess/#usages","title":"Usages","text":"used by used in type used Database storage_process_set range StorageProcess"},{"location":"StorageProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StorageProcess/#schema-source","title":"Schema Source","text":""},{"location":"StorageProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:StorageProcess native nmdc:StorageProcess related OBI:0302893"},{"location":"StorageProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"StorageProcess/#direct","title":"Direct","text":"
name: StorageProcess\ndescription: A planned process with the objective to preserve and protect material\n  entities by placing them in an identified  location which may have a controlled\n  environment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0302893\nis_a: PlannedProcess\nslots:\n- substances_used\n- contained_in\n- temperature\nslot_usage:\n  substances_used:\n    name: substances_used\n    description: The substance(s) that a processed sample is stored in.\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:StorageProcess\n\n
"},{"location":"StorageProcess/#induced","title":"Induced","text":"
name: StorageProcess\ndescription: A planned process with the objective to preserve and protect material\n  entities by placing them in an identified  location which may have a controlled\n  environment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0302893\nis_a: PlannedProcess\nslot_usage:\n  substances_used:\n    name: substances_used\n    description: The substance(s) that a processed sample is stored in.\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  substances_used:\n    name: substances_used\n    description: The substance(s) that a processed sample is stored in.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: substances_used\n    owner: StorageProcess\n    domain_of:\n    - Extraction\n    - StorageProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    - MobilePhaseSegment\n    range: PortionOfSubstance\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  contained_in:\n    name: contained_in\n    description: A type of container.\n    examples:\n    - value: test tube\n    - value: falcon tube\n    - value: whirlpak\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: contained_in\n    owner: StorageProcess\n    domain_of:\n    - SubSamplingProcess\n    - StorageProcess\n    range: ContainerCategoryEnum\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: StorageProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: StorageProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: StorageProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: StorageProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: StorageProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: StorageProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: StorageProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:StorageProcess\n\n
"},{"location":"StrandedOrientationEnum/","title":"Enum: StrandedOrientationEnum","text":"

This enumeration specifies information about stranded RNA library preparations.

URI: StrandedOrientationEnum

"},{"location":"StrandedOrientationEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description antisense orientation None Orientation that is complementary (non-coding) to a sequence of messenger RNA sense orientation None Orientation that corresponds to the coding sequence of messenger RNA"},{"location":"StrandedOrientationEnum/#slots","title":"Slots","text":"Name Description stranded_orientation Lists the strand orientiation for a stranded RNA library preparation"},{"location":"StrandedOrientationEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StrandedOrientationEnum/#schema-source","title":"Schema Source","text":""},{"location":"StrandedOrientationEnum/#linkml-source","title":"LinkML Source","text":"
name: StrandedOrientationEnum\ndescription: This enumeration specifies information about stranded RNA library preparations.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  antisense orientation:\n    text: antisense orientation\n    description: Orientation that is complementary (non-coding) to a sequence of messenger\n      RNA.\n    comments:\n    - See https://www.genome.gov/genetics-glossary/antisense\n    exact_mappings:\n    - SO:0000077\n  sense orientation:\n    text: sense orientation\n    description: Orientation that corresponds to the coding sequence of messenger\n      RNA.\n\n
"},{"location":"String/","title":"Type: String","text":"

A character string

URI: xsd:string

"},{"location":"String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"String/#schema-source","title":"Schema Source","text":""},{"location":"String/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:string exact schema:Text"},{"location":"Study/","title":"Class: Study","text":"

A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.

URI: nmdc:Study

classDiagram\n  class Study\n  click Study href \"../Study\"\n    NamedThing <|-- Study\n      click NamedThing href \"../NamedThing\"\n\n\n\n  Study : alternative_descriptions\n\n  Study : alternative_identifiers\n\n  Study : alternative_names\n\n  Study : alternative_titles\n\n  Study : associated_dois\n\n      Study --> \"*\" Doi : associated_dois\n    click Doi href \"../Doi\"\n\n  Study : description\n\n  Study : ecosystem\n\n  Study : ecosystem_category\n\n  Study : ecosystem_subtype\n\n  Study : ecosystem_type\n\n  Study : emsl_project_identifiers\n\n  Study : funding_sources\n\n  Study : gnps_task_identifiers\n\n  Study : gold_study_identifiers\n\n  Study : has_credit_associations\n\n      Study --> \"*\" CreditAssociation : has_credit_associations\n    click CreditAssociation href \"../CreditAssociation\"\n\n  Study : homepage_website\n\n  Study : id\n\n  Study : insdc_bioproject_identifiers\n\n  Study : jgi_portal_study_identifiers\n\n  Study : mgnify_project_identifiers\n\n  Study : name\n\n  Study : neon_study_identifiers\n\n  Study : notes\n\n  Study : objective\n\n  Study : part_of\n\n      Study --> \"*\" Study : part_of\n    click Study href \"../Study\"\n\n  Study : principal_investigator\n\n      Study --> \"0..1\" PersonValue : principal_investigator\n    click PersonValue href \"../PersonValue\"\n\n  Study : protocol_link\n\n      Study --> \"*\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  Study : related_identifiers\n\n  Study : specific_ecosystem\n\n  Study : study_category\n\n      Study --> \"1\" StudyCategoryEnum : study_category\n    click StudyCategoryEnum href \"../StudyCategoryEnum\"\n\n  Study : study_image\n\n      Study --> \"*\" ImageValue : study_image\n    click ImageValue href \"../ImageValue\"\n\n  Study : title\n\n  Study : type\n\n  Study : websites\n\n\n\n
"},{"location":"Study/#inheritance","title":"Inheritance","text":""},{"location":"Study/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance emsl_project_identifiers * ExternalIdentifier Identifiers that link a NMDC study to the EMSL user facility website hosting ... direct gnps_task_identifiers * ExternalIdentifier identifiers that link a NMDC study to a web-based report about metabolomics a... direct gold_study_identifiers * ExternalIdentifier identifiers for corresponding project(s) in GOLD direct insdc_bioproject_identifiers * ExternalIdentifier Unique identifier for a bioproject submitted to INSDC that relates to the NMD... direct jgi_portal_study_identifiers * ExternalIdentifier Identifiers that link a NMDC study to a website hosting raw and analyzed data... direct mgnify_project_identifiers * ExternalIdentifier identifiers for corresponding project in MGnify direct neon_study_identifiers * ExternalIdentifier direct related_identifiers 0..1 String Unique identifier for a study submitted to additional resources direct alternative_descriptions * String A list of alternative descriptions for the entity direct alternative_names * String A list of alternative names used to refer to the entity direct alternative_titles * String A list of alternative titles for the entity direct ecosystem 0..1 String An ecosystem is a combination of a physical environment (abiotic factors) and... direct ecosystem_category 0..1 String Ecosystem categories represent divisions within the ecosystem based on specif... direct ecosystem_subtype 0..1 String Ecosystem subtypes represent further subdivision of Ecosystem types into more... direct ecosystem_type 0..1 String Ecosystem types represent things having common characteristics within the Eco... direct specific_ecosystem 0..1 String Specific ecosystems represent specific features of the environment like aphot... direct associated_dois * Doi A list of DOIs associated with a resource, such as a list of DOIS associated ... direct funding_sources * String A list of organizations, along with the award numbers, that underwrite financ... direct has_credit_associations * CreditAssociation This slot links a study to a credit association direct homepage_website * String The website address (URL) of an entity's homepage direct notes 0..1 String direct objective 0..1 String The scientific objectives associated with the entity direct part_of * Study Links a study or consortium to a parent (or umbrella) study or consortium direct principal_investigator 0..1 PersonValue Principal Investigator who led the study and/or generated the dataset direct protocol_link * Protocol direct study_category 1 StudyCategoryEnum The type of research initiative direct study_image * ImageValue Links a study to one or more images direct title 0..1 String A name given to the entity that differs from the name/label programmatically ... direct websites * String A list of websites that are associated with the entity direct id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String A brief, link-free summary of a Study NamedThing alternative_identifiers * Uriorcurie Unique identifier for a study submitted to additional resources NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"Study/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing associated_studies range Study MassSpectrometry associated_studies range Study Database study_set range Study Biosample associated_studies range Study Study part_of range Study DataGeneration associated_studies range Study"},{"location":"Study/#aliases","title":"Aliases","text":""},{"location":"Study/#comments","title":"Comments","text":""},{"location":"Study/#todos","title":"TODOs","text":""},{"location":"Study/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Study/#schema-source","title":"Schema Source","text":""},{"location":"Study/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:Study native nmdc:Study exact OBI:0000066, SIO:000747, NCIT:C41198, ISA:Investigation broad prov:Activity"},{"location":"Study/#linkml-source","title":"LinkML Source","text":""},{"location":"Study/#direct","title":"Direct","text":"
name: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n  the key objective of its underlying projects.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: A study (project) groups together data submitted to the archive and\n      controls its release date. A study accession is typically used when citing data\n      submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n  but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research initiative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslots:\n- emsl_project_identifiers\n- gnps_task_identifiers\n- gold_study_identifiers\n- insdc_bioproject_identifiers\n- jgi_portal_study_identifiers\n- mgnify_project_identifiers\n- neon_study_identifiers\n- related_identifiers\n- alternative_descriptions\n- alternative_names\n- alternative_titles\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- specific_ecosystem\n- associated_dois\n- funding_sources\n- has_credit_associations\n- homepage_website\n- notes\n- objective\n- part_of\n- principal_investigator\n- protocol_link\n- study_category\n- study_image\n- title\n- websites\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a name for the study your samples will belong with.\n  websites:\n    name: websites\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the Principal Investigator's research lab webpage or the study\n          webpage associated with this collection of samples. Multiple links can be\n          provided.\n  homepage_website:\n    name: homepage_website\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the consortium's homepage if the study_category is a consortium.\n  description:\n    name: description\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a brief description of your study.\n    description: A brief, link-free summary of a Study\n    comments:\n    - Include links in other Study slots, such as websites or dois.\n  notes:\n    name: notes\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Add any additional notes or comments about this study.\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Matches that which has been submitted to NMDC\n  alternative_names:\n    name: alternative_names\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Project, study, or sample set names the are also associated with this\n          submission or other names / identifiers for this study.\n  related_identifiers:\n    name: related_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Similar, but not necessarily identical to that which has been submitted to NMDC\n  insdc_bioproject_identifiers:\n    name: insdc_bioproject_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the NCBI BioProject Accession Number associated with the listed\n          NCBI BioProject Title.\n    description: Unique identifier for a bioproject submitted to INSDC that relates\n      to the NMDC submitted study.\n  part_of:\n    name: part_of\n    description: Links a study or consortium to a parent (or umbrella) study or consortium.\n    comments:\n    - Value is the id of the umbrella study or consortium.\n    range: Study\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  protocol_link:\n    name: protocol_link\n    multivalued: true\n    inlined_as_list: true\nclass_uri: nmdc:Study\n\n
"},{"location":"Study/#induced","title":"Induced","text":"
name: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n  the key objective of its underlying projects.\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: A study (project) groups together data submitted to the archive and\n      controls its release date. A study accession is typically used when citing data\n      submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n  but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research initiative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a name for the study your samples will belong with.\n  websites:\n    name: websites\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the Principal Investigator's research lab webpage or the study\n          webpage associated with this collection of samples. Multiple links can be\n          provided.\n  homepage_website:\n    name: homepage_website\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the consortium's homepage if the study_category is a consortium.\n  description:\n    name: description\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a brief description of your study.\n    description: A brief, link-free summary of a Study\n    comments:\n    - Include links in other Study slots, such as websites or dois.\n  notes:\n    name: notes\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Add any additional notes or comments about this study.\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Matches that which has been submitted to NMDC\n  alternative_names:\n    name: alternative_names\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Project, study, or sample set names the are also associated with this\n          submission or other names / identifiers for this study.\n  related_identifiers:\n    name: related_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Similar, but not necessarily identical to that which has been submitted to NMDC\n  insdc_bioproject_identifiers:\n    name: insdc_bioproject_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the NCBI BioProject Accession Number associated with the listed\n          NCBI BioProject Title.\n    description: Unique identifier for a bioproject submitted to INSDC that relates\n      to the NMDC submitted study.\n  part_of:\n    name: part_of\n    description: Links a study or consortium to a parent (or umbrella) study or consortium.\n    comments:\n    - Value is the id of the umbrella study or consortium.\n    range: Study\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  protocol_link:\n    name: protocol_link\n    multivalued: true\n    inlined_as_list: true\nattributes:\n  emsl_project_identifiers:\n    name: emsl_project_identifiers\n    description: Identifiers that link a NMDC study to the EMSL user facility website\n      hosting the project description of an EMSL user project\n    title: EMSL Project Identifiers\n    todos:\n    - elaborate on description\n    notes:\n    - these identifiers are all currently 5 digits long but that could change in the\n      future\n    examples:\n    - value: emsl.project:60141\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/927#issuecomment-1802136437\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - emsl_identifiers\n    alias: emsl_project_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^emsl\\.project:[0-9]{5}$\n  gnps_task_identifiers:\n    name: gnps_task_identifiers\n    description: identifiers that link a NMDC study to a web-based report about metabolomics\n      analysis progress and results\n    title: GNPS task identifiers\n    comments:\n    - this could be considered a related identifier, as the metabolomics progress\n      and results aren't a study per se\n    - this identifier was registered with bioregistry but not identifiers.org\n    examples:\n    - value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysis/\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - gnps_identifiers\n    alias: gnps_task_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^gnps\\.task:[a-f0-9]+$\n  gold_study_identifiers:\n    name: gold_study_identifiers\n    description: identifiers for corresponding project(s) in GOLD\n    title: GOLD Study Identifiers\n    comments:\n    - uses the prefix GS (but possibly in a different case)\n    examples:\n    - value: https://bioregistry.io/gold:Gs0110115\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/studies\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - gold_identifiers\n    alias: gold_study_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^gold:Gs[0-9]+$\n  insdc_bioproject_identifiers:\n    name: insdc_bioproject_identifiers\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide the NCBI BioProject Accession Number associated with the listed\n          NCBI BioProject Title.\n    description: Unique identifier for a bioproject submitted to INSDC that relates\n      to the NMDC submitted study.\n    comments:\n    - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n      one to one\n    examples:\n    - value: https://bioregistry.io/bioproject:PRJNA366857\n      description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2\n        metatranscriptome\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://www.ncbi.nlm.nih.gov/bioproject/\n    - https://www.ddbj.nig.ac.jp/bioproject/index-e.html\n    aliases:\n    - NCBI bioproject identifiers\n    - DDBJ bioproject identifiers\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - insdc_identifiers\n    alias: insdc_bioproject_identifiers\n    owner: Study\n    domain_of:\n    - NucleotideSequencing\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n  jgi_portal_study_identifiers:\n    name: jgi_portal_study_identifiers\n    id_prefixes:\n    - jgi.proposal\n    description: Identifiers that link a NMDC study to a website hosting raw and analyzed\n      data for a JGI proposal.  The suffix of the curie can used to query the GOLD\n      API and is interoperable with an award DOI from OSTI and a GOLD study identifier.\n    title: JGI Portal Study identifiers\n    comments:\n    - Could this could be considered a related identifier?\n    - Curie suffix is the Site Award Number from an OSTI award page\n    - Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD\n      study identifier gold:Gs0154044\n    - bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\n    examples:\n    - value: jgi.proposal:507130\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - jgi_portal_identifiers\n    alias: jgi_portal_study_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^jgi.proposal:\\d+$\n  mgnify_project_identifiers:\n    name: mgnify_project_identifiers\n    description: identifiers for corresponding project in MGnify\n    examples:\n    - value: https://bioregistry.io/mgnify.proj:MGYS00005757\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - mgnify_identifiers\n    alias: mgnify_project_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^mgnify.proj:[A-Z]+[0-9]+$\n  neon_study_identifiers:\n    name: neon_study_identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: study_identifiers\n    mixins:\n    - neon_identifiers\n    alias: neon_study_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: external_identifier\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  related_identifiers:\n    name: related_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Similar, but not necessarily identical to that which has been submitted to NMDC\n    title: Related Identifiers\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: related_identifiers\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n  alternative_descriptions:\n    name: alternative_descriptions\n    description: A list of alternative descriptions for the entity. The distinction\n      between description and alternative descriptions is application-specific.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_descriptions\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n    multivalued: true\n  alternative_names:\n    name: alternative_names\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Project, study, or sample set names the are also associated with this\n          submission or other names / identifiers for this study.\n    description: A list of alternative names used to refer to the entity. The distinction\n      between name and alternative names is application-specific.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - dcterms:alternative\n    - skos:altLabel\n    rank: 1000\n    alias: alternative_names\n    owner: Study\n    domain_of:\n    - ChemicalEntity\n    - Study\n    range: string\n    multivalued: true\n  alternative_titles:\n    name: alternative_titles\n    description: A list of alternative titles for the entity. The distinction between\n      title and alternative titles is application-specific.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - dcterms:alternative\n    rank: 1000\n    alias: alternative_titles\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n    multivalued: true\n  ecosystem:\n    name: ecosystem\n    description: An ecosystem is a combination of a physical environment (abiotic\n      factors) and all the organisms (biotic factors) that interact with this environment.\n      Ecosystem is in position 1/5 in a GOLD path.\n    comments:\n    - The abiotic factors play a profound role on the type and composition of organisms\n      in a given environment. The GOLD Ecosystem at the top of the five-level classification\n      system is aimed at capturing the broader environment from which an organism\n      or environmental sample is collected. The three broad groups under Ecosystem\n      are Environmental, Host-associated, and Engineered. They represent samples collected\n      from a natural environment or from another organism or from engineered environments\n      like bioreactors respectively.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_category:\n    name: ecosystem_category\n    description: Ecosystem categories represent divisions within the ecosystem based\n      on specific characteristics of the environment from where an organism or sample\n      is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n    comments:\n    - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n      Ecosystem categories for Host-associated samples can be individual hosts or\n      phyla and for engineered samples it may be manipulated environments like bioreactors,\n      solid waste etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_category\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_subtype:\n    name: ecosystem_subtype\n    description: Ecosystem subtypes represent further subdivision of Ecosystem types\n      into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n      path.\n    comments:\n    - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n      (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n      the Ecosystem subtype category.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_subtype\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  ecosystem_type:\n    name: ecosystem_type\n    description: Ecosystem types represent things having common characteristics within\n      the Ecosystem Category. These common characteristics based grouping is still\n      broad but specific to the characteristics of a given environment. Ecosystem\n      type is in position 3/5 in a GOLD path.\n    comments:\n    - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n      or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n      air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n      type can represent Respiratory system, Digestive system, Roots etc.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: ecosystem_type\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  specific_ecosystem:\n    name: specific_ecosystem\n    description: Specific ecosystems represent specific features of the environment\n      like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n      Specific ecosystem is in position 5/5 in a GOLD path.\n    comments:\n    - Specific ecosystems help to define samples based on very specific characteristics\n      of an environment under the five-level classification system.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://gold.jgi.doe.gov/help\n    rank: 1000\n    is_a: gold_path_field\n    alias: specific_ecosystem\n    owner: Study\n    domain_of:\n    - Biosample\n    - Study\n    range: string\n  associated_dois:\n    name: associated_dois\n    description: A list of DOIs associated with a resource, such as a list of DOIS\n      associated with a Study.\n    examples:\n    - value: '[{''doi'': ''doi:10.46936/intm.proj.2021.60141/60000423'', ''doi_provider'':\n        ''emsl'', ''doi_category'': ''award_doi''}, {''doi'': ''doi:10.1101/2022.12.12.520098'',\n        ''doi_category'': ''publication_doi''}, {''doi'': ''doi:10.48321/D1Z60Q'',\n        ''doi_category'': ''data_management_plan_doi'', ''doi_provider'': ''gsc''}]'\n      description: Provides a list of two DOIs; specifically, an EMSL award DOI and\n        a publication DOI.\n    in_subset:\n    - data_portal_subset\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - Associated DOIs\n    - Associated digital object identifiers\n    rank: 1000\n    alias: associated_dois\n    owner: Study\n    domain_of:\n    - Study\n    range: Doi\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  funding_sources:\n    name: funding_sources\n    description: A list of organizations, along with the award numbers, that underwrite\n      financial support for projects of a particular type. Typically, they process\n      applications and award funds to the chosen qualified applicants.\n    comments:\n    - Include only the name of the funding organization and the award or contract\n      number.\n    examples:\n    - value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n    - value: U.S. Department of Energy, Office of Science, Office of Biological and\n        Environmental Research (BER) under contract DE-AC05-00OR2275\n    from_schema: https://w3id.org/nmdc/nmdc\n    close_mappings:\n    - NCIT:C39409\n    rank: 1000\n    alias: funding_sources\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n    multivalued: true\n  has_credit_associations:\n    name: has_credit_associations\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Other researchers associated with this study.\n    description: 'This slot links a study to a credit association.  The credit association\n      will be linked to a person value and to a CRediT Contributor Roles term. Overall\n      semantics: person should get credit X for their participation in the study'\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: prov:qualifiedAssociation\n    alias: has_credit_associations\n    owner: Study\n    domain_of:\n    - Study\n    range: CreditAssociation\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  homepage_website:\n    name: homepage_website\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the consortium's homepage if the study_category is a consortium.\n    description: The website address (URL) of an entity's homepage.\n    examples:\n    - value: https://www.neonscience.org/\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    is_a: websites\n    alias: homepage_website\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n    multivalued: true\n    pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n    maximum_cardinality: 1\n  notes:\n    name: notes\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Add any additional notes or comments about this study.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: notes\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n  objective:\n    name: objective\n    description: The scientific objectives associated with the entity. It SHOULD correspond\n      to scientific norms for objectives field in a structured abstract.\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - SIO:000337\n    rank: 1000\n    alias: objective\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n  part_of:\n    name: part_of\n    description: Links a study or consortium to a parent (or umbrella) study or consortium.\n    comments:\n    - Value is the id of the umbrella study or consortium.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - is part of\n    rank: 1000\n    slot_uri: dcterms:isPartOf\n    alias: part_of\n    owner: Study\n    domain_of:\n    - FieldResearchSite\n    - Study\n    range: Study\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  principal_investigator:\n    name: principal_investigator\n    description: Principal Investigator who led the study and/or generated the dataset.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - PI\n    rank: 1000\n    alias: principal_investigator\n    owner: Study\n    domain_of:\n    - Study\n    - DataGeneration\n    range: PersonValue\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: Study\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n    multivalued: true\n    inlined_as_list: true\n  study_category:\n    name: study_category\n    description: The type of research initiative\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: study_category\n    owner: Study\n    domain_of:\n    - Study\n    range: StudyCategoryEnum\n    required: true\n  study_image:\n    name: study_image\n    description: Links a study to one or more images.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: study_image\n    owner: Study\n    domain_of:\n    - Study\n    range: ImageValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  title:\n    name: title\n    description: A name given to the entity that differs from the name/label programmatically\n      assigned to it. For example, when extracting study information for GOLD, the\n      GOLD system has assigned a name/label. However, for display purposes, we may\n      also wish the capture the title of the proposal that was used to fund the study.\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - dcterms:title\n    rank: 1000\n    alias: title\n    owner: Study\n    domain_of:\n    - Study\n    range: string\n  websites:\n    name: websites\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Link to the Principal Investigator's research lab webpage or the study\n          webpage associated with this collection of samples. Multiple links can be\n          provided.\n    description: A list of websites that are associated with the entity.\n    comments:\n    - DOIs should not be included as websites. Instead, use the associated_dois slot.\n    - A consortium's homepage website should be included in the homepage_website slot,\n      not in websites.\n    - consortium is a convenience term for a Study whose study_category value is consortium\n    - the website slot and its subproperties are virtually identical to the url slot,\n      except that they are multivalued and url is single-valued.\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - nmdc:url\n    rank: 1000\n    alias: websites\n    owner: Study\n    domain_of:\n    - PersonValue\n    - Study\n    range: string\n    multivalued: true\n    pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Study\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a name for the study your samples will belong with.\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: Study\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    annotations:\n      tooltip:\n        tag: tooltip\n        value: Provide a brief description of your study.\n    description: A brief, link-free summary of a Study\n    comments:\n    - Include links in other Study slots, such as websites or dois.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: Study\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: Unique identifier for a study submitted to additional resources.\n      Matches that which has been submitted to NMDC\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: Study\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: Study\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:Study\n\n
"},{"location":"StudyCategoryEnum/","title":"Enum: StudyCategoryEnum","text":"

URI: StudyCategoryEnum

"},{"location":"StudyCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description research_study None A detailed examination, analysis, or critical inspection of a hypothesis-driv... consortium None A group formed to undertake a venture that is beyond the capabilities of the ..."},{"location":"StudyCategoryEnum/#slots","title":"Slots","text":"Name Description study_category The type of research initiative"},{"location":"StudyCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StudyCategoryEnum/#schema-source","title":"Schema Source","text":""},{"location":"StudyCategoryEnum/#linkml-source","title":"LinkML Source","text":"
name: StudyCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  research_study:\n    text: research_study\n    description: A detailed examination, analysis, or critical inspection of a hypothesis-driven\n      experiment.\n    exact_mappings:\n    - SIO:001066\n    - NCIT:C63536\n    - ISA:Study\n    close_mappings:\n    - OBI:0000355\n  consortium:\n    text: consortium\n    description: A group formed to undertake a venture that is beyond the capabilities\n      of the individual members. Each member of the consortium brings a high level\n      of expertise in a specific area to ensure the successful completion of the project.\n    comments:\n    - A consortium has collections of data, those data do not come from a hypothesis-driven\n      experiment.\n    exact_mappings:\n    - NCIT:C61538\n\n
"},{"location":"SubSamplingProcess/","title":"Class: SubSamplingProcess","text":"

Separating a sample aliquot from the starting material for downstream activity.

__

URI: nmdc:SubSamplingProcess

classDiagram\n  class SubSamplingProcess\n  click SubSamplingProcess href \"../SubSamplingProcess\"\n    MaterialProcessing <|-- SubSamplingProcess\n      click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n  SubSamplingProcess : alternative_identifiers\n\n  SubSamplingProcess : contained_in\n\n      SubSamplingProcess --> \"0..1\" ContainerCategoryEnum : contained_in\n    click ContainerCategoryEnum href \"../ContainerCategoryEnum\"\n\n  SubSamplingProcess : container_size\n\n      SubSamplingProcess --> \"0..1\" QuantityValue : container_size\n    click QuantityValue href \"../QuantityValue\"\n\n  SubSamplingProcess : description\n\n  SubSamplingProcess : end_date\n\n  SubSamplingProcess : has_failure_categorization\n\n      SubSamplingProcess --> \"*\" FailureCategorization : has_failure_categorization\n    click FailureCategorization href \"../FailureCategorization\"\n\n  SubSamplingProcess : has_input\n\n      SubSamplingProcess --> \"*\" NamedThing : has_input\n    click NamedThing href \"../NamedThing\"\n\n  SubSamplingProcess : has_output\n\n      SubSamplingProcess --> \"*\" ProcessedSample : has_output\n    click ProcessedSample href \"../ProcessedSample\"\n\n  SubSamplingProcess : id\n\n  SubSamplingProcess : instrument_used\n\n      SubSamplingProcess --> \"*\" Instrument : instrument_used\n    click Instrument href \"../Instrument\"\n\n  SubSamplingProcess : mass\n\n      SubSamplingProcess --> \"0..1\" QuantityValue : mass\n    click QuantityValue href \"../QuantityValue\"\n\n  SubSamplingProcess : name\n\n  SubSamplingProcess : processing_institution\n\n      SubSamplingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n    click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n  SubSamplingProcess : protocol_link\n\n      SubSamplingProcess --> \"0..1\" Protocol : protocol_link\n    click Protocol href \"../Protocol\"\n\n  SubSamplingProcess : qc_comment\n\n  SubSamplingProcess : qc_status\n\n      SubSamplingProcess --> \"0..1\" StatusEnum : qc_status\n    click StatusEnum href \"../StatusEnum\"\n\n  SubSamplingProcess : sampled_portion\n\n      SubSamplingProcess --> \"*\" SamplePortionEnum : sampled_portion\n    click SamplePortionEnum href \"../SamplePortionEnum\"\n\n  SubSamplingProcess : start_date\n\n  SubSamplingProcess : temperature\n\n      SubSamplingProcess --> \"0..1\" QuantityValue : temperature\n    click QuantityValue href \"../QuantityValue\"\n\n  SubSamplingProcess : type\n\n  SubSamplingProcess : volume\n\n      SubSamplingProcess --> \"0..1\" QuantityValue : volume\n    click QuantityValue href \"../QuantityValue\"\n\n\n\n
"},{"location":"SubSamplingProcess/#inheritance","title":"Inheritance","text":""},{"location":"SubSamplingProcess/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance container_size 0..1 QuantityValue The volume of the container an analyte is stored in or an activity takes plac... direct contained_in 0..1 ContainerCategoryEnum A type of container direct temperature 0..1 QuantityValue The value of a temperature measurement or temperature used in a process direct volume 0..1 QuantityValue The output volume of the SubSampling Process direct mass 0..1 QuantityValue The output mass of the SubSampling Process direct sampled_portion * SamplePortionEnum The portion of the sample that is taken for downstream activity direct instrument_used * Instrument What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing has_input * NamedThing\u00a0or\u00a0Biosample\u00a0or\u00a0ProcessedSample An input to a process PlannedProcess has_output * ProcessedSample The subsample PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"SubSamplingProcess/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubSamplingProcess/#schema-source","title":"Schema Source","text":""},{"location":"SubSamplingProcess/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:SubSamplingProcess native nmdc:SubSamplingProcess related OBI:0000744"},{"location":"SubSamplingProcess/#linkml-source","title":"LinkML Source","text":""},{"location":"SubSamplingProcess/#direct","title":"Direct","text":"
name: SubSamplingProcess\ndescription: 'Separating a sample aliquot from the starting material for downstream\n  activity.\n\n  '\nnotes:\n- A subsample may be (a) a portion of the sample obtained by selection or division;\n  (b) an individual unit of the lot taken as part of the sample; (c) the final unit\n  of multistage sampling. The term 'subsample' is used either in the sense of a 'sample\n  of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent\n  from the context or is defined.\n- TODO - Montana to visit slot descriptions\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0000744\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslots:\n- container_size\n- contained_in\n- temperature\n- volume\n- mass\n- sampled_portion\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The output volume of the SubSampling Process.\n  mass:\n    name: mass\n    description: The output mass of the SubSampling Process.\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The subsample.\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nclass_uri: nmdc:SubSamplingProcess\n\n
"},{"location":"SubSamplingProcess/#induced","title":"Induced","text":"
name: SubSamplingProcess\ndescription: 'Separating a sample aliquot from the starting material for downstream\n  activity.\n\n  '\nnotes:\n- A subsample may be (a) a portion of the sample obtained by selection or division;\n  (b) an individual unit of the lot taken as part of the sample; (c) the final unit\n  of multistage sampling. The term 'subsample' is used either in the sense of a 'sample\n  of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent\n  from the context or is defined.\n- TODO - Montana to visit slot descriptions\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0000744\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslot_usage:\n  id:\n    name: id\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  volume:\n    name: volume\n    description: The output volume of the SubSampling Process.\n  mass:\n    name: mass\n    description: The output mass of the SubSampling Process.\n  has_input:\n    name: has_input\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The subsample.\n    range: ProcessedSample\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\nattributes:\n  container_size:\n    name: container_size\n    description: The volume of the container an analyte is stored in or an activity\n      takes place in\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: container_size\n    owner: SubSamplingProcess\n    domain_of:\n    - SubSamplingProcess\n    - FiltrationProcess\n    range: QuantityValue\n  contained_in:\n    name: contained_in\n    description: A type of container.\n    examples:\n    - value: test tube\n    - value: falcon tube\n    - value: whirlpak\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: contained_in\n    owner: SubSamplingProcess\n    domain_of:\n    - SubSamplingProcess\n    - StorageProcess\n    range: ContainerCategoryEnum\n  temperature:\n    name: temperature\n    description: The value of a temperature measurement or temperature used in a process.\n    notes:\n    - Not to be confused with the MIXS:0000113\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: temperature\n    owner: SubSamplingProcess\n    domain_of:\n    - ChromatographyConfiguration\n    - SubSamplingProcess\n    - StorageProcess\n    - ChromatographicSeparationProcess\n    - DissolvingProcess\n    - ChemicalConversionProcess\n    range: QuantityValue\n  volume:\n    name: volume\n    description: The output volume of the SubSampling Process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    contributors:\n    - ORCID:0009-0001-1555-1601\n    - ORCID:0000-0002-8683-0050\n    rank: 1000\n    alias: volume\n    owner: SubSamplingProcess\n    domain_of:\n    - Extraction\n    - SubSamplingProcess\n    - FiltrationProcess\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    range: QuantityValue\n  mass:\n    name: mass\n    description: The output mass of the SubSampling Process.\n    title: mass\n    from_schema: https://w3id.org/nmdc/nmdc\n    exact_mappings:\n    - PATO:0000125\n    rank: 1000\n    alias: mass\n    owner: SubSamplingProcess\n    domain_of:\n    - SubSamplingProcess\n    - PortionOfSubstance\n    range: QuantityValue\n  sampled_portion:\n    name: sampled_portion\n    description: The portion of the sample that is taken for downstream activity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: sampled_portion\n    owner: SubSamplingProcess\n    domain_of:\n    - SubSamplingProcess\n    range: SamplePortionEnum\n    multivalued: true\n  instrument_used:\n    name: instrument_used\n    description: What instrument was used during DataGeneration or MaterialProcessing.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: instrument_used\n    owner: SubSamplingProcess\n    domain_of:\n    - MaterialProcessing\n    - DataGeneration\n    range: Instrument\n    multivalued: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n    any_of:\n    - range: Biosample\n    - range: ProcessedSample\n  has_output:\n    name: has_output\n    description: The subsample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessedSample\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: SubSamplingProcess\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: SubSamplingProcess\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: SubSamplingProcess\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: SubSamplingProcess\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: SubSamplingProcess\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: SubSamplingProcess\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:SubSamplingProcess\n\n
"},{"location":"SubstanceRoleEnum/","title":"Enum: SubstanceRoleEnum","text":"

URI: SubstanceRoleEnum

"},{"location":"SubstanceRoleEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description buffer CHEBI:35225 Maintains the pH of the solution within a specific range to stabilize analyte... acid CHEBI:37527 Donates a proton or accepts an electron pair in a chemical reaction base CHEBI:22695 Accepts a proton or donates an electron pair in a chemical reaction ms_proteolytic_enzyme MS:1002986 Enzyme that catalyzes the hydrolysis of proteins and is used in mass spectrom... solvent CHEBI:46787 Dissolves the sample or reagents to facilitate reactions or extraction surfactant CHEBI:35195 Reduces surface tension and aids in the solubilization of substances derivatizing_agent None Chemically modifies analytes to improve detection or separation solubilizing_agent None"},{"location":"SubstanceRoleEnum/#slots","title":"Slots","text":"Name Description substance_role The role of a substance in a process"},{"location":"SubstanceRoleEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstanceRoleEnum/#schema-source","title":"Schema Source","text":""},{"location":"SubstanceRoleEnum/#linkml-source","title":"LinkML Source","text":"
name: SubstanceRoleEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  buffer:\n    text: buffer\n    description: Maintains the pH of the solution within a specific range to stabilize\n      analytes or reactions.\n    meaning: CHEBI:35225\n  acid:\n    text: acid\n    description: Donates a proton or accepts an electron pair in a chemical reaction.\n    meaning: CHEBI:37527\n  base:\n    text: base\n    description: Accepts a proton or donates an electron pair in a chemical reaction.\n    meaning: CHEBI:22695\n  ms_proteolytic_enzyme:\n    text: ms_proteolytic_enzyme\n    description: Enzyme that catalyzes the hydrolysis of proteins and is used in mass\n      spectrometry based proteomics\n    meaning: MS:1002986\n  solvent:\n    text: solvent\n    description: Dissolves the sample or reagents to facilitate reactions or extraction.\n    meaning: CHEBI:46787\n  surfactant:\n    text: surfactant\n    description: Reduces surface tension and aids in the solubilization of substances.\n    meaning: CHEBI:35195\n  derivatizing_agent:\n    text: derivatizing_agent\n    description: Chemically modifies analytes to improve detection or separation.\n  solubilizing_agent:\n    text: solubilizing_agent\n\n
"},{"location":"SubstructureTypeEnum/","title":"Enum: SubstructureTypeEnum","text":"

URI: SubstructureTypeEnum

"},{"location":"SubstructureTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crawlspace None slab on grade None basement None"},{"location":"SubstructureTypeEnum/#slots","title":"Slots","text":"Name Description substructure_type The substructure or under building is that largely hidden section of the buil..."},{"location":"SubstructureTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstructureTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"SubstructureTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: substructure_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  crawlspace:\n    text: crawlspace\n  slab on grade:\n    text: slab on grade\n  basement:\n    text: basement\n\n
"},{"location":"SurfAirContEnum/","title":"Enum: SurfAirContEnum","text":"

URI: SurfAirContEnum

"},{"location":"SurfAirContEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dust None organic matter None particulate matter None volatile organic compounds None biological contaminants None radon None nutrients None biocides None"},{"location":"SurfAirContEnum/#slots","title":"Slots","text":"Name Description surf_air_cont Contaminant identified on surface"},{"location":"SurfAirContEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfAirContEnum/#schema-source","title":"Schema Source","text":""},{"location":"SurfAirContEnum/#linkml-source","title":"LinkML Source","text":"
name: surf_air_cont_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  dust:\n    text: dust\n  organic matter:\n    text: organic matter\n  particulate matter:\n    text: particulate matter\n  volatile organic compounds:\n    text: volatile organic compounds\n  biological contaminants:\n    text: biological contaminants\n  radon:\n    text: radon\n  nutrients:\n    text: nutrients\n  biocides:\n    text: biocides\n\n
"},{"location":"SurfMaterialEnum/","title":"Enum: SurfMaterialEnum","text":"

URI: SurfMaterialEnum

"},{"location":"SurfMaterialEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description adobe None carpet None cinder blocks None concrete None hay bales None glass None metal None paint None plastic None stainless steel None stone None stucco None tile None vinyl None wood None"},{"location":"SurfMaterialEnum/#slots","title":"Slots","text":"Name Description surf_material Surface materials at the point of sampling"},{"location":"SurfMaterialEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfMaterialEnum/#schema-source","title":"Schema Source","text":""},{"location":"SurfMaterialEnum/#linkml-source","title":"LinkML Source","text":"
name: surf_material_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  adobe:\n    text: adobe\n  carpet:\n    text: carpet\n  cinder blocks:\n    text: cinder blocks\n  concrete:\n    text: concrete\n  hay bales:\n    text: hay bales\n  glass:\n    text: glass\n  metal:\n    text: metal\n  paint:\n    text: paint\n  plastic:\n    text: plastic\n  stainless steel:\n    text: stainless steel\n  stone:\n    text: stone\n  stucco:\n    text: stucco\n  tile:\n    text: tile\n  vinyl:\n    text: vinyl\n  wood:\n    text: wood\n\n
"},{"location":"TextValue/","title":"Class: TextValue","text":"

A basic string value

URI: nmdc:TextValue

classDiagram\n  class TextValue\n  click TextValue href \"../TextValue\"\n    AttributeValue <|-- TextValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  TextValue : has_raw_value\n\n  TextValue : language\n\n  TextValue : type\n\n\n\n
"},{"location":"TextValue/#inheritance","title":"Inheritance","text":""},{"location":"TextValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance language 0..1 LanguageCode Should use ISO 639-1 code e direct has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"TextValue/#usages","title":"Usages","text":"used by used in type used NucleotideSequencing target_gene range TextValue NucleotideSequencing target_subfragment range TextValue LibraryPreparation nucl_acid_amp range TextValue LibraryPreparation pcr_cond range TextValue LibraryPreparation pcr_primers range TextValue FieldResearchSite cur_vegetation range TextValue FieldResearchSite geo_loc_name range TextValue FieldResearchSite local_class range TextValue FieldResearchSite soil_type range TextValue Biosample host_disease_stat range TextValue Biosample add_recov_method range TextValue Biosample additional_info range TextValue Biosample address range TextValue Biosample adj_room range TextValue Biosample aero_struc range TextValue Biosample agrochem_addition range TextValue Biosample air_PM_concen range TextValue Biosample air_temp_regm range TextValue Biosample al_sat_meth range TextValue Biosample alkalinity_method range TextValue Biosample ances_data range TextValue Biosample antibiotic_regm range TextValue Biosample aromatics_pc range TextValue Biosample asphaltenes_pc range TextValue Biosample atmospheric_data range TextValue Biosample avg_occup range TextValue Biosample basin range TextValue Biosample bathroom_count range TextValue Biosample bedroom_count range TextValue Biosample biocide range TextValue Biosample biocide_admin_method range TextValue Biosample biomass range TextValue Biosample biotic_regm range TextValue Biosample built_struc_set range TextValue Biosample built_struc_type range TextValue Biosample ceil_struc range TextValue Biosample ceil_water_mold range TextValue Biosample chem_mutagen range TextValue Biosample chem_treatment range TextValue Biosample climate_environment range TextValue Biosample cool_syst_id range TextValue Biosample crop_rotation range TextValue Biosample cult_root_med range TextValue Biosample cur_vegetation range TextValue Biosample cur_vegetation_meth range TextValue Biosample diether_lipids range TextValue Biosample door_water_mold range TextValue Biosample elevator range TextValue Biosample emulsions range TextValue Biosample env_package range TextValue Biosample escalator range TextValue Biosample ext_door range TextValue Biosample fertilizer_regm range TextValue Biosample field range TextValue Biosample fireplace_type range TextValue Biosample floor_count range TextValue Biosample fungicide_regm range TextValue Biosample gaseous_environment range TextValue Biosample gaseous_substances range TextValue Biosample genetic_mod range TextValue Biosample geo_loc_name range TextValue Biosample gravidity range TextValue Biosample gravity range TextValue Biosample growth_hormone_regm range TextValue Biosample hall_count range TextValue Biosample hcr_pressure range TextValue Biosample hcr_temp range TextValue Biosample heat_system_id range TextValue Biosample heavy_metals range TextValue Biosample heavy_metals_meth range TextValue Biosample herbicide_regm range TextValue Biosample horizon_meth range TextValue Biosample host_body_habitat range TextValue Biosample host_color range TextValue Biosample host_common_name range TextValue Biosample host_diet range TextValue Biosample host_genotype range TextValue Biosample host_growth_cond range TextValue Biosample host_last_meal range TextValue Biosample host_life_stage range TextValue Biosample host_shape range TextValue Biosample host_subject_id range TextValue Biosample host_substrate range TextValue Biosample humidity_regm range TextValue Biosample inorg_particles range TextValue Biosample light_regm range TextValue Biosample link_addit_analys range TextValue Biosample link_class_info range TextValue Biosample link_climate_info range TextValue Biosample local_class range TextValue Biosample local_class_meth range TextValue Biosample mechanical_damage range TextValue Biosample mineral_nutr_regm range TextValue Biosample misc_param range TextValue Biosample n_alkanes range TextValue Biosample org_particles range TextValue Biosample particle_class range TextValue Biosample permeability range TextValue Biosample perturbation range TextValue Biosample pesticide_regm range TextValue Biosample ph_meth range TextValue Biosample ph_regm range TextValue Biosample phaeopigments range TextValue Biosample phosplipid_fatt_acid range TextValue Biosample plant_product range TextValue Biosample pollutants range TextValue Biosample porosity range TextValue Biosample pre_treatment range TextValue Biosample previous_land_use range TextValue Biosample primary_treatment range TextValue Biosample radiation_regm range TextValue Biosample rainfall_regm range TextValue Biosample reactor_type range TextValue Biosample reservoir range TextValue Biosample resins_pc range TextValue Biosample room_count range TextValue Biosample room_dim range TextValue Biosample room_door_dist range TextValue Biosample room_door_share range TextValue Biosample room_hallway range TextValue Biosample room_net_area range TextValue Biosample room_vol range TextValue Biosample room_wall_share range TextValue Biosample root_cond range TextValue Biosample root_med_carbon range TextValue Biosample root_med_macronutr range TextValue Biosample root_med_micronutr range TextValue Biosample root_med_regl range TextValue Biosample root_med_solid range TextValue Biosample root_med_suppl range TextValue Biosample salinity_meth range TextValue Biosample salt_regm range TextValue Biosample samp_loc_corr_rate range TextValue Biosample samp_preserv range TextValue Biosample samp_room_id range TextValue Biosample samp_sort_meth range TextValue Biosample samp_store_dur range TextValue Biosample samp_store_loc range TextValue Biosample samp_time_out range TextValue Biosample samp_transport_cond range TextValue Biosample samp_tvdss range TextValue Biosample samp_type range TextValue Biosample samp_well_name range TextValue Biosample saturates_pc range TextValue Biosample season range TextValue Biosample season_environment range TextValue Biosample secondary_treatment range TextValue Biosample sewage_type range TextValue Biosample shading_device_loc range TextValue Biosample shading_device_mat range TextValue Biosample sieving range TextValue Biosample size_frac range TextValue Biosample soil_type range TextValue Biosample soil_type_meth range TextValue Biosample soluble_inorg_mat range TextValue Biosample soluble_org_mat range TextValue Biosample source_mat_id range TextValue Biosample space_typ_state range TextValue Biosample standing_water_regm range TextValue Biosample store_cond range TextValue Biosample suspend_solids range TextValue Biosample tertiary_treatment range TextValue Biosample tiss_cult_growth_med range TextValue Biosample tot_org_c_meth range TextValue Biosample ventilation_type range TextValue Biosample viscosity range TextValue Biosample volatile_org_comp range TextValue Biosample wall_water_mold range TextValue Biosample wastewater_type range TextValue Biosample water_temp_regm range TextValue Biosample watering_regm range TextValue Biosample win range TextValue Biosample wind_direction range TextValue Biosample window_open_freq range TextValue Biosample window_size range TextValue Biosample window_status range TextValue Biosample window_water_mold range TextValue"},{"location":"TextValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TextValue/#schema-source","title":"Schema Source","text":""},{"location":"TextValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:TextValue native nmdc:TextValue"},{"location":"TextValue/#linkml-source","title":"LinkML Source","text":""},{"location":"TextValue/#direct","title":"Direct","text":"
name: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- language\nclass_uri: nmdc:TextValue\n\n
"},{"location":"TextValue/#induced","title":"Induced","text":"
name: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n  language:\n    name: language\n    description: Should use ISO 639-1 code e.g. \"en\", \"fr\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: language\n    owner: TextValue\n    domain_of:\n    - TextValue\n    range: language code\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: TextValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: TextValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:TextValue\n\n
"},{"location":"TidalStageEnum/","title":"Enum: TidalStageEnum","text":"

URI: TidalStageEnum

"},{"location":"TidalStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low tide None ebb tide None flood tide None high tide None"},{"location":"TidalStageEnum/#slots","title":"Slots","text":"Name Description tidal_stage Stage of tide"},{"location":"TidalStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TidalStageEnum/#schema-source","title":"Schema Source","text":""},{"location":"TidalStageEnum/#linkml-source","title":"LinkML Source","text":"
name: tidal_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  low tide:\n    text: low tide\n  ebb tide:\n    text: ebb tide\n  flood tide:\n    text: flood tide\n  high tide:\n    text: high tide\n\n
"},{"location":"TillageEnum/","title":"Enum: TillageEnum","text":"

URI: TillageEnum

"},{"location":"TillageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drill None cutting disc None ridge till None strip tillage None zonal tillage None chisel None tined None mouldboard None disc plough None"},{"location":"TillageEnum/#slots","title":"Slots","text":"Name Description tillage Note method(s) used for tilling"},{"location":"TillageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TillageEnum/#schema-source","title":"Schema Source","text":""},{"location":"TillageEnum/#linkml-source","title":"LinkML Source","text":"
name: tillage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  drill:\n    text: drill\n  cutting disc:\n    text: cutting disc\n  ridge till:\n    text: ridge till\n  strip tillage:\n    text: strip tillage\n  zonal tillage:\n    text: zonal tillage\n  chisel:\n    text: chisel\n  tined:\n    text: tined\n  mouldboard:\n    text: mouldboard\n  disc plough:\n    text: disc plough\n\n
"},{"location":"Time/","title":"Type: Time","text":"

A time object represents a (local) time of day, independent of any particular day

URI: xsd:time

"},{"location":"Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Time/#schema-source","title":"Schema Source","text":""},{"location":"Time/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:time native nmdc:time exact schema:Time"},{"location":"TimestampValue/","title":"Class: TimestampValue","text":"

A value that is a timestamp. The range should be ISO-8601

URI: nmdc:TimestampValue

classDiagram\n  class TimestampValue\n  click TimestampValue href \"../TimestampValue\"\n    AttributeValue <|-- TimestampValue\n      click AttributeValue href \"../AttributeValue\"\n\n\n\n  TimestampValue : has_raw_value\n\n  TimestampValue : type\n\n\n\n
"},{"location":"TimestampValue/#inheritance","title":"Inheritance","text":""},{"location":"TimestampValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance has_raw_value 0..1 String The value that was specified for an annotation in raw form, i AttributeValue type 1 Uriorcurie the class_uri of the class that has been instantiated AttributeValue"},{"location":"TimestampValue/#usages","title":"Usages","text":"used by used in type used Biosample collection_date range TimestampValue Biosample date_last_rain range TimestampValue Biosample iw_bt_date_well range TimestampValue Biosample last_clean range TimestampValue Biosample prod_start_date range TimestampValue"},{"location":"TimestampValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TimestampValue/#schema-source","title":"Schema Source","text":""},{"location":"TimestampValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:TimestampValue native nmdc:TimestampValue"},{"location":"TimestampValue/#linkml-source","title":"LinkML Source","text":""},{"location":"TimestampValue/#direct","title":"Direct","text":"
name: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nclass_uri: nmdc:TimestampValue\n\n
"},{"location":"TimestampValue/#induced","title":"Induced","text":"
name: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n  has_raw_value:\n    name: has_raw_value\n    description: The value that was specified for an annotation in raw form, i.e.\n      a string. E.g. \"2 cm\" or \"2-4 cm\"\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_raw_value\n    owner: TimestampValue\n    domain_of:\n    - AttributeValue\n    range: string\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: TimestampValue\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:TimestampValue\n\n
"},{"location":"TrainLineEnum/","title":"Enum: TrainLineEnum","text":"

URI: TrainLineEnum

"},{"location":"TrainLineEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description red None green None orange None"},{"location":"TrainLineEnum/#slots","title":"Slots","text":"Name Description train_line The subway line name"},{"location":"TrainLineEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainLineEnum/#schema-source","title":"Schema Source","text":""},{"location":"TrainLineEnum/#linkml-source","title":"LinkML Source","text":"
name: train_line_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  red:\n    text: red\n  green:\n    text: green\n  orange:\n    text: orange\n\n
"},{"location":"TrainStatLocEnum/","title":"Enum: TrainStatLocEnum","text":"

URI: TrainStatLocEnum

"},{"location":"TrainStatLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description south station above ground None south station underground None south station amtrak None forest hills None riverside None"},{"location":"TrainStatLocEnum/#slots","title":"Slots","text":"Name Description train_stat_loc The train station collection location"},{"location":"TrainStatLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStatLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"TrainStatLocEnum/#linkml-source","title":"LinkML Source","text":"
name: train_stat_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  south station above ground:\n    text: south station above ground\n  south station underground:\n    text: south station underground\n  south station amtrak:\n    text: south station amtrak\n  forest hills:\n    text: forest hills\n  riverside:\n    text: riverside\n\n
"},{"location":"TrainStopLocEnum/","title":"Enum: TrainStopLocEnum","text":"

URI: TrainStopLocEnum

"},{"location":"TrainStopLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description end None mid None downtown None"},{"location":"TrainStopLocEnum/#slots","title":"Slots","text":"Name Description train_stop_loc The train stop collection location"},{"location":"TrainStopLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStopLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"TrainStopLocEnum/#linkml-source","title":"LinkML Source","text":"
name: train_stop_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  end:\n    text: end\n  mid:\n    text: mid\n  downtown:\n    text: downtown\n\n
"},{"location":"Unit/","title":"Type: Unit","text":"

URI: xsd:string

"},{"location":"Unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Unit/#schema-source","title":"Schema Source","text":""},{"location":"Unit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native nmdc:unit undefined qud:Unit, UO:0000000"},{"location":"Uri/","title":"Type: Uri","text":"

a complete URI

URI: xsd:anyURI

"},{"location":"Uri/#comments","title":"Comments","text":""},{"location":"Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Uri/#schema-source","title":"Schema Source","text":""},{"location":"Uri/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:anyURI native nmdc:uri close schema:URL"},{"location":"Uriorcurie/","title":"Type: Uriorcurie","text":"

a URI or a CURIE

URI: xsd:anyURI

"},{"location":"Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Uriorcurie/#schema-source","title":"Schema Source","text":""},{"location":"Uriorcurie/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:anyURI native nmdc:uriorcurie"},{"location":"VisMediaEnum/","title":"Enum: VisMediaEnum","text":"

URI: VisMediaEnum

"},{"location":"VisMediaEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description photos None videos None commonly of the building None site context (adjacent buildings, vegetation, terrain, streets) None interiors None equipment None 3D scans None"},{"location":"VisMediaEnum/#slots","title":"Slots","text":"Name Description vis_media The building visual media"},{"location":"VisMediaEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"VisMediaEnum/#schema-source","title":"Schema Source","text":""},{"location":"VisMediaEnum/#linkml-source","title":"LinkML Source","text":"
name: vis_media_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  photos:\n    text: photos\n  videos:\n    text: videos\n  commonly of the building:\n    text: commonly of the building\n  site context (adjacent buildings, vegetation, terrain, streets):\n    text: site context (adjacent buildings, vegetation, terrain, streets)\n  interiors:\n    text: interiors\n  equipment:\n    text: equipment\n  3D scans:\n    text: 3D scans\n\n
"},{"location":"WallConstTypeEnum/","title":"Enum: WallConstTypeEnum","text":"

URI: WallConstTypeEnum

"},{"location":"WallConstTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description frame construction None joisted masonry None light noncombustible None masonry noncombustible None modified fire resistive None fire resistive None"},{"location":"WallConstTypeEnum/#slots","title":"Slots","text":"Name Description wall_const_type The building class of the wall defined by the composition of the building ele..."},{"location":"WallConstTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallConstTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallConstTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_const_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  frame construction:\n    text: frame construction\n  joisted masonry:\n    text: joisted masonry\n  light noncombustible:\n    text: light noncombustible\n  masonry noncombustible:\n    text: masonry noncombustible\n  modified fire resistive:\n    text: modified fire resistive\n  fire resistive:\n    text: fire resistive\n\n
"},{"location":"WallFinishMatEnum/","title":"Enum: WallFinishMatEnum","text":"

URI: WallFinishMatEnum

"},{"location":"WallFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plaster None gypsum plaster None veneer plaster None gypsum board None tile None terrazzo None stone facing None acoustical treatment None wood None metal None masonry None"},{"location":"WallFinishMatEnum/#slots","title":"Slots","text":"Name Description wall_finish_mat The material utilized to finish the outer most layer of the wall"},{"location":"WallFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallFinishMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallFinishMatEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  plaster:\n    text: plaster\n  gypsum plaster:\n    text: gypsum plaster\n  veneer plaster:\n    text: veneer plaster\n  gypsum board:\n    text: gypsum board\n  tile:\n    text: tile\n  terrazzo:\n    text: terrazzo\n  stone facing:\n    text: stone facing\n  acoustical treatment:\n    text: acoustical treatment\n  wood:\n    text: wood\n  metal:\n    text: metal\n  masonry:\n    text: masonry\n\n
"},{"location":"WallLocEnum/","title":"Enum: WallLocEnum","text":"

URI: WallLocEnum

"},{"location":"WallLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WallLocEnum/#slots","title":"Slots","text":"Name Description wall_loc The relative location of the wall within the room"},{"location":"WallLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallLocEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n\n
"},{"location":"WallSurfTreatmentEnum/","title":"Enum: WallSurfTreatmentEnum","text":"

URI: WallSurfTreatmentEnum

"},{"location":"WallSurfTreatmentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description painted None wall paper None no treatment None paneling None stucco None fabric None"},{"location":"WallSurfTreatmentEnum/#slots","title":"Slots","text":"Name Description wall_surf_treatment The surface treatment of interior wall"},{"location":"WallSurfTreatmentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallSurfTreatmentEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallSurfTreatmentEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_surf_treatment_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  painted:\n    text: painted\n  wall paper:\n    text: wall paper\n  no treatment:\n    text: no treatment\n  paneling:\n    text: paneling\n  stucco:\n    text: stucco\n  fabric:\n    text: fabric\n\n
"},{"location":"WallTextureEnum/","title":"Enum: WallTextureEnum","text":"

URI: WallTextureEnum

"},{"location":"WallTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"WallTextureEnum/#slots","title":"Slots","text":"Name Description wall_texture The feel, appearance, or consistency of a wall surface"},{"location":"WallTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallTextureEnum/#schema-source","title":"Schema Source","text":""},{"location":"WallTextureEnum/#linkml-source","title":"LinkML Source","text":"
name: wall_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  crows feet:\n    text: crows feet\n  crows-foot stomp:\n    text: crows-foot stomp\n  ? ''\n  : text: ''\n  double skip:\n    text: double skip\n  hawk and trowel:\n    text: hawk and trowel\n  knockdown:\n    text: knockdown\n  popcorn:\n    text: popcorn\n  orange peel:\n    text: orange peel\n  rosebud stomp:\n    text: rosebud stomp\n  Santa-Fe texture:\n    text: Santa-Fe texture\n  skip trowel:\n    text: skip trowel\n  smooth:\n    text: smooth\n  stomp knockdown:\n    text: stomp knockdown\n  swirl:\n    text: swirl\n\n
"},{"location":"WaterFeatTypeEnum/","title":"Enum: WaterFeatTypeEnum","text":"

URI: WaterFeatTypeEnum

"},{"location":"WaterFeatTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fountain None pool None standing feature None stream None waterfall None"},{"location":"WaterFeatTypeEnum/#slots","title":"Slots","text":"Name Description water_feat_type The type of water feature present within the building being sampled"},{"location":"WaterFeatTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WaterFeatTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"WaterFeatTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: water_feat_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  fountain:\n    text: fountain\n  pool:\n    text: pool\n  standing feature:\n    text: standing feature\n  stream:\n    text: stream\n  waterfall:\n    text: waterfall\n\n
"},{"location":"WeekdayEnum/","title":"Enum: WeekdayEnum","text":"

URI: WeekdayEnum

"},{"location":"WeekdayEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Monday None Tuesday None Wednesday None Thursday None Friday None Saturday None Sunday None"},{"location":"WeekdayEnum/#slots","title":"Slots","text":"Name Description weekday The day of the week when sampling occurred"},{"location":"WeekdayEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WeekdayEnum/#schema-source","title":"Schema Source","text":""},{"location":"WeekdayEnum/#linkml-source","title":"LinkML Source","text":"
name: weekday_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  Monday:\n    text: Monday\n  Tuesday:\n    text: Tuesday\n  Wednesday:\n    text: Wednesday\n  Thursday:\n    text: Thursday\n  Friday:\n    text: Friday\n  Saturday:\n    text: Saturday\n  Sunday:\n    text: Sunday\n\n
"},{"location":"WindowCondEnum/","title":"Enum: WindowCondEnum","text":"

URI: WindowCondEnum

"},{"location":"WindowCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"WindowCondEnum/#slots","title":"Slots","text":"Name Description window_cond The physical condition of the window at the time of sampling"},{"location":"WindowCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCondEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowCondEnum/#linkml-source","title":"LinkML Source","text":"
name: window_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  damaged:\n    text: damaged\n  needs repair:\n    text: needs repair\n  new:\n    text: new\n  rupture:\n    text: rupture\n  visible wear:\n    text: visible wear\n\n
"},{"location":"WindowCoverEnum/","title":"Enum: WindowCoverEnum","text":"

URI: WindowCoverEnum

"},{"location":"WindowCoverEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description blinds None curtains None none None"},{"location":"WindowCoverEnum/#slots","title":"Slots","text":"Name Description window_cover The type of window covering"},{"location":"WindowCoverEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCoverEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowCoverEnum/#linkml-source","title":"LinkML Source","text":"
name: window_cover_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  blinds:\n    text: blinds\n  curtains:\n    text: curtains\n  none:\n    text: none\n\n
"},{"location":"WindowHorizPosEnum/","title":"Enum: WindowHorizPosEnum","text":"

URI: WindowHorizPosEnum

"},{"location":"WindowHorizPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description left None middle None right None"},{"location":"WindowHorizPosEnum/#slots","title":"Slots","text":"Name Description window_horiz_pos The horizontal position of the window on the wall"},{"location":"WindowHorizPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowHorizPosEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowHorizPosEnum/#linkml-source","title":"LinkML Source","text":"
name: window_horiz_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  left:\n    text: left\n  middle:\n    text: middle\n  right:\n    text: right\n\n
"},{"location":"WindowLocEnum/","title":"Enum: WindowLocEnum","text":"

URI: WindowLocEnum

"},{"location":"WindowLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WindowLocEnum/#slots","title":"Slots","text":"Name Description window_loc The relative location of the window within the room"},{"location":"WindowLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowLocEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowLocEnum/#linkml-source","title":"LinkML Source","text":"
name: window_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  north:\n    text: north\n  south:\n    text: south\n  east:\n    text: east\n  west:\n    text: west\n\n
"},{"location":"WindowMatEnum/","title":"Enum: WindowMatEnum","text":"

URI: WindowMatEnum

"},{"location":"WindowMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clad None fiberglass None metal None vinyl None wood None"},{"location":"WindowMatEnum/#slots","title":"Slots","text":"Name Description window_mat The type of material used to finish a window"},{"location":"WindowMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowMatEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowMatEnum/#linkml-source","title":"LinkML Source","text":"
name: window_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  clad:\n    text: clad\n  fiberglass:\n    text: fiberglass\n  metal:\n    text: metal\n  vinyl:\n    text: vinyl\n  wood:\n    text: wood\n\n
"},{"location":"WindowTypeEnum/","title":"Enum: WindowTypeEnum","text":"

URI: WindowTypeEnum

"},{"location":"WindowTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description single-hung sash window None horizontal sash window None fixed window None"},{"location":"WindowTypeEnum/#slots","title":"Slots","text":"Name Description window_type The type of windows"},{"location":"WindowTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowTypeEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowTypeEnum/#linkml-source","title":"LinkML Source","text":"
name: window_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  single-hung sash window:\n    text: single-hung sash window\n  horizontal sash window:\n    text: horizontal sash window\n  fixed window:\n    text: fixed window\n\n
"},{"location":"WindowVertPosEnum/","title":"Enum: WindowVertPosEnum","text":"

URI: WindowVertPosEnum

"},{"location":"WindowVertPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bottom None middle None top None low None high None"},{"location":"WindowVertPosEnum/#slots","title":"Slots","text":"Name Description window_vert_pos The vertical position of the window on the wall"},{"location":"WindowVertPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowVertPosEnum/#schema-source","title":"Schema Source","text":""},{"location":"WindowVertPosEnum/#linkml-source","title":"LinkML Source","text":"
name: window_vert_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  bottom:\n    text: bottom\n  middle:\n    text: middle\n  top:\n    text: top\n  low:\n    text: low\n  high:\n    text: high\n\n
"},{"location":"WorkflowExecution/","title":"Class: WorkflowExecution","text":"

Represents an instance of an execution of a particular workflow

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:WorkflowExecution

Note

Mermaid class diagram too large to render.

"},{"location":"WorkflowExecution/#inheritance","title":"Inheritance","text":""},{"location":"WorkflowExecution/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance ended_at_time 0..1 String direct execution_resource 1 ExecutionResourceEnum The computing resource or facility where the workflow was executed direct git_url 1 String The url that points to the exact github location of a workflow direct started_at_time 1 String direct version 0..1 String direct was_informed_by 1 DataGeneration direct has_input 1..* NamedThing An input to a process PlannedProcess has_output * NamedThing An output from a process PlannedProcess processing_institution 0..1 ProcessingInstitutionEnum The organization that processed the sample PlannedProcess protocol_link 0..1 Protocol PlannedProcess start_date 0..1 String The date on which any process or activity was started PlannedProcess end_date 0..1 String The date on which any process or activity was ended PlannedProcess qc_status 0..1 StatusEnum Stores information about the result of a process (ie the process of sequencin... PlannedProcess qc_comment 0..1 String Slot to store additional comments about laboratory or workflow output PlannedProcess has_failure_categorization * FailureCategorization PlannedProcess id 1 Uriorcurie A unique identifier for a thing NamedThing name 0..1 String A human readable label for an entity NamedThing description 0..1 String a human-readable description of a thing NamedThing alternative_identifiers * Uriorcurie A list of alternative identifiers for the entity NamedThing type 1 Uriorcurie the class_uri of the class that has been instantiated NamedThing"},{"location":"WorkflowExecution/#usages","title":"Usages","text":"used by used in type used FunctionalAnnotationAggMember metagenome_annotation_id range WorkflowExecution Database workflow_execution_set range WorkflowExecution FunctionalAnnotation was_generated_by any_of[range] WorkflowExecution DataObject was_generated_by range WorkflowExecution DataObject was_generated_by any_of[range] WorkflowExecution"},{"location":"WorkflowExecution/#aliases","title":"Aliases","text":""},{"location":"WorkflowExecution/#comments","title":"Comments","text":""},{"location":"WorkflowExecution/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WorkflowExecution/#schema-source","title":"Schema Source","text":""},{"location":"WorkflowExecution/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self nmdc:WorkflowExecution native nmdc:WorkflowExecution"},{"location":"WorkflowExecution/#linkml-source","title":"LinkML Source","text":""},{"location":"WorkflowExecution/#direct","title":"Direct","text":"
name: WorkflowExecution\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: An analysis contains secondary analysis results derived from sequence\n      reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) subclasses of WorkflowExecution is a distinct\n  run with start and stop times, potentially with different inputs and outputs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: PlannedProcess\nabstract: true\nslots:\n- ended_at_time\n- execution_resource\n- git_url\n- started_at_time\n- version\n- was_informed_by\nslot_usage:\n  started_at_time:\n    name: started_at_time\n    required: true\n  git_url:\n    name: git_url\n    required: true\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  execution_resource:\n    name: execution_resource\n    required: true\n  was_informed_by:\n    name: was_informed_by\n    required: true\nclass_uri: nmdc:WorkflowExecution\nrules:\n- preconditions:\n    slot_conditions:\n      qc_status:\n        name: qc_status\n        equals_string: pass\n  postconditions:\n    slot_conditions:\n      has_output:\n        name: has_output\n        required: true\n  description: If qc_status has a value of pass, then the has_output slot is required.\n  title: qc_status_pass_has_output_required\n- preconditions:\n    slot_conditions:\n      qc_status:\n        name: qc_status\n        value_presence: ABSENT\n  postconditions:\n    slot_conditions:\n      has_output:\n        name: has_output\n        required: true\n  description: If qc_status is not specified, then the has_output slot is required.\n  title: qc_status_pass_null_has_output_required\n\n
"},{"location":"WorkflowExecution/#induced","title":"Induced","text":"
name: WorkflowExecution\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n  embl.ena:\n    source: embl.ena\n    description: An analysis contains secondary analysis results derived from sequence\n      reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) subclasses of WorkflowExecution is a distinct\n  run with start and stop times, potentially with different inputs and outputs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n  started_at_time:\n    name: started_at_time\n    required: true\n  git_url:\n    name: git_url\n    required: true\n  has_input:\n    name: has_input\n    required: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  execution_resource:\n    name: execution_resource\n    required: true\n  was_informed_by:\n    name: was_informed_by\n    required: true\nattributes:\n  ended_at_time:\n    name: ended_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:endedAtTime\n    rank: 1000\n    alias: ended_at_time\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: string\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  execution_resource:\n    name: execution_resource\n    description: The computing resource or facility where the workflow was executed.\n    examples:\n    - value: NERSC-Cori\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: execution_resource\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: ExecutionResourceEnum\n    required: true\n  git_url:\n    name: git_url\n    description: The url that points to the exact github location of a workflow.\n    examples:\n    - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n    - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: git_url\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n  started_at_time:\n    name: started_at_time\n    notes:\n    - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n      It may not be complete, but it is good enough for now.'\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:startedAtTime\n    rank: 1000\n    alias: started_at_time\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: string\n    required: true\n    pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n  version:\n    name: version\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: version\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: string\n  was_informed_by:\n    name: was_informed_by\n    from_schema: https://w3id.org/nmdc/nmdc\n    mappings:\n    - prov:wasInformedBy\n    rank: 1000\n    alias: was_informed_by\n    owner: WorkflowExecution\n    domain_of:\n    - WorkflowExecution\n    range: DataGeneration\n    required: true\n  has_input:\n    name: has_input\n    description: An input to a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - input\n    rank: 1000\n    alias: has_input\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    required: true\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  has_output:\n    name: has_output\n    description: An output from a process.\n    from_schema: https://w3id.org/nmdc/nmdc\n    aliases:\n    - output\n    rank: 1000\n    alias: has_output\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: NamedThing\n    multivalued: true\n    structured_pattern:\n      syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n      interpolated: true\n  processing_institution:\n    name: processing_institution\n    description: The organization that processed the sample.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: processing_institution\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: ProcessingInstitutionEnum\n  protocol_link:\n    name: protocol_link\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: protocol_link\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    - Study\n    range: Protocol\n  start_date:\n    name: start_date\n    description: The date on which any process or activity was started\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: start_date\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  end_date:\n    name: end_date\n    description: The date on which any process or activity was ended\n    todos:\n    - add date string validation pattern\n    comments:\n    - We are using string representations of dates until all components of our ecosystem\n      can handle ISO 8610 dates\n    - The date should be formatted as YYYY-MM-DD\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: end_date\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  qc_status:\n    name: qc_status\n    description: Stores information about the result of a process (ie the process\n      of sequencing a library may have for qc_status of 'fail' if not enough data\n      was generated)\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_status\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: StatusEnum\n  qc_comment:\n    name: qc_comment\n    description: Slot to store additional comments about laboratory or workflow output.\n      For workflow output it may describe the particular workflow stage that failed.\n      (ie Failed at call-stage due to a malformed fastq file).\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: qc_comment\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: string\n  has_failure_categorization:\n    name: has_failure_categorization\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: has_failure_categorization\n    owner: WorkflowExecution\n    domain_of:\n    - PlannedProcess\n    range: FailureCategorization\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  id:\n    name: id\n    description: A unique identifier for a thing. Must be either a CURIE shorthand\n      for a URI or a complete URI\n    notes:\n    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n      will be accepted\n    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n      via per-class id slot usage assertions\n    - minting authority shoulders should probably be enumerated and checked in the\n      pattern\n    examples:\n    - value: nmdc:mgmag-00-x012.1_7_c1\n      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: WorkflowExecution\n    domain_of:\n    - NamedThing\n    range: uriorcurie\n    required: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  name:\n    name: name\n    description: A human readable label for an entity\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: name\n    owner: WorkflowExecution\n    domain_of:\n    - PersonValue\n    - NamedThing\n    - Protocol\n    range: string\n  description:\n    name: description\n    description: a human-readable description of a thing\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    slot_uri: dcterms:description\n    alias: description\n    owner: WorkflowExecution\n    domain_of:\n    - ImageValue\n    - NamedThing\n    range: string\n  alternative_identifiers:\n    name: alternative_identifiers\n    description: A list of alternative identifiers for the entity.\n    from_schema: https://w3id.org/nmdc/nmdc\n    rank: 1000\n    alias: alternative_identifiers\n    owner: WorkflowExecution\n    domain_of:\n    - MetaboliteIdentification\n    - NamedThing\n    range: uriorcurie\n    multivalued: true\n    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n  type:\n    name: type\n    description: the class_uri of the class that has been instantiated\n    notes:\n    - replaces legacy nmdc:type slot\n    - makes it easier to read example data files\n    - required for polymorphic MongoDB collections\n    examples:\n    - value: nmdc:Biosample\n    - value: nmdc:Study\n    from_schema: https://w3id.org/nmdc/nmdc\n    see_also:\n    - https://github.com/microbiomedata/nmdc-schema/issues/1048\n    - https://github.com/microbiomedata/nmdc-schema/issues/1233\n    - https://github.com/microbiomedata/nmdc-schema/issues/248\n    rank: 1000\n    slot_uri: rdf:type\n    designates_type: true\n    alias: type\n    owner: WorkflowExecution\n    domain_of:\n    - EukEval\n    - FunctionalAnnotationAggMember\n    - MobilePhaseSegment\n    - PortionOfSubstance\n    - MagBin\n    - MetaboliteIdentification\n    - PeptideQuantification\n    - ProteinQuantification\n    - GenomeFeature\n    - FunctionalAnnotation\n    - AttributeValue\n    - NamedThing\n    - FailureCategorization\n    - Protocol\n    - CreditAssociation\n    - Doi\n    range: uriorcurie\n    required: true\nclass_uri: nmdc:WorkflowExecution\nrules:\n- preconditions:\n    slot_conditions:\n      qc_status:\n        name: qc_status\n        equals_string: pass\n  postconditions:\n    slot_conditions:\n      has_output:\n        name: has_output\n        required: true\n  description: If qc_status has a value of pass, then the has_output slot is required.\n  title: qc_status_pass_has_output_required\n- preconditions:\n    slot_conditions:\n      qc_status:\n        name: qc_status\n        value_presence: ABSENT\n  postconditions:\n    slot_conditions:\n      has_output:\n        name: has_output\n        required: true\n  description: If qc_status is not specified, then the has_output slot is required.\n  title: qc_status_pass_null_has_output_required\n\n
"},{"location":"WorkflowSubset/","title":"Subset: WorkflowSubset","text":"

Subset consisting of just the workflow execution activities

URI: WorkflowSubset

"},{"location":"WorkflowSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WorkflowSubset/#schema-source","title":"Schema Source","text":""},{"location":"WorkflowSubset/#classes-in-subset","title":"Classes in subset","text":"Class Description MagsAnalysis A workflow execution activity that uses computational binning tools to group ... MetabolomicsAnalysis MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... MetagenomeSequencing Initial sequencing activity that precedes any analysis MetaproteomicsAnalysis MetatranscriptomeAnnotation MetatranscriptomeAssembly MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... NomAnalysis ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... WorkflowExecution Represents an instance of an execution of a particular workflow"},{"location":"YesNoEnum/","title":"Enum: YesNoEnum","text":"

replaces DnaDnaseEnum and DnaseRnaEnum

URI: YesNoEnum

"},{"location":"YesNoEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description no None yes None"},{"location":"YesNoEnum/#slots","title":"Slots","text":"Name Description dna_dnase dnase_rna"},{"location":"YesNoEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"YesNoEnum/#schema-source","title":"Schema Source","text":""},{"location":"YesNoEnum/#linkml-source","title":"LinkML Source","text":"
name: YesNoEnum\ndescription: replaces DnaDnaseEnum and DnaseRnaEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n  'no':\n    text: 'no'\n  'yes':\n    text: 'yes'\n\n
"},{"location":"about/","title":"About","text":""},{"location":"about/#nmdc-schema","title":"NMDC Schema","text":"

Schema resources for the National Microbiome Data Collaborative (NMDC)

The purpose of the NMDC Schema is to define metadata for the National Microbiome Data Collaborative (NMDC). The NMDC is a multi-organizational effort to enable integrated microbiome data across diverse areas in medicine, agriculture, bioenergy, and the environment. This integrated platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science.

The NMDC schema is used during the translation process to specify how metadata elements are related.

"},{"location":"about/#credits","title":"Credits","text":"

this project was made using the LinkML framework

"},{"location":"abs_air_humidity/","title":"Slot: absolute air humidity (abs_air_humidity)","text":"

Actual mass of water vapor - mh20 - present in the air water vapor mixture

URI: MIXS:0000122

"},{"location":"abs_air_humidity/#inheritance","title":"Inheritance","text":""},{"location":"abs_air_humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"abs_air_humidity/#properties","title":"Properties","text":""},{"location":"abs_air_humidity/#aliases","title":"Aliases","text":""},{"location":"abs_air_humidity/#examples","title":"Examples","text":"Value 9 gram per gram"},{"location":"abs_air_humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"abs_air_humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"abs_air_humidity/#schema-source","title":"Schema Source","text":""},{"location":"abs_air_humidity/#linkml-source","title":"LinkML Source","text":"
name: abs_air_humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per gram, kilogram per kilogram, kilogram, pound\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Actual mass of water vapor - mh20 - present in the air water vapor mixture\ntitle: absolute air humidity\nexamples:\n- value: 9 gram per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- absolute air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000122\nalias: abs_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"add_date/","title":"Slot: add_date","text":"

The date on which the information was added to the database.

URI: nmdc:add_date

"},{"location":"add_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no Biosample Biological source material which can be characterized by an experiment no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"add_date/#properties","title":"Properties","text":""},{"location":"add_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"add_date/#schema-source","title":"Schema Source","text":""},{"location":"add_date/#linkml-source","title":"LinkML Source","text":"
name: add_date\ndescription: The date on which the information was added to the database.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: add_date\ndomain_of:\n- Biosample\n- DataGeneration\nrange: string\n\n
"},{"location":"add_recov_method/","title":"Slot: secondary and tertiary recovery methods and start date (add_recov_method)","text":"

Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0001009

"},{"location":"add_recov_method/#inheritance","title":"Inheritance","text":""},{"location":"add_recov_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"add_recov_method/#properties","title":"Properties","text":""},{"location":"add_recov_method/#aliases","title":"Aliases","text":""},{"location":"add_recov_method/#examples","title":"Examples","text":"Value Polymer Addition;2018-06-21T14:30Z"},{"location":"add_recov_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"add_recov_method/#annotations","title":"Annotations","text":"property value expected_value enumeration;timestamp"},{"location":"add_recov_method/#schema-source","title":"Schema Source","text":""},{"location":"add_recov_method/#linkml-source","title":"LinkML Source","text":"
name: add_recov_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration;timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n  for increase of hydrocarbon recovery from resource and start date for each one of\n  them. If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: secondary and tertiary recovery methods and start date\nexamples:\n- value: Polymer Addition;2018-06-21T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary and tertiary recovery methods and start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001009\nalias: add_recov_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"additional_info/","title":"Slot: additional info (additional_info)","text":"

Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary

URI: MIXS:0000300

"},{"location":"additional_info/#inheritance","title":"Inheritance","text":""},{"location":"additional_info/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"additional_info/#properties","title":"Properties","text":""},{"location":"additional_info/#aliases","title":"Aliases","text":""},{"location":"additional_info/#examples","title":"Examples","text":"Value"},{"location":"additional_info/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"additional_info/#annotations","title":"Annotations","text":"property value expected_value text"},{"location":"additional_info/#schema-source","title":"Schema Source","text":""},{"location":"additional_info/#linkml-source","title":"LinkML Source","text":"
name: additional_info\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information that doesn't fit anywhere else. Can also be used to propose\n  new entries for fields with controlled vocabulary\ntitle: additional info\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- additional info\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000300\nalias: additional_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"address/","title":"Slot: address (address)","text":"

The street name and building number where the sampling occurred.

URI: MIXS:0000218

"},{"location":"address/#inheritance","title":"Inheritance","text":""},{"location":"address/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"address/#properties","title":"Properties","text":""},{"location":"address/#aliases","title":"Aliases","text":""},{"location":"address/#examples","title":"Examples","text":"Value"},{"location":"address/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"address/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"address/#schema-source","title":"Schema Source","text":""},{"location":"address/#linkml-source","title":"LinkML Source","text":"
name: address\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The street name and building number where the sampling occurred.\ntitle: address\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- address\nrank: 1000\nis_a: core field\nstring_serialization: '{integer}{text}'\nslot_uri: MIXS:0000218\nalias: address\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"adj_room/","title":"Slot: adjacent rooms (adj_room)","text":"

List of rooms (room number, room name) immediately adjacent to the sampling room

URI: MIXS:0000219

"},{"location":"adj_room/#inheritance","title":"Inheritance","text":""},{"location":"adj_room/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"adj_room/#properties","title":"Properties","text":""},{"location":"adj_room/#aliases","title":"Aliases","text":""},{"location":"adj_room/#examples","title":"Examples","text":"Value"},{"location":"adj_room/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"adj_room/#annotations","title":"Annotations","text":"property value expected_value room name;room number"},{"location":"adj_room/#schema-source","title":"Schema Source","text":""},{"location":"adj_room/#linkml-source","title":"LinkML Source","text":"
name: adj_room\nannotations:\n  expected_value:\n    tag: expected_value\n    value: room name;room number\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of rooms (room number, room name) immediately adjacent to the sampling\n  room\ntitle: adjacent rooms\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- adjacent rooms\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000219\nalias: adj_room\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"aero_struc/","title":"Slot: aerospace structure (aero_struc)","text":"

Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together

URI: MIXS:0000773

"},{"location":"aero_struc/#inheritance","title":"Inheritance","text":""},{"location":"aero_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"aero_struc/#properties","title":"Properties","text":""},{"location":"aero_struc/#aliases","title":"Aliases","text":""},{"location":"aero_struc/#examples","title":"Examples","text":"Value plane"},{"location":"aero_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"aero_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"aero_struc/#schema-source","title":"Schema Source","text":""},{"location":"aero_struc/#linkml-source","title":"LinkML Source","text":"
name: aero_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Aerospace structures typically consist of thin plates with stiffeners\n  for the external surfaces, bulkheads and frames to support the shape and fasteners\n  such as welds, rivets, screws and bolts to hold the components together\ntitle: aerospace structure\nexamples:\n- value: plane\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aerospace structure\nrank: 1000\nis_a: core field\nstring_serialization: '[plane|glider]'\nslot_uri: MIXS:0000773\nalias: aero_struc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"agrochem_addition/","title":"Slot: history/agrochemical additions (agrochem_addition)","text":"

Addition of fertilizers, pesticides, etc. - amount and time of applications

URI: MIXS:0000639

"},{"location":"agrochem_addition/#inheritance","title":"Inheritance","text":""},{"location":"agrochem_addition/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"agrochem_addition/#properties","title":"Properties","text":""},{"location":"agrochem_addition/#aliases","title":"Aliases","text":""},{"location":"agrochem_addition/#examples","title":"Examples","text":"Value roundup;5 milligram per liter;2018-06-21"},{"location":"agrochem_addition/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"agrochem_addition/#annotations","title":"Annotations","text":"property value expected_value agrochemical name;agrochemical amount;timestamp"},{"location":"agrochem_addition/#schema-source","title":"Schema Source","text":""},{"location":"agrochem_addition/#linkml-source","title":"LinkML Source","text":"
name: agrochem_addition\nannotations:\n  expected_value:\n    tag: expected_value\n    value: agrochemical name;agrochemical amount;timestamp\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Addition of fertilizers, pesticides, etc. - amount and time of applications\ntitle: history/agrochemical additions\nexamples:\n- value: roundup;5 milligram per liter;2018-06-21\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/agrochemical additions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{timestamp}'\nslot_uri: MIXS:0000639\nalias: agrochem_addition\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"air_PM_concen/","title":"Slot: air particulate matter concentration (air_PM_concen)","text":"

Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM

URI: MIXS:0000108

"},{"location":"air_PM_concen/#inheritance","title":"Inheritance","text":""},{"location":"air_PM_concen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"air_PM_concen/#properties","title":"Properties","text":""},{"location":"air_PM_concen/#aliases","title":"Aliases","text":""},{"location":"air_PM_concen/#examples","title":"Examples","text":"Value PM2.5;10 microgram per cubic meter"},{"location":"air_PM_concen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"air_PM_concen/#annotations","title":"Annotations","text":"property value expected_value particulate matter name;measurement value"},{"location":"air_PM_concen/#schema-source","title":"Schema Source","text":""},{"location":"air_PM_concen/#linkml-source","title":"LinkML Source","text":"
name: air_PM_concen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: particulate matter name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micrograms per cubic meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of substances that remain suspended in the air, and comprise\n  mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple\n  PM's by entering numeric values preceded by name of PM\ntitle: air particulate matter concentration\nexamples:\n- value: PM2.5;10 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air particulate matter concentration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000108\nalias: air_PM_concen\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"air_temp/","title":"Slot: air temperature (air_temp)","text":"

Temperature of the air at the time of sampling

URI: MIXS:0000124

"},{"location":"air_temp/#inheritance","title":"Inheritance","text":""},{"location":"air_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"air_temp/#properties","title":"Properties","text":""},{"location":"air_temp/#aliases","title":"Aliases","text":""},{"location":"air_temp/#examples","title":"Examples","text":"Value 20 degree Celsius"},{"location":"air_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"air_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"air_temp/#schema-source","title":"Schema Source","text":""},{"location":"air_temp/#linkml-source","title":"LinkML Source","text":"
name: air_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Temperature of the air at the time of sampling\ntitle: air temperature\nexamples:\n- value: 20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000124\nalias: air_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"air_temp_regm/","title":"Slot: air temperature regimen (air_temp_regm)","text":"

Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens

URI: MIXS:0000551

"},{"location":"air_temp_regm/#inheritance","title":"Inheritance","text":""},{"location":"air_temp_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"air_temp_regm/#properties","title":"Properties","text":""},{"location":"air_temp_regm/#aliases","title":"Aliases","text":""},{"location":"air_temp_regm/#examples","title":"Examples","text":"Value 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"air_temp_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"air_temp_regm/#annotations","title":"Annotations","text":"property value expected_value temperature value;treatment interval and duration"},{"location":"air_temp_regm/#schema-source","title":"Schema Source","text":""},{"location":"air_temp_regm/#linkml-source","title":"LinkML Source","text":"
name: air_temp_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: temperature value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to varying temperatures;\n  should include the temperature, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include different temperature regimens\ntitle: air temperature regimen\nexamples:\n- value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000551\nalias: air_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"al_sat/","title":"Slot: extreme_unusual_properties/Al saturation (al_sat)","text":"

Aluminum saturation (esp. For tropical soils)

URI: MIXS:0000607

"},{"location":"al_sat/#inheritance","title":"Inheritance","text":""},{"location":"al_sat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"al_sat/#properties","title":"Properties","text":""},{"location":"al_sat/#aliases","title":"Aliases","text":""},{"location":"al_sat/#examples","title":"Examples","text":"Value"},{"location":"al_sat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"al_sat/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"al_sat/#schema-source","title":"Schema Source","text":""},{"location":"al_sat/#linkml-source","title":"LinkML Source","text":"
name: al_sat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Aluminum saturation (esp. For tropical soils)\ntitle: extreme_unusual_properties/Al saturation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000607\nalias: al_sat\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"al_sat_meth/","title":"Slot: extreme_unusual_properties/Al saturation method (al_sat_meth)","text":"

Reference or method used in determining Al saturation

URI: MIXS:0000324

"},{"location":"al_sat_meth/#inheritance","title":"Inheritance","text":""},{"location":"al_sat_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"al_sat_meth/#properties","title":"Properties","text":""},{"location":"al_sat_meth/#aliases","title":"Aliases","text":""},{"location":"al_sat_meth/#examples","title":"Examples","text":"Value"},{"location":"al_sat_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"al_sat_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or URL"},{"location":"al_sat_meth/#schema-source","title":"Schema Source","text":""},{"location":"al_sat_meth/#linkml-source","title":"LinkML Source","text":"
name: al_sat_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or URL\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining Al saturation\ntitle: extreme_unusual_properties/Al saturation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000324\nalias: al_sat_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"alkalinity/","title":"Slot: alkalinity (alkalinity)","text":"

Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate

URI: MIXS:0000421

"},{"location":"alkalinity/#inheritance","title":"Inheritance","text":""},{"location":"alkalinity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"alkalinity/#properties","title":"Properties","text":""},{"location":"alkalinity/#aliases","title":"Aliases","text":""},{"location":"alkalinity/#examples","title":"Examples","text":"Value 50 milligram per liter"},{"location":"alkalinity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alkalinity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"alkalinity/#schema-source","title":"Schema Source","text":""},{"location":"alkalinity/#linkml-source","title":"LinkML Source","text":"
name: alkalinity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milliequivalent per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Alkalinity, the ability of a solution to neutralize acids to the equivalence\n  point of carbonate or bicarbonate\ntitle: alkalinity\nexamples:\n- value: 50 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000421\nalias: alkalinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"alkalinity_method/","title":"Slot: alkalinity method (alkalinity_method)","text":"

Method used for alkalinity measurement

URI: MIXS:0000298

"},{"location":"alkalinity_method/#inheritance","title":"Inheritance","text":""},{"location":"alkalinity_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"alkalinity_method/#properties","title":"Properties","text":""},{"location":"alkalinity_method/#aliases","title":"Aliases","text":""},{"location":"alkalinity_method/#examples","title":"Examples","text":"Value titration"},{"location":"alkalinity_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alkalinity_method/#annotations","title":"Annotations","text":"property value expected_value description of method"},{"location":"alkalinity_method/#schema-source","title":"Schema Source","text":""},{"location":"alkalinity_method/#linkml-source","title":"LinkML Source","text":"
name: alkalinity_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: description of method\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Method used for alkalinity measurement\ntitle: alkalinity method\nexamples:\n- value: titration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000298\nalias: alkalinity_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"alkyl_diethers/","title":"Slot: alkyl diethers (alkyl_diethers)","text":"

Concentration of alkyl diethers

URI: MIXS:0000490

"},{"location":"alkyl_diethers/#inheritance","title":"Inheritance","text":""},{"location":"alkyl_diethers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"alkyl_diethers/#properties","title":"Properties","text":""},{"location":"alkyl_diethers/#aliases","title":"Aliases","text":""},{"location":"alkyl_diethers/#examples","title":"Examples","text":"Value 0.005 mole per liter"},{"location":"alkyl_diethers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alkyl_diethers/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"alkyl_diethers/#schema-source","title":"Schema Source","text":""},{"location":"alkyl_diethers/#linkml-source","title":"LinkML Source","text":"
name: alkyl_diethers\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of alkyl diethers\ntitle: alkyl diethers\nexamples:\n- value: 0.005 mole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkyl diethers\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000490\nalias: alkyl_diethers\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"all_proteins/","title":"Slot: all_proteins","text":"

the list of protein identifiers that are associated with the peptide sequence

URI: nmdc:all_proteins

"},{"location":"all_proteins/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"all_proteins/#properties","title":"Properties","text":""},{"location":"all_proteins/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"all_proteins/#schema-source","title":"Schema Source","text":""},{"location":"all_proteins/#linkml-source","title":"LinkML Source","text":"
name: all_proteins\ndescription: the list of protein identifiers that are associated with the peptide\n  sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: all_proteins\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\nmultivalued: true\n\n
"},{"location":"alt/","title":"Slot: altitude (alt)","text":"

Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air

URI: MIXS:0000094

"},{"location":"alt/#inheritance","title":"Inheritance","text":""},{"location":"alt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"alt/#properties","title":"Properties","text":""},{"location":"alt/#aliases","title":"Aliases","text":""},{"location":"alt/#examples","title":"Examples","text":"Value 100 meter"},{"location":"alt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alt/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"alt/#schema-source","title":"Schema Source","text":""},{"location":"alt/#linkml-source","title":"LinkML Source","text":"
name: alt\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\ndescription: Altitude is a term used to identify heights of objects such as airplanes,\n  space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric\n  layers and clouds. It is used to measure the height of an object which is above\n  the earth's surface. In this context, the altitude measurement is the vertical distance\n  between the earth's surface above sea level and the sampled position in the air\ntitle: altitude\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- altitude\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000094\nalias: alt\ndomain_of:\n- agriculture\n- air\n- built environment\n- core\n- food-animal and animal feed\n- food-farm environment\n- food-food production facility\n- food-human foods\n- host-associated\n- human-associated\n- human-gut\n- human-oral\n- human-skin\n- human-vaginal\n- hydrocarbon resources-cores\n- hydrocarbon resources-fluids_swabs\n- microbial mat_biofilm\n- miscellaneous natural or artificial environment\n- plant-associated\n- sediment\n- soil\n- symbiont-associated\n- wastewater_sludge\n- water\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"alternative_descriptions/","title":"Slot: alternative_descriptions","text":"

A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.

URI: nmdc:alternative_descriptions

"},{"location":"alternative_descriptions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_descriptions/#properties","title":"Properties","text":""},{"location":"alternative_descriptions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alternative_descriptions/#schema-source","title":"Schema Source","text":""},{"location":"alternative_descriptions/#linkml-source","title":"LinkML Source","text":"
name: alternative_descriptions\ndescription: A list of alternative descriptions for the entity. The distinction between\n  description and alternative descriptions is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternative_descriptions\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\n
"},{"location":"alternative_identifiers/","title":"Slot: alternative_identifiers","text":"

A list of alternative identifiers for the entity.

URI: nmdc:alternative_identifiers

"},{"location":"alternative_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"alternative_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no Site no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MaterialEntity no MetatranscriptomeAssembly no Configuration A set of parameters that define the actions of a process and is shared among ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DataObject An object that primarily consists of symbols that represent information no PlannedProcess no EnvironmentalMaterialTerm no NamedThing a databased entity or concept/class no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no ProcessedSample no ChemicalEntity An atom or molecule that can be represented with a chemical formula no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no Instrument A material entity that is designed to perform a function in a scientific inve... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no GeneProduct A molecule encoded by a gene that has an evolved function no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Study A study summarizes the overall goal of a research initiative and outlines the... yes MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no CalibrationInformation A calibration object that is associated with a process no Extraction A material separation in which a desired component of an input material is se... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no OntologyClass no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ProtocolExecution A PlannedProces that has PlannedProcess parts no Manifest no OrthologyGroup A set of genes or gene products in which all members are orthologous no Biosample Biological source material which can be characterized by an experiment yes LibraryPreparation no"},{"location":"alternative_identifiers/#properties","title":"Properties","text":""},{"location":"alternative_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alternative_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"alternative_identifiers/#linkml-source","title":"LinkML Source","text":"
name: alternative_identifiers\ndescription: A list of alternative identifiers for the entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternative_identifiers\ndomain_of:\n- MetaboliteIdentification\n- NamedThing\nrange: uriorcurie\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"alternative_names/","title":"Slot: alternative_names","text":"

A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.

URI: nmdc:alternative_names

"},{"location":"alternative_names/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"alternative_names/#properties","title":"Properties","text":""},{"location":"alternative_names/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alternative_names/#schema-source","title":"Schema Source","text":""},{"location":"alternative_names/#linkml-source","title":"LinkML Source","text":"
name: alternative_names\ndescription: A list of alternative names used to refer to the entity. The distinction\n  between name and alternative names is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\n- skos:altLabel\nrank: 1000\nalias: alternative_names\ndomain_of:\n- ChemicalEntity\n- Study\nrange: string\nmultivalued: true\n\n
"},{"location":"alternative_titles/","title":"Slot: alternative_titles","text":"

A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.

URI: nmdc:alternative_titles

"},{"location":"alternative_titles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_titles/#properties","title":"Properties","text":""},{"location":"alternative_titles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"alternative_titles/#schema-source","title":"Schema Source","text":""},{"location":"alternative_titles/#linkml-source","title":"LinkML Source","text":"
name: alternative_titles\ndescription: A list of alternative titles for the entity. The distinction between\n  title and alternative titles is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\nrank: 1000\nalias: alternative_titles\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\n
"},{"location":"aminopept_act/","title":"Slot: aminopeptidase activity (aminopept_act)","text":"

Measurement of aminopeptidase activity

URI: MIXS:0000172

"},{"location":"aminopept_act/#inheritance","title":"Inheritance","text":""},{"location":"aminopept_act/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"aminopept_act/#properties","title":"Properties","text":""},{"location":"aminopept_act/#aliases","title":"Aliases","text":""},{"location":"aminopept_act/#examples","title":"Examples","text":"Value 0.269 mole per liter per hour"},{"location":"aminopept_act/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"aminopept_act/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"aminopept_act/#schema-source","title":"Schema Source","text":""},{"location":"aminopept_act/#linkml-source","title":"LinkML Source","text":"
name: aminopept_act\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per liter per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of aminopeptidase activity\ntitle: aminopeptidase activity\nexamples:\n- value: 0.269 mole per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aminopeptidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000172\nalias: aminopept_act\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ammonium/","title":"Slot: ammonium (ammonium)","text":"

Concentration of ammonium in the sample

URI: MIXS:0000427

"},{"location":"ammonium/#inheritance","title":"Inheritance","text":""},{"location":"ammonium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ammonium/#properties","title":"Properties","text":""},{"location":"ammonium/#aliases","title":"Aliases","text":""},{"location":"ammonium/#examples","title":"Examples","text":"Value 1.5 milligram per liter"},{"location":"ammonium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ammonium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ammonium/#schema-source","title":"Schema Source","text":""},{"location":"ammonium/#linkml-source","title":"LinkML Source","text":"
name: ammonium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of ammonium in the sample\ntitle: ammonium\nexamples:\n- value: 1.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ammonium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000427\nalias: ammonium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ammonium_nitrogen/","title":"Slot: ammonium nitrogen (ammonium_nitrogen)","text":"

Concentration of ammonium nitrogen in the sample

URI: nmdc:ammonium_nitrogen

"},{"location":"ammonium_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ammonium_nitrogen/#properties","title":"Properties","text":""},{"location":"ammonium_nitrogen/#aliases","title":"Aliases","text":""},{"location":"ammonium_nitrogen/#examples","title":"Examples","text":"Value 2.3 mg/kg"},{"location":"ammonium_nitrogen/#see-also","title":"See Also","text":""},{"location":"ammonium_nitrogen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ammonium_nitrogen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ammonium_nitrogen/#schema-source","title":"Schema Source","text":""},{"location":"ammonium_nitrogen/#linkml-source","title":"LinkML Source","text":"
name: ammonium_nitrogen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of ammonium nitrogen in the sample\ntitle: ammonium nitrogen\nexamples:\n- value: 2.3 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- ammonium_nitrogen\n- NH4-N\nrank: 1000\nalias: ammonium_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"amount_light/","title":"Slot: amount of light (amount_light)","text":"

The unit of illuminance and luminous emittance, measuring luminous flux per unit area

URI: MIXS:0000140

"},{"location":"amount_light/#inheritance","title":"Inheritance","text":""},{"location":"amount_light/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"amount_light/#properties","title":"Properties","text":""},{"location":"amount_light/#aliases","title":"Aliases","text":""},{"location":"amount_light/#examples","title":"Examples","text":"Value"},{"location":"amount_light/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"amount_light/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"amount_light/#schema-source","title":"Schema Source","text":""},{"location":"amount_light/#linkml-source","title":"LinkML Source","text":"
name: amount_light\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: lux, lumens per square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The unit of illuminance and luminous emittance, measuring luminous flux\n  per unit area\ntitle: amount of light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount of light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000140\nalias: amount_light\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"analysis_identifiers/","title":"Slot: analysis_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:analysis_identifiers

"},{"location":"analysis_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"analysis_identifiers/#properties","title":"Properties","text":""},{"location":"analysis_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"analysis_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"analysis_identifiers/#linkml-source","title":"LinkML Source","text":"
name: analysis_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"analysis_type/","title":"Slot: analysis/data type (analysis_type)","text":"

Select all the data types associated or available for this biosample

URI: nmdc:analysis_type

"},{"location":"analysis_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"analysis_type/#properties","title":"Properties","text":""},{"location":"analysis_type/#examples","title":"Examples","text":"Value metagenomics; metabolomics; proteomics"},{"location":"analysis_type/#see-also","title":"See Also","text":""},{"location":"analysis_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"analysis_type/#schema-source","title":"Schema Source","text":""},{"location":"analysis_type/#linkml-source","title":"LinkML Source","text":"
name: analysis_type\ndescription: Select all the data types associated or available for this biosample\ntitle: analysis/data type\nexamples:\n- value: metagenomics; metabolomics; proteomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIxS:investigation_type\nrank: 3\nalias: analysis_type\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: AnalysisTypeEnum\nrecommended: true\nmultivalued: true\n\n
"},{"location":"analyte_category/","title":"Slot: analyte_category","text":"

The type of analyte(s) that were measured in the data generation process and analyzed

_ in the Workflow Chain_

__

URI: nmdc:analyte_category

"},{"location":"analyte_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"analyte_category/#properties","title":"Properties","text":""},{"location":"analyte_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"analyte_category/#schema-source","title":"Schema Source","text":""},{"location":"analyte_category/#linkml-source","title":"LinkML Source","text":"
name: analyte_category\ndescription: \"The type of analyte(s) that were measured in the data generation process\\\n  \\ and analyzed\\n  in the Workflow Chain\\n\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: analyte_category\ndomain_of:\n- DataGeneration\nrange: AnalyteCategoryEnum\nrequired: true\n\n
"},{"location":"ances_data/","title":"Slot: ancestral data (ances_data)","text":"

Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)

URI: MIXS:0000247

"},{"location":"ances_data/#inheritance","title":"Inheritance","text":""},{"location":"ances_data/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ances_data/#properties","title":"Properties","text":""},{"location":"ances_data/#aliases","title":"Aliases","text":""},{"location":"ances_data/#examples","title":"Examples","text":"Value A/3*B"},{"location":"ances_data/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ances_data/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"ances_data/#schema-source","title":"Schema Source","text":""},{"location":"ances_data/#linkml-source","title":"LinkML Source","text":"
name: ances_data\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information about either pedigree or other ancestral information description\n  (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A\n  x B) x B] x B)\ntitle: ancestral data\nexamples:\n- value: A/3*B\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ancestral data\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000247\nalias: ances_data\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"annual_precpt/","title":"Slot: mean annual precipitation (annual_precpt)","text":"

The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.

URI: MIXS:0000644

"},{"location":"annual_precpt/#inheritance","title":"Inheritance","text":""},{"location":"annual_precpt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"annual_precpt/#properties","title":"Properties","text":""},{"location":"annual_precpt/#aliases","title":"Aliases","text":""},{"location":"annual_precpt/#examples","title":"Examples","text":"Value"},{"location":"annual_precpt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"annual_precpt/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"annual_precpt/#schema-source","title":"Schema Source","text":""},{"location":"annual_precpt/#linkml-source","title":"LinkML Source","text":"
name: annual_precpt\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average of all annual precipitation values known, or an estimated\n  equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean annual precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000644\nalias: annual_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"annual_temp/","title":"Slot: mean annual temperature (annual_temp)","text":"

Mean annual temperature

URI: MIXS:0000642

"},{"location":"annual_temp/#inheritance","title":"Inheritance","text":""},{"location":"annual_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"annual_temp/#properties","title":"Properties","text":""},{"location":"annual_temp/#aliases","title":"Aliases","text":""},{"location":"annual_temp/#examples","title":"Examples","text":"Value 12.5 degree Celsius"},{"location":"annual_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"annual_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"annual_temp/#schema-source","title":"Schema Source","text":""},{"location":"annual_temp/#linkml-source","title":"LinkML Source","text":"
name: annual_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Mean annual temperature\ntitle: mean annual temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000642\nalias: annual_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"antibiotic_regm/","title":"Slot: antibiotic regimen (antibiotic_regm)","text":"

Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens

URI: MIXS:0000553

"},{"location":"antibiotic_regm/#inheritance","title":"Inheritance","text":""},{"location":"antibiotic_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"antibiotic_regm/#properties","title":"Properties","text":""},{"location":"antibiotic_regm/#aliases","title":"Aliases","text":""},{"location":"antibiotic_regm/#examples","title":"Examples","text":"Value penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"antibiotic_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"antibiotic_regm/#annotations","title":"Annotations","text":"property value expected_value antibiotic name;antibiotic amount;treatment interval and duration"},{"location":"antibiotic_regm/#schema-source","title":"Schema Source","text":""},{"location":"antibiotic_regm/#linkml-source","title":"LinkML Source","text":"
name: antibiotic_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: antibiotic name;antibiotic amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving antibiotic administration; should\n  include the name of antibiotic, amount administered, treatment regimen including\n  how many times the treatment was repeated, how long each treatment lasted, and the\n  start and end time of the entire treatment; can include multiple antibiotic regimens\ntitle: antibiotic regimen\nexamples:\n- value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- antibiotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000553\nalias: antibiotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"api/","title":"Slot: API gravity (api)","text":"

API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)

URI: MIXS:0000157

"},{"location":"api/#inheritance","title":"Inheritance","text":""},{"location":"api/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"api/#properties","title":"Properties","text":""},{"location":"api/#aliases","title":"Aliases","text":""},{"location":"api/#examples","title":"Examples","text":"Value"},{"location":"api/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"api/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"api/#schema-source","title":"Schema Source","text":""},{"location":"api/#linkml-source","title":"LinkML Source","text":"
name: api\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degrees API\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'API gravity is a measure of how heavy or light a petroleum liquid is\n  compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e\n  API)'\ntitle: API gravity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- API gravity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000157\nalias: api\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"applied_roles/","title":"Slot: applied_roles","text":"

URI: nmdc:applied_roles

"},{"location":"applied_roles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applied_roles/#properties","title":"Properties","text":""},{"location":"applied_roles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"applied_roles/#annotations","title":"Annotations","text":"property value tooltip Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/"},{"location":"applied_roles/#schema-source","title":"Schema Source","text":""},{"location":"applied_roles/#linkml-source","title":"LinkML Source","text":"
name: applied_roles\nannotations:\n  tooltip:\n    tag: tooltip\n    value: 'Identify all CRediT roles associated with this contributor. CRediT Information:\n      https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: applied_roles\ndomain_of:\n- CreditAssociation\nrange: CreditEnum\nrequired: true\nmultivalued: true\n\n
"},{"location":"applies_to_person/","title":"Slot: applies_to_person","text":"

URI: nmdc:applies_to_person

"},{"location":"applies_to_person/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applies_to_person/#properties","title":"Properties","text":""},{"location":"applies_to_person/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"applies_to_person/#schema-source","title":"Schema Source","text":""},{"location":"applies_to_person/#linkml-source","title":"LinkML Source","text":"
name: applies_to_person\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: applies_to_person\ndomain_of:\n- CreditAssociation\nrange: PersonValue\nrequired: true\n\n
"},{"location":"arch_struc/","title":"Slot: architectural structure (arch_struc)","text":"

An architectural structure is a human-made, free-standing, immobile outdoor construction

URI: MIXS:0000774

"},{"location":"arch_struc/#inheritance","title":"Inheritance","text":""},{"location":"arch_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"arch_struc/#properties","title":"Properties","text":""},{"location":"arch_struc/#aliases","title":"Aliases","text":""},{"location":"arch_struc/#examples","title":"Examples","text":"Value shed"},{"location":"arch_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"arch_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"arch_struc/#schema-source","title":"Schema Source","text":""},{"location":"arch_struc/#linkml-source","title":"LinkML Source","text":"
name: arch_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: An architectural structure is a human-made, free-standing, immobile outdoor\n  construction\ntitle: architectural structure\nexamples:\n- value: shed\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- architectural structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000774\nalias: arch_struc\ndomain_of:\n- Biosample\nrange: arch_struc_enum\nmultivalued: false\n\n
"},{"location":"aromatics_pc/","title":"Slot: aromatics wt% (aromatics_pc)","text":"

Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)

URI: MIXS:0000133

"},{"location":"aromatics_pc/#inheritance","title":"Inheritance","text":""},{"location":"aromatics_pc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"aromatics_pc/#properties","title":"Properties","text":""},{"location":"aromatics_pc/#aliases","title":"Aliases","text":""},{"location":"aromatics_pc/#examples","title":"Examples","text":"Value"},{"location":"aromatics_pc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"aromatics_pc/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"aromatics_pc/#schema-source","title":"Schema Source","text":""},{"location":"aromatics_pc/#linkml-source","title":"LinkML Source","text":"
name: aromatics_pc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n  that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n  There are three main methods to obtain SARA results. The most popular one is known\n  as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: aromatics wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aromatics wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000133\nalias: aromatics_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"asm_score/","title":"Slot: asm_score","text":"

A score for comparing metagenomic assembly quality from same sample.

URI: nmdc:asm_score

"},{"location":"asm_score/#inheritance","title":"Inheritance","text":""},{"location":"asm_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"asm_score/#properties","title":"Properties","text":""},{"location":"asm_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"asm_score/#schema-source","title":"Schema Source","text":""},{"location":"asm_score/#linkml-source","title":"LinkML Source","text":"
name: asm_score\ndescription: A score for comparing metagenomic assembly quality from same sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: asm_score\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"asphaltenes_pc/","title":"Slot: asphaltenes wt% (asphaltenes_pc)","text":"

Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)

URI: MIXS:0000135

"},{"location":"asphaltenes_pc/#inheritance","title":"Inheritance","text":""},{"location":"asphaltenes_pc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"asphaltenes_pc/#properties","title":"Properties","text":""},{"location":"asphaltenes_pc/#aliases","title":"Aliases","text":""},{"location":"asphaltenes_pc/#examples","title":"Examples","text":"Value"},{"location":"asphaltenes_pc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"asphaltenes_pc/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"asphaltenes_pc/#schema-source","title":"Schema Source","text":""},{"location":"asphaltenes_pc/#linkml-source","title":"LinkML Source","text":"
name: asphaltenes_pc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n  that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n  There are three main methods to obtain SARA results. The most popular one is known\n  as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: asphaltenes wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- asphaltenes wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000135\nalias: asphaltenes_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"assembly_identifiers/","title":"Slot: assembly_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:assembly_identifiers

"},{"location":"assembly_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"assembly_identifiers/#properties","title":"Properties","text":""},{"location":"assembly_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"assembly_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"assembly_identifiers/#linkml-source","title":"LinkML Source","text":"
name: assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: assembly_identifiers\nrange: string\n\n
"},{"location":"associated_dois/","title":"Slot: associated_dois","text":"

A list of DOIs associated with a resource, such as a list of DOIS associated with a Study.

URI: nmdc:associated_dois

"},{"location":"associated_dois/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"associated_dois/#properties","title":"Properties","text":""},{"location":"associated_dois/#aliases","title":"Aliases","text":""},{"location":"associated_dois/#examples","title":"Examples","text":"Value [{'doi': 'doi:10.46936/intm.proj.2021.60141/60000423', 'doi_provider': 'emsl', 'doi_category': 'award_doi'}, {'doi': 'doi:10.1101/2022.12.12.520098', 'doi_category': 'publication_doi'}, {'doi': 'doi:10.48321/D1Z60Q', 'doi_category': 'data_management_plan_doi', 'doi_provider': 'gsc'}]"},{"location":"associated_dois/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"associated_dois/#schema-source","title":"Schema Source","text":""},{"location":"associated_dois/#linkml-source","title":"LinkML Source","text":"
name: associated_dois\ndescription: A list of DOIs associated with a resource, such as a list of DOIS associated\n  with a Study.\nexamples:\n- value: '[{''doi'': ''doi:10.46936/intm.proj.2021.60141/60000423'', ''doi_provider'':\n    ''emsl'', ''doi_category'': ''award_doi''}, {''doi'': ''doi:10.1101/2022.12.12.520098'',\n    ''doi_category'': ''publication_doi''}, {''doi'': ''doi:10.48321/D1Z60Q'', ''doi_category'':\n    ''data_management_plan_doi'', ''doi_provider'': ''gsc''}]'\n  description: Provides a list of two DOIs; specifically, an EMSL award DOI and a\n    publication DOI.\nin_subset:\n- data_portal_subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Associated DOIs\n- Associated digital object identifiers\nrank: 1000\nalias: associated_dois\ndomain_of:\n- Study\nrange: Doi\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"associated_studies/","title":"Slot: associated_studies","text":"

The study associated with a resource.

URI: nmdc:associated_studies

"},{"location":"associated_studies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no Biosample Biological source material which can be characterized by an experiment yes DataGeneration The methods and processes used to generate omics data from a biosample or org... yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"associated_studies/#properties","title":"Properties","text":""},{"location":"associated_studies/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"associated_studies/#schema-source","title":"Schema Source","text":""},{"location":"associated_studies/#linkml-source","title":"LinkML Source","text":"
name: associated_studies\ndescription: The study associated with a resource.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: associated_studies\ndomain_of:\n- Biosample\n- DataGeneration\nrange: Study\nrequired: true\nmultivalued: true\nstructured_pattern:\n  syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n  interpolated: true\n\n
"},{"location":"atmospheric_data/","title":"Slot: atmospheric data (atmospheric_data)","text":"

Measurement of atmospheric data; can include multiple data

URI: MIXS:0001097

"},{"location":"atmospheric_data/#inheritance","title":"Inheritance","text":""},{"location":"atmospheric_data/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"atmospheric_data/#properties","title":"Properties","text":""},{"location":"atmospheric_data/#aliases","title":"Aliases","text":""},{"location":"atmospheric_data/#examples","title":"Examples","text":"Value wind speed;9 knots"},{"location":"atmospheric_data/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"atmospheric_data/#annotations","title":"Annotations","text":"property value expected_value atmospheric data name;measurement value"},{"location":"atmospheric_data/#schema-source","title":"Schema Source","text":""},{"location":"atmospheric_data/#linkml-source","title":"LinkML Source","text":"
name: atmospheric_data\nannotations:\n  expected_value:\n    tag: expected_value\n    value: atmospheric data name;measurement value\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Measurement of atmospheric data; can include multiple data\ntitle: atmospheric data\nexamples:\n- value: wind speed;9 knots\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- atmospheric data\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0001097\nalias: atmospheric_data\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"avg_dew_point/","title":"Slot: average dew point (avg_dew_point)","text":"

The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day

URI: MIXS:0000141

"},{"location":"avg_dew_point/#inheritance","title":"Inheritance","text":""},{"location":"avg_dew_point/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"avg_dew_point/#properties","title":"Properties","text":""},{"location":"avg_dew_point/#aliases","title":"Aliases","text":""},{"location":"avg_dew_point/#examples","title":"Examples","text":"Value 25.5 degree Celsius"},{"location":"avg_dew_point/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"avg_dew_point/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"avg_dew_point/#schema-source","title":"Schema Source","text":""},{"location":"avg_dew_point/#linkml-source","title":"LinkML Source","text":"
name: avg_dew_point\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average of dew point measures taken at the beginning of every hour\n  over a 24 hour period on the sampling day\ntitle: average dew point\nexamples:\n- value: 25.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000141\nalias: avg_dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"avg_occup/","title":"Slot: average daily occupancy (avg_occup)","text":"

Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.

URI: MIXS:0000775

"},{"location":"avg_occup/#inheritance","title":"Inheritance","text":""},{"location":"avg_occup/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"avg_occup/#properties","title":"Properties","text":""},{"location":"avg_occup/#aliases","title":"Aliases","text":""},{"location":"avg_occup/#examples","title":"Examples","text":"Value 2"},{"location":"avg_occup/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"avg_occup/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"avg_occup/#schema-source","title":"Schema Source","text":""},{"location":"avg_occup/#linkml-source","title":"LinkML Source","text":"
name: avg_occup\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Daily average occupancy of room. Indicate the number of person(s) daily\n  occupying the sampling room.\ntitle: average daily occupancy\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average daily occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000775\nalias: avg_occup\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"avg_temp/","title":"Slot: average temperature (avg_temp)","text":"

The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day

URI: MIXS:0000142

"},{"location":"avg_temp/#inheritance","title":"Inheritance","text":""},{"location":"avg_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"avg_temp/#properties","title":"Properties","text":""},{"location":"avg_temp/#aliases","title":"Aliases","text":""},{"location":"avg_temp/#examples","title":"Examples","text":"Value 12.5 degree Celsius"},{"location":"avg_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"avg_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"avg_temp/#schema-source","title":"Schema Source","text":""},{"location":"avg_temp/#linkml-source","title":"LinkML Source","text":"
name: avg_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average of temperatures taken at the beginning of every hour over\n  a 24 hour period on the sampling day\ntitle: average temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000142\nalias: avg_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"bac_prod/","title":"Slot: bacterial production (bac_prod)","text":"

Bacterial production in the water column measured by isotope uptake

URI: MIXS:0000683

"},{"location":"bac_prod/#inheritance","title":"Inheritance","text":""},{"location":"bac_prod/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bac_prod/#properties","title":"Properties","text":""},{"location":"bac_prod/#aliases","title":"Aliases","text":""},{"location":"bac_prod/#examples","title":"Examples","text":"Value 5 milligram per cubic meter per day"},{"location":"bac_prod/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bac_prod/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bac_prod/#schema-source","title":"Schema Source","text":""},{"location":"bac_prod/#linkml-source","title":"LinkML Source","text":"
name: bac_prod\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter per day\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Bacterial production in the water column measured by isotope uptake\ntitle: bacterial production\nexamples:\n- value: 5 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000683\nalias: bac_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"bac_resp/","title":"Slot: bacterial respiration (bac_resp)","text":"

Measurement of bacterial respiration in the water column

URI: MIXS:0000684

"},{"location":"bac_resp/#inheritance","title":"Inheritance","text":""},{"location":"bac_resp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bac_resp/#properties","title":"Properties","text":""},{"location":"bac_resp/#aliases","title":"Aliases","text":""},{"location":"bac_resp/#examples","title":"Examples","text":"Value 300 micromole oxygen per liter per hour"},{"location":"bac_resp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bac_resp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bac_resp/#schema-source","title":"Schema Source","text":""},{"location":"bac_resp/#linkml-source","title":"LinkML Source","text":"
name: bac_resp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter per day, micromole oxygen per liter per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of bacterial respiration in the water column\ntitle: bacterial respiration\nexamples:\n- value: 300 micromole oxygen per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial respiration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000684\nalias: bac_resp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"bacteria_carb_prod/","title":"Slot: bacterial carbon production (bacteria_carb_prod)","text":"

Measurement of bacterial carbon production

URI: MIXS:0000173

"},{"location":"bacteria_carb_prod/#inheritance","title":"Inheritance","text":""},{"location":"bacteria_carb_prod/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bacteria_carb_prod/#properties","title":"Properties","text":""},{"location":"bacteria_carb_prod/#aliases","title":"Aliases","text":""},{"location":"bacteria_carb_prod/#examples","title":"Examples","text":"Value 2.53 microgram per liter per hour"},{"location":"bacteria_carb_prod/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bacteria_carb_prod/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bacteria_carb_prod/#schema-source","title":"Schema Source","text":""},{"location":"bacteria_carb_prod/#linkml-source","title":"LinkML Source","text":"
name: bacteria_carb_prod\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: nanogram per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of bacterial carbon production\ntitle: bacterial carbon production\nexamples:\n- value: 2.53 microgram per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial carbon production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000173\nalias: bacteria_carb_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"barometric_press/","title":"Slot: barometric pressure (barometric_press)","text":"

Force per unit area exerted against a surface by the weight of air above that surface

URI: MIXS:0000096

"},{"location":"barometric_press/#inheritance","title":"Inheritance","text":""},{"location":"barometric_press/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"barometric_press/#properties","title":"Properties","text":""},{"location":"barometric_press/#aliases","title":"Aliases","text":""},{"location":"barometric_press/#examples","title":"Examples","text":"Value 5 millibar"},{"location":"barometric_press/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"barometric_press/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"barometric_press/#schema-source","title":"Schema Source","text":""},{"location":"barometric_press/#linkml-source","title":"LinkML Source","text":"
name: barometric_press\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millibar\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Force per unit area exerted against a surface by the weight of air above\n  that surface\ntitle: barometric pressure\nexamples:\n- value: 5 millibar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- barometric pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000096\nalias: barometric_press\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"basin/","title":"Slot: basin name (basin)","text":"

Name of the basin (e.g. Campos)

URI: MIXS:0000290

"},{"location":"basin/#inheritance","title":"Inheritance","text":""},{"location":"basin/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"basin/#properties","title":"Properties","text":""},{"location":"basin/#aliases","title":"Aliases","text":""},{"location":"basin/#examples","title":"Examples","text":"Value"},{"location":"basin/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"basin/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"basin/#schema-source","title":"Schema Source","text":""},{"location":"basin/#linkml-source","title":"LinkML Source","text":"
name: basin\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of the basin (e.g. Campos)\ntitle: basin name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- basin name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000290\nalias: basin\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"bathroom_count/","title":"Slot: bathroom count (bathroom_count)","text":"

The number of bathrooms in the building

URI: MIXS:0000776

"},{"location":"bathroom_count/#inheritance","title":"Inheritance","text":""},{"location":"bathroom_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bathroom_count/#properties","title":"Properties","text":""},{"location":"bathroom_count/#aliases","title":"Aliases","text":""},{"location":"bathroom_count/#examples","title":"Examples","text":"Value 1"},{"location":"bathroom_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bathroom_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"bathroom_count/#schema-source","title":"Schema Source","text":""},{"location":"bathroom_count/#linkml-source","title":"LinkML Source","text":"
name: bathroom_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of bathrooms in the building\ntitle: bathroom count\nexamples:\n- value: '1'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bathroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000776\nalias: bathroom_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"bedroom_count/","title":"Slot: bedroom count (bedroom_count)","text":"

The number of bedrooms in the building

URI: MIXS:0000777

"},{"location":"bedroom_count/#inheritance","title":"Inheritance","text":""},{"location":"bedroom_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bedroom_count/#properties","title":"Properties","text":""},{"location":"bedroom_count/#aliases","title":"Aliases","text":""},{"location":"bedroom_count/#examples","title":"Examples","text":"Value 2"},{"location":"bedroom_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bedroom_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"bedroom_count/#schema-source","title":"Schema Source","text":""},{"location":"bedroom_count/#linkml-source","title":"LinkML Source","text":"
name: bedroom_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of bedrooms in the building\ntitle: bedroom count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bedroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000777\nalias: bedroom_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"benzene/","title":"Slot: benzene (benzene)","text":"

Concentration of benzene in the sample

URI: MIXS:0000153

"},{"location":"benzene/#inheritance","title":"Inheritance","text":""},{"location":"benzene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"benzene/#properties","title":"Properties","text":""},{"location":"benzene/#aliases","title":"Aliases","text":""},{"location":"benzene/#examples","title":"Examples","text":"Value"},{"location":"benzene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"benzene/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"benzene/#schema-source","title":"Schema Source","text":""},{"location":"benzene/#linkml-source","title":"LinkML Source","text":"
name: benzene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of benzene in the sample\ntitle: benzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- benzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000153\nalias: benzene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"best_protein/","title":"Slot: best_protein","text":"

the specific protein identifier most correctly associated with the peptide sequence

URI: nmdc:best_protein

"},{"location":"best_protein/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"best_protein/#properties","title":"Properties","text":""},{"location":"best_protein/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"best_protein/#schema-source","title":"Schema Source","text":""},{"location":"best_protein/#linkml-source","title":"LinkML Source","text":"
name: best_protein\ndescription: the specific protein identifier most correctly associated with the peptide\n  sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: best_protein\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\n\n
"},{"location":"bin_name/","title":"Slot: bin_name","text":"

URI: nmdc:bin_name

"},{"location":"bin_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_name/#properties","title":"Properties","text":""},{"location":"bin_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bin_name/#schema-source","title":"Schema Source","text":""},{"location":"bin_name/#linkml-source","title":"LinkML Source","text":"
name: bin_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_name\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"bin_quality/","title":"Slot: bin_quality","text":"

URI: nmdc:bin_quality

"},{"location":"bin_quality/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_quality/#properties","title":"Properties","text":""},{"location":"bin_quality/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bin_quality/#schema-source","title":"Schema Source","text":""},{"location":"bin_quality/#linkml-source","title":"LinkML Source","text":"
name: bin_quality\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_quality\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"binned_contig_num/","title":"Slot: binned_contig_num","text":"

URI: nmdc:binned_contig_num

"},{"location":"binned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"binned_contig_num/#properties","title":"Properties","text":""},{"location":"binned_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"binned_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"binned_contig_num/#linkml-source","title":"LinkML Source","text":"
name: binned_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: binned_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"biochem_oxygen_dem/","title":"Slot: biochemical oxygen demand (biochem_oxygen_dem)","text":"

Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period

URI: MIXS:0000653

"},{"location":"biochem_oxygen_dem/#inheritance","title":"Inheritance","text":""},{"location":"biochem_oxygen_dem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biochem_oxygen_dem/#properties","title":"Properties","text":""},{"location":"biochem_oxygen_dem/#aliases","title":"Aliases","text":""},{"location":"biochem_oxygen_dem/#examples","title":"Examples","text":"Value"},{"location":"biochem_oxygen_dem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biochem_oxygen_dem/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"biochem_oxygen_dem/#schema-source","title":"Schema Source","text":""},{"location":"biochem_oxygen_dem/#linkml-source","title":"LinkML Source","text":"
name: biochem_oxygen_dem\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Amount of dissolved oxygen needed by aerobic biological organisms in\n  a body of water to break down organic material present in a given water sample at\n  certain temperature over a specific time period\ntitle: biochemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biochemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000653\nalias: biochem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"biocide/","title":"Slot: biocide administration (biocide)","text":"

List of biocides (commercial name of product and supplier) and date of administration

URI: MIXS:0001011

"},{"location":"biocide/#inheritance","title":"Inheritance","text":""},{"location":"biocide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biocide/#properties","title":"Properties","text":""},{"location":"biocide/#aliases","title":"Aliases","text":""},{"location":"biocide/#examples","title":"Examples","text":"Value ALPHA 1427;Baker Hughes;2008-01-23"},{"location":"biocide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biocide/#annotations","title":"Annotations","text":"property value expected_value name;name;timestamp"},{"location":"biocide/#schema-source","title":"Schema Source","text":""},{"location":"biocide/#linkml-source","title":"LinkML Source","text":"
name: biocide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;name;timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of biocides (commercial name of product and supplier) and date of\n  administration\ntitle: biocide administration\nexamples:\n- value: ALPHA 1427;Baker Hughes;2008-01-23\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001011\nalias: biocide\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"biocide_admin_method/","title":"Slot: biocide administration method (biocide_admin_method)","text":"

Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)

URI: MIXS:0000456

"},{"location":"biocide_admin_method/#inheritance","title":"Inheritance","text":""},{"location":"biocide_admin_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biocide_admin_method/#properties","title":"Properties","text":""},{"location":"biocide_admin_method/#aliases","title":"Aliases","text":""},{"location":"biocide_admin_method/#examples","title":"Examples","text":"Value"},{"location":"biocide_admin_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biocide_admin_method/#annotations","title":"Annotations","text":"property value expected_value measurement value;frequency;duration;duration"},{"location":"biocide_admin_method/#schema-source","title":"Schema Source","text":""},{"location":"biocide_admin_method/#linkml-source","title":"LinkML Source","text":"
name: biocide_admin_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;frequency;duration;duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Method of biocide administration (dose, frequency, duration, time elapsed\n  between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)\ntitle: biocide administration method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\nslot_uri: MIXS:0000456\nalias: biocide_admin_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"biogas_retention_time/","title":"Slot: biogas_retention_time","text":"

URI: nmdc:biogas_retention_time

"},{"location":"biogas_retention_time/#properties","title":"Properties","text":""},{"location":"biogas_retention_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biogas_retention_time/#schema-source","title":"Schema Source","text":""},{"location":"biogas_retention_time/#linkml-source","title":"LinkML Source","text":"
name: biogas_retention_time\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_retention_time\nrange: string\n\n
"},{"location":"biogas_temperature/","title":"Slot: biogas_temperature","text":"

URI: nmdc:biogas_temperature

"},{"location":"biogas_temperature/#properties","title":"Properties","text":""},{"location":"biogas_temperature/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biogas_temperature/#schema-source","title":"Schema Source","text":""},{"location":"biogas_temperature/#linkml-source","title":"LinkML Source","text":"
name: biogas_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_temperature\nrange: string\n\n
"},{"location":"biol_stat/","title":"Slot: biological status (biol_stat)","text":"

The level of genome modification.

URI: MIXS:0000858

"},{"location":"biol_stat/#inheritance","title":"Inheritance","text":""},{"location":"biol_stat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biol_stat/#properties","title":"Properties","text":""},{"location":"biol_stat/#aliases","title":"Aliases","text":""},{"location":"biol_stat/#examples","title":"Examples","text":"Value natural"},{"location":"biol_stat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biol_stat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"biol_stat/#schema-source","title":"Schema Source","text":""},{"location":"biol_stat/#linkml-source","title":"LinkML Source","text":"
name: biol_stat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The level of genome modification.\ntitle: biological status\nexamples:\n- value: natural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000858\nalias: biol_stat\ndomain_of:\n- Biosample\nrange: biol_stat_enum\nmultivalued: false\n\n
"},{"location":"biomass/","title":"Slot: biomass (biomass)","text":"

Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements

URI: MIXS:0000174

"},{"location":"biomass/#inheritance","title":"Inheritance","text":""},{"location":"biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biomass/#properties","title":"Properties","text":""},{"location":"biomass/#aliases","title":"Aliases","text":""},{"location":"biomass/#examples","title":"Examples","text":"Value total;20 gram"},{"location":"biomass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biomass/#annotations","title":"Annotations","text":"property value expected_value biomass type;measurement value"},{"location":"biomass/#schema-source","title":"Schema Source","text":""},{"location":"biomass/#linkml-source","title":"LinkML Source","text":"
name: biomass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: biomass type;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: ton, kilogram, gram\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n  e.g. Microbial, total. Can include multiple measurements\ntitle: biomass\nexamples:\n- value: total;20 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biomass\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000174\nalias: biomass\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biomaterial_purity/","title":"Slot: biomaterial_purity","text":"

URI: nmdc:biomaterial_purity

"},{"location":"biomaterial_purity/#inheritance","title":"Inheritance","text":""},{"location":"biomaterial_purity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProcessedSample no"},{"location":"biomaterial_purity/#properties","title":"Properties","text":""},{"location":"biomaterial_purity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biomaterial_purity/#schema-source","title":"Schema Source","text":""},{"location":"biomaterial_purity/#linkml-source","title":"LinkML Source","text":"
name: biomaterial_purity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biomaterial_purity\ndomain_of:\n- ProcessedSample\nrange: QuantityValue\n\n
"},{"location":"biosample_categories/","title":"Slot: Categories the biosample belongs to (biosample_categories)","text":"

URI: nmdc:biosample_categories

"},{"location":"biosample_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biosample_categories/#properties","title":"Properties","text":""},{"location":"biosample_categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biosample_categories/#schema-source","title":"Schema Source","text":""},{"location":"biosample_categories/#linkml-source","title":"LinkML Source","text":"
name: biosample_categories\ntitle: Categories the biosample belongs to\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biosample_categories\ndomain_of:\n- Biosample\nrange: BiosampleCategoryEnum\nmultivalued: true\n\n
"},{"location":"biosample_identifiers/","title":"Slot: biosample_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:biosample_identifiers

"},{"location":"biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"biosample_identifiers/#properties","title":"Properties","text":""},{"location":"biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: biosample_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"biosample_set/","title":"Slot: biosample_set","text":"

This property links a database object to the set of samples within it.

URI: nmdc:biosample_set

"},{"location":"biosample_set/#inheritance","title":"Inheritance","text":""},{"location":"biosample_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"biosample_set/#properties","title":"Properties","text":""},{"location":"biosample_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biosample_set/#schema-source","title":"Schema Source","text":""},{"location":"biosample_set/#linkml-source","title":"LinkML Source","text":"
name: biosample_set\ndescription: This property links a database object to the set of samples within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: biosample_set\ndomain_of:\n- Database\nrange: Biosample\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"biotic_regm/","title":"Slot: biotic regimen (biotic_regm)","text":"

Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.

URI: MIXS:0001038

"},{"location":"biotic_regm/#inheritance","title":"Inheritance","text":""},{"location":"biotic_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biotic_regm/#properties","title":"Properties","text":""},{"location":"biotic_regm/#aliases","title":"Aliases","text":""},{"location":"biotic_regm/#examples","title":"Examples","text":"Value sample inoculated with Rhizobium spp. Culture"},{"location":"biotic_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_regm/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"biotic_regm/#schema-source","title":"Schema Source","text":""},{"location":"biotic_regm/#linkml-source","title":"LinkML Source","text":"
name: biotic_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information about treatment(s) involving use of biotic factors, such\n  as bacteria, viruses or fungi.\ntitle: biotic regimen\nexamples:\n- value: sample inoculated with Rhizobium spp. Culture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001038\nalias: biotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"biotic_relationship/","title":"Slot: observed biotic relationship (biotic_relationship)","text":"

Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object

URI: MIXS:0000028

"},{"location":"biotic_relationship/#inheritance","title":"Inheritance","text":""},{"location":"biotic_relationship/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biotic_relationship/#properties","title":"Properties","text":""},{"location":"biotic_relationship/#aliases","title":"Aliases","text":""},{"location":"biotic_relationship/#examples","title":"Examples","text":"Value free living"},{"location":"biotic_relationship/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"biotic_relationship/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"biotic_relationship/#schema-source","title":"Schema Source","text":""},{"location":"biotic_relationship/#linkml-source","title":"LinkML Source","text":"
name: biotic_relationship\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\ndescription: Description of relationship(s) between the subject organism and other\n  organism(s) it is associated with. E.g., parasite on species X; mutualist with species\n  Y. The target organism is the subject of the relationship, and the other organism(s)\n  is the object\ntitle: observed biotic relationship\nexamples:\n- value: free living\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed biotic relationship\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000028\nalias: biotic_relationship\ndomain_of:\n- Biosample\nrange: biotic_relationship_enum\nmultivalued: false\n\n
"},{"location":"bishomohopanol/","title":"Slot: bishomohopanol (bishomohopanol)","text":"

Concentration of bishomohopanol

URI: MIXS:0000175

"},{"location":"bishomohopanol/#inheritance","title":"Inheritance","text":""},{"location":"bishomohopanol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bishomohopanol/#properties","title":"Properties","text":""},{"location":"bishomohopanol/#aliases","title":"Aliases","text":""},{"location":"bishomohopanol/#examples","title":"Examples","text":"Value 14 microgram per liter"},{"location":"bishomohopanol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bishomohopanol/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bishomohopanol/#schema-source","title":"Schema Source","text":""},{"location":"bishomohopanol/#linkml-source","title":"LinkML Source","text":"
name: bishomohopanol\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, microgram per gram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of bishomohopanol\ntitle: bishomohopanol\nexamples:\n- value: 14 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bishomohopanol\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000175\nalias: bishomohopanol\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"blood_press_diast/","title":"Slot: host blood pressure diastolic (blood_press_diast)","text":"

Resting diastolic blood pressure, measured as mm mercury

URI: MIXS:0000258

"},{"location":"blood_press_diast/#inheritance","title":"Inheritance","text":""},{"location":"blood_press_diast/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"blood_press_diast/#properties","title":"Properties","text":""},{"location":"blood_press_diast/#aliases","title":"Aliases","text":""},{"location":"blood_press_diast/#examples","title":"Examples","text":"Value"},{"location":"blood_press_diast/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"blood_press_diast/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"blood_press_diast/#schema-source","title":"Schema Source","text":""},{"location":"blood_press_diast/#linkml-source","title":"LinkML Source","text":"
name: blood_press_diast\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter mercury\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Resting diastolic blood pressure, measured as mm mercury\ntitle: host blood pressure diastolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure diastolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000258\nalias: blood_press_diast\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"blood_press_syst/","title":"Slot: host blood pressure systolic (blood_press_syst)","text":"

Resting systolic blood pressure, measured as mm mercury

URI: MIXS:0000259

"},{"location":"blood_press_syst/#inheritance","title":"Inheritance","text":""},{"location":"blood_press_syst/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"blood_press_syst/#properties","title":"Properties","text":""},{"location":"blood_press_syst/#aliases","title":"Aliases","text":""},{"location":"blood_press_syst/#examples","title":"Examples","text":"Value"},{"location":"blood_press_syst/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"blood_press_syst/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"blood_press_syst/#schema-source","title":"Schema Source","text":""},{"location":"blood_press_syst/#linkml-source","title":"LinkML Source","text":"
name: blood_press_syst\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter mercury\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Resting systolic blood pressure, measured as mm mercury\ntitle: host blood pressure systolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure systolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000259\nalias: blood_press_syst\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"bromide/","title":"Slot: bromide (bromide)","text":"

Concentration of bromide

URI: MIXS:0000176

"},{"location":"bromide/#inheritance","title":"Inheritance","text":""},{"location":"bromide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bromide/#properties","title":"Properties","text":""},{"location":"bromide/#aliases","title":"Aliases","text":""},{"location":"bromide/#examples","title":"Examples","text":"Value 0.05 parts per million"},{"location":"bromide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bromide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"bromide/#schema-source","title":"Schema Source","text":""},{"location":"bromide/#linkml-source","title":"LinkML Source","text":"
name: bromide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of bromide\ntitle: bromide\nexamples:\n- value: 0.05 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bromide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000176\nalias: bromide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"build_docs/","title":"Slot: design, construction, and operation documents (build_docs)","text":"

The building design, construction and operation documents

URI: MIXS:0000787

"},{"location":"build_docs/#inheritance","title":"Inheritance","text":""},{"location":"build_docs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"build_docs/#properties","title":"Properties","text":""},{"location":"build_docs/#aliases","title":"Aliases","text":""},{"location":"build_docs/#examples","title":"Examples","text":"Value maintenance plans"},{"location":"build_docs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"build_docs/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"build_docs/#schema-source","title":"Schema Source","text":""},{"location":"build_docs/#linkml-source","title":"LinkML Source","text":"
name: build_docs\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The building design, construction and operation documents\ntitle: design, construction, and operation documents\nexamples:\n- value: maintenance plans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- design, construction, and operation documents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000787\nalias: build_docs\ndomain_of:\n- Biosample\nrange: build_docs_enum\nmultivalued: false\n\n
"},{"location":"build_occup_type/","title":"Slot: building occupancy type (build_occup_type)","text":"

The primary function for which a building or discrete part of a building is intended to be used

URI: MIXS:0000761

"},{"location":"build_occup_type/#inheritance","title":"Inheritance","text":""},{"location":"build_occup_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"build_occup_type/#properties","title":"Properties","text":""},{"location":"build_occup_type/#aliases","title":"Aliases","text":""},{"location":"build_occup_type/#examples","title":"Examples","text":"Value market"},{"location":"build_occup_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"build_occup_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"build_occup_type/#schema-source","title":"Schema Source","text":""},{"location":"build_occup_type/#linkml-source","title":"LinkML Source","text":"
name: build_occup_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: The primary function for which a building or discrete part of a building\n  is intended to be used\ntitle: building occupancy type\nexamples:\n- value: market\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building occupancy type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000761\nalias: build_occup_type\ndomain_of:\n- Biosample\nrange: build_occup_type_enum\nmultivalued: true\n\n
"},{"location":"building_setting/","title":"Slot: building setting (building_setting)","text":"

A location (geography) where a building is set

URI: MIXS:0000768

"},{"location":"building_setting/#inheritance","title":"Inheritance","text":""},{"location":"building_setting/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"building_setting/#properties","title":"Properties","text":""},{"location":"building_setting/#aliases","title":"Aliases","text":""},{"location":"building_setting/#examples","title":"Examples","text":"Value rural"},{"location":"building_setting/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"building_setting/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"building_setting/#schema-source","title":"Schema Source","text":""},{"location":"building_setting/#linkml-source","title":"LinkML Source","text":"
name: building_setting\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A location (geography) where a building is set\ntitle: building setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building setting\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000768\nalias: building_setting\ndomain_of:\n- Biosample\nrange: building_setting_enum\nmultivalued: false\n\n
"},{"location":"built_struc_age/","title":"Slot: built structure age (built_struc_age)","text":"

The age of the built structure since construction

URI: MIXS:0000145

"},{"location":"built_struc_age/#inheritance","title":"Inheritance","text":""},{"location":"built_struc_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"built_struc_age/#properties","title":"Properties","text":""},{"location":"built_struc_age/#aliases","title":"Aliases","text":""},{"location":"built_struc_age/#examples","title":"Examples","text":"Value 15"},{"location":"built_struc_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"built_struc_age/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"built_struc_age/#schema-source","title":"Schema Source","text":""},{"location":"built_struc_age/#linkml-source","title":"LinkML Source","text":"
name: built_struc_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: year\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The age of the built structure since construction\ntitle: built structure age\nexamples:\n- value: '15'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000145\nalias: built_struc_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"built_struc_set/","title":"Slot: built structure setting (built_struc_set)","text":"

The characterization of the location of the built structure as high or low human density

URI: MIXS:0000778

"},{"location":"built_struc_set/#inheritance","title":"Inheritance","text":""},{"location":"built_struc_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"built_struc_set/#properties","title":"Properties","text":""},{"location":"built_struc_set/#aliases","title":"Aliases","text":""},{"location":"built_struc_set/#examples","title":"Examples","text":"Value rural"},{"location":"built_struc_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"built_struc_set/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"built_struc_set/#schema-source","title":"Schema Source","text":""},{"location":"built_struc_set/#linkml-source","title":"LinkML Source","text":"
name: built_struc_set\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The characterization of the location of the built structure as high or\n  low human density\ntitle: built structure setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure setting\nrank: 1000\nis_a: core field\nstring_serialization: '[urban|rural]'\nslot_uri: MIXS:0000778\nalias: built_struc_set\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"built_struc_type/","title":"Slot: built structure type (built_struc_type)","text":"

A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads

URI: MIXS:0000721

"},{"location":"built_struc_type/#inheritance","title":"Inheritance","text":""},{"location":"built_struc_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"built_struc_type/#properties","title":"Properties","text":""},{"location":"built_struc_type/#aliases","title":"Aliases","text":""},{"location":"built_struc_type/#examples","title":"Examples","text":"Value"},{"location":"built_struc_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"built_struc_type/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"built_struc_type/#schema-source","title":"Schema Source","text":""},{"location":"built_struc_type/#linkml-source","title":"LinkML Source","text":"
name: built_struc_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A physical structure that is a body or assemblage of bodies in space\n  to form a system capable of supporting loads\ntitle: built structure type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000721\nalias: built_struc_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"bulk_elect_conductivity/","title":"Slot: bulk electrical conductivity (bulk_elect_conductivity)","text":"

Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.

URI: nmdc:bulk_elect_conductivity

"},{"location":"bulk_elect_conductivity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bulk_elect_conductivity/#properties","title":"Properties","text":""},{"location":"bulk_elect_conductivity/#examples","title":"Examples","text":"Value JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')"},{"location":"bulk_elect_conductivity/#comments","title":"Comments","text":""},{"location":"bulk_elect_conductivity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"bulk_elect_conductivity/#schema-source","title":"Schema Source","text":""},{"location":"bulk_elect_conductivity/#linkml-source","title":"LinkML Source","text":"
name: bulk_elect_conductivity\ndescription: Electrical conductivity is a measure of the ability to carry electric\n  current, which is mostly dictated by the chemistry of and amount of water.\ntitle: bulk electrical conductivity\ncomments:\n- Provide the value output of the field instrument.\nexamples:\n- value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')\n  description: The conductivity measurement was 0.017 millisiemens per centimeter.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bulk_elect_conductivity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"calcium/","title":"Slot: calcium (calcium)","text":"

Concentration of calcium in the sample

URI: MIXS:0000432

"},{"location":"calcium/#inheritance","title":"Inheritance","text":""},{"location":"calcium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"calcium/#properties","title":"Properties","text":""},{"location":"calcium/#aliases","title":"Aliases","text":""},{"location":"calcium/#examples","title":"Examples","text":"Value 0.2 micromole per liter"},{"location":"calcium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calcium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"calcium/#schema-source","title":"Schema Source","text":""},{"location":"calcium/#linkml-source","title":"LinkML Source","text":"
name: calcium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, micromole per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of calcium in the sample\ntitle: calcium\nexamples:\n- value: 0.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- calcium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000432\nalias: calcium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"calibration_object/","title":"Slot: calibration_object","text":"

the file containing calibration data object

URI: nmdc:calibration_object

"},{"location":"calibration_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process no"},{"location":"calibration_object/#properties","title":"Properties","text":""},{"location":"calibration_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calibration_object/#schema-source","title":"Schema Source","text":""},{"location":"calibration_object/#linkml-source","title":"LinkML Source","text":"
name: calibration_object\ndescription: the file containing calibration data object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_object\ndomain_of:\n- CalibrationInformation\nrange: DataObject\n\n
"},{"location":"calibration_set/","title":"Slot: calibration_set","text":"

This property links a database object to the set of calibrations within it.

URI: nmdc:calibration_set

"},{"location":"calibration_set/#inheritance","title":"Inheritance","text":""},{"location":"calibration_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"calibration_set/#properties","title":"Properties","text":""},{"location":"calibration_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calibration_set/#schema-source","title":"Schema Source","text":""},{"location":"calibration_set/#linkml-source","title":"LinkML Source","text":"
name: calibration_set\ndescription: This property links a database object to the set of calibrations within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: calibration_set\ndomain_of:\n- Database\nrange: CalibrationInformation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"calibration_standard/","title":"Slot: calibration_standard","text":"

the reference standard(s) used for calibration

URI: nmdc:calibration_standard

"},{"location":"calibration_standard/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process no"},{"location":"calibration_standard/#properties","title":"Properties","text":""},{"location":"calibration_standard/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calibration_standard/#schema-source","title":"Schema Source","text":""},{"location":"calibration_standard/#linkml-source","title":"LinkML Source","text":"
name: calibration_standard\ndescription: the reference standard(s) used for calibration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_standard\ndomain_of:\n- CalibrationInformation\nrange: CalibrationStandardEnum\n\n
"},{"location":"calibration_target/","title":"Slot: calibration_target","text":"

the target measurement of the calibration

URI: nmdc:calibration_target

"},{"location":"calibration_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process yes"},{"location":"calibration_target/#properties","title":"Properties","text":""},{"location":"calibration_target/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"calibration_target/#schema-source","title":"Schema Source","text":""},{"location":"calibration_target/#linkml-source","title":"LinkML Source","text":"
name: calibration_target\ndescription: the target measurement of the calibration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_target\ndomain_of:\n- CalibrationInformation\nrange: CalibrationTargetEnum\n\n
"},{"location":"carb_dioxide/","title":"Slot: carbon dioxide (carb_dioxide)","text":"

Carbon dioxide (gas) amount or concentration at the time of sampling

URI: MIXS:0000097

"},{"location":"carb_dioxide/#inheritance","title":"Inheritance","text":""},{"location":"carb_dioxide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"carb_dioxide/#properties","title":"Properties","text":""},{"location":"carb_dioxide/#aliases","title":"Aliases","text":""},{"location":"carb_dioxide/#examples","title":"Examples","text":"Value 410 parts per million"},{"location":"carb_dioxide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"carb_dioxide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"carb_dioxide/#schema-source","title":"Schema Source","text":""},{"location":"carb_dioxide/#linkml-source","title":"LinkML Source","text":"
name: carb_dioxide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Carbon dioxide (gas) amount or concentration at the time of sampling\ntitle: carbon dioxide\nexamples:\n- value: 410 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000097\nalias: carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"carb_monoxide/","title":"Slot: carbon monoxide (carb_monoxide)","text":"

Carbon monoxide (gas) amount or concentration at the time of sampling

URI: MIXS:0000098

"},{"location":"carb_monoxide/#inheritance","title":"Inheritance","text":""},{"location":"carb_monoxide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"carb_monoxide/#properties","title":"Properties","text":""},{"location":"carb_monoxide/#aliases","title":"Aliases","text":""},{"location":"carb_monoxide/#examples","title":"Examples","text":"Value 0.1 parts per million"},{"location":"carb_monoxide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"carb_monoxide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"carb_monoxide/#schema-source","title":"Schema Source","text":""},{"location":"carb_monoxide/#linkml-source","title":"LinkML Source","text":"
name: carb_monoxide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Carbon monoxide (gas) amount or concentration at the time of sampling\ntitle: carbon monoxide\nexamples:\n- value: 0.1 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon monoxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000098\nalias: carb_monoxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"carb_nitro_ratio/","title":"Slot: carbon/nitrogen ratio (carb_nitro_ratio)","text":"

Ratio of amount or concentrations of carbon to nitrogen

URI: MIXS:0000310

"},{"location":"carb_nitro_ratio/#inheritance","title":"Inheritance","text":""},{"location":"carb_nitro_ratio/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"carb_nitro_ratio/#properties","title":"Properties","text":""},{"location":"carb_nitro_ratio/#aliases","title":"Aliases","text":""},{"location":"carb_nitro_ratio/#examples","title":"Examples","text":"Value 0.417361111"},{"location":"carb_nitro_ratio/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"carb_nitro_ratio/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"carb_nitro_ratio/#schema-source","title":"Schema Source","text":""},{"location":"carb_nitro_ratio/#linkml-source","title":"LinkML Source","text":"
name: carb_nitro_ratio\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Ratio of amount or concentrations of carbon to nitrogen\ntitle: carbon/nitrogen ratio\nexamples:\n- value: '0.417361111'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon/nitrogen ratio\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000310\nalias: carb_nitro_ratio\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ceil_area/","title":"Slot: ceiling area (ceil_area)","text":"

The area of the ceiling space within the room

URI: MIXS:0000148

"},{"location":"ceil_area/#inheritance","title":"Inheritance","text":""},{"location":"ceil_area/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_area/#properties","title":"Properties","text":""},{"location":"ceil_area/#aliases","title":"Aliases","text":""},{"location":"ceil_area/#examples","title":"Examples","text":"Value 25 square meter"},{"location":"ceil_area/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_area/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ceil_area/#schema-source","title":"Schema Source","text":""},{"location":"ceil_area/#linkml-source","title":"LinkML Source","text":"
name: ceil_area\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The area of the ceiling space within the room\ntitle: ceiling area\nexamples:\n- value: 25 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000148\nalias: ceil_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ceil_cond/","title":"Slot: ceiling condition (ceil_cond)","text":"

The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas

URI: MIXS:0000779

"},{"location":"ceil_cond/#inheritance","title":"Inheritance","text":""},{"location":"ceil_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_cond/#properties","title":"Properties","text":""},{"location":"ceil_cond/#aliases","title":"Aliases","text":""},{"location":"ceil_cond/#examples","title":"Examples","text":"Value damaged"},{"location":"ceil_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_cond/#schema-source","title":"Schema Source","text":""},{"location":"ceil_cond/#linkml-source","title":"LinkML Source","text":"
name: ceil_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the ceiling at the time of sampling; photos\n  or video preferred; use drawings to indicate location of damaged areas\ntitle: ceiling condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000779\nalias: ceil_cond\ndomain_of:\n- Biosample\nrange: ceil_cond_enum\nmultivalued: false\n\n
"},{"location":"ceil_finish_mat/","title":"Slot: ceiling finish material (ceil_finish_mat)","text":"

The type of material used to finish a ceiling

URI: MIXS:0000780

"},{"location":"ceil_finish_mat/#inheritance","title":"Inheritance","text":""},{"location":"ceil_finish_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_finish_mat/#properties","title":"Properties","text":""},{"location":"ceil_finish_mat/#aliases","title":"Aliases","text":""},{"location":"ceil_finish_mat/#examples","title":"Examples","text":"Value stucco"},{"location":"ceil_finish_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_finish_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_finish_mat/#schema-source","title":"Schema Source","text":""},{"location":"ceil_finish_mat/#linkml-source","title":"LinkML Source","text":"
name: ceil_finish_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of material used to finish a ceiling\ntitle: ceiling finish material\nexamples:\n- value: stucco\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000780\nalias: ceil_finish_mat\ndomain_of:\n- Biosample\nrange: ceil_finish_mat_enum\nmultivalued: false\n\n
"},{"location":"ceil_struc/","title":"Slot: ceiling structure (ceil_struc)","text":"

The construction format of the ceiling

URI: MIXS:0000782

"},{"location":"ceil_struc/#inheritance","title":"Inheritance","text":""},{"location":"ceil_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_struc/#properties","title":"Properties","text":""},{"location":"ceil_struc/#aliases","title":"Aliases","text":""},{"location":"ceil_struc/#examples","title":"Examples","text":"Value concrete"},{"location":"ceil_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_struc/#schema-source","title":"Schema Source","text":""},{"location":"ceil_struc/#linkml-source","title":"LinkML Source","text":"
name: ceil_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The construction format of the ceiling\ntitle: ceiling structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling structure\nrank: 1000\nis_a: core field\nstring_serialization: '[wood frame|concrete]'\nslot_uri: MIXS:0000782\nalias: ceil_struc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ceil_texture/","title":"Slot: ceiling texture (ceil_texture)","text":"

The feel, appearance, or consistency of a ceiling surface

URI: MIXS:0000783

"},{"location":"ceil_texture/#inheritance","title":"Inheritance","text":""},{"location":"ceil_texture/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_texture/#properties","title":"Properties","text":""},{"location":"ceil_texture/#aliases","title":"Aliases","text":""},{"location":"ceil_texture/#examples","title":"Examples","text":"Value popcorn"},{"location":"ceil_texture/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_texture/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_texture/#schema-source","title":"Schema Source","text":""},{"location":"ceil_texture/#linkml-source","title":"LinkML Source","text":"
name: ceil_texture\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The feel, appearance, or consistency of a ceiling surface\ntitle: ceiling texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000783\nalias: ceil_texture\ndomain_of:\n- Biosample\nrange: ceil_texture_enum\nmultivalued: false\n\n
"},{"location":"ceil_thermal_mass/","title":"Slot: ceiling thermal mass (ceil_thermal_mass)","text":"

The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow

URI: MIXS:0000143

"},{"location":"ceil_thermal_mass/#inheritance","title":"Inheritance","text":""},{"location":"ceil_thermal_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_thermal_mass/#properties","title":"Properties","text":""},{"location":"ceil_thermal_mass/#aliases","title":"Aliases","text":""},{"location":"ceil_thermal_mass/#examples","title":"Examples","text":"Value"},{"location":"ceil_thermal_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_thermal_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ceil_thermal_mass/#schema-source","title":"Schema Source","text":""},{"location":"ceil_thermal_mass/#linkml-source","title":"LinkML Source","text":"
name: ceil_thermal_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: joule per degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The ability of the ceiling to provide inertia against temperature fluctuations.\n  Generally this means concrete that is exposed. A metal deck that supports a concrete\n  slab will act thermally as long as it is exposed to room air flow\ntitle: ceiling thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000143\nalias: ceil_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ceil_type/","title":"Slot: ceiling type (ceil_type)","text":"

The type of ceiling according to the ceiling's appearance or construction

URI: MIXS:0000784

"},{"location":"ceil_type/#inheritance","title":"Inheritance","text":""},{"location":"ceil_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_type/#properties","title":"Properties","text":""},{"location":"ceil_type/#aliases","title":"Aliases","text":""},{"location":"ceil_type/#examples","title":"Examples","text":"Value coffered"},{"location":"ceil_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_type/#schema-source","title":"Schema Source","text":""},{"location":"ceil_type/#linkml-source","title":"LinkML Source","text":"
name: ceil_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of ceiling according to the ceiling's appearance or construction\ntitle: ceiling type\nexamples:\n- value: coffered\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000784\nalias: ceil_type\ndomain_of:\n- Biosample\nrange: ceil_type_enum\nmultivalued: false\n\n
"},{"location":"ceil_water_mold/","title":"Slot: ceiling signs of water/mold (ceil_water_mold)","text":"

Signs of the presence of mold or mildew on the ceiling

URI: MIXS:0000781

"},{"location":"ceil_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"ceil_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ceil_water_mold/#properties","title":"Properties","text":""},{"location":"ceil_water_mold/#aliases","title":"Aliases","text":""},{"location":"ceil_water_mold/#examples","title":"Examples","text":"Value presence of mold visible"},{"location":"ceil_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ceil_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ceil_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"ceil_water_mold/#linkml-source","title":"LinkML Source","text":"
name: ceil_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on the ceiling\ntitle: ceiling signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000781\nalias: ceil_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"chem_administration/","title":"Slot: chemical administration (chem_administration)","text":"

List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi

URI: MIXS:0000751

"},{"location":"chem_administration/#inheritance","title":"Inheritance","text":""},{"location":"chem_administration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_administration/#properties","title":"Properties","text":""},{"location":"chem_administration/#aliases","title":"Aliases","text":""},{"location":"chem_administration/#examples","title":"Examples","text":"Value agar [CHEBI:2509];2018-05-11T20:00Z"},{"location":"chem_administration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_administration/#annotations","title":"Annotations","text":"property value expected_value CHEBI;timestamp"},{"location":"chem_administration/#schema-source","title":"Schema Source","text":""},{"location":"chem_administration/#linkml-source","title":"LinkML Source","text":"
name: chem_administration\nannotations:\n  expected_value:\n    tag: expected_value\n    value: CHEBI;timestamp\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: List of chemical compounds administered to the host or site where sampling\n  occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple\n  compounds. For chemical entities of biological interest ontology (chebi) (v 163),\n  http://purl.bioontology.org/ontology/chebi\ntitle: chemical administration\nexamples:\n- value: agar [CHEBI:2509];2018-05-11T20:00Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical administration\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]};{timestamp}'\nslot_uri: MIXS:0000751\nalias: chem_administration\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"chem_mutagen/","title":"Slot: chemical mutagen (chem_mutagen)","text":"

Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens

URI: MIXS:0000555

"},{"location":"chem_mutagen/#inheritance","title":"Inheritance","text":""},{"location":"chem_mutagen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_mutagen/#properties","title":"Properties","text":""},{"location":"chem_mutagen/#aliases","title":"Aliases","text":""},{"location":"chem_mutagen/#examples","title":"Examples","text":"Value nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"chem_mutagen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_mutagen/#annotations","title":"Annotations","text":"property value expected_value mutagen name;mutagen amount;treatment interval and duration"},{"location":"chem_mutagen/#schema-source","title":"Schema Source","text":""},{"location":"chem_mutagen/#linkml-source","title":"LinkML Source","text":"
name: chem_mutagen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: mutagen name;mutagen amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Treatment involving use of mutagens; should include the name of mutagen,\n  amount administered, treatment regimen including how many times the treatment was\n  repeated, how long each treatment lasted, and the start and end time of the entire\n  treatment; can include multiple mutagen regimens\ntitle: chemical mutagen\nexamples:\n- value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical mutagen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000555\nalias: chem_mutagen\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"chem_oxygen_dem/","title":"Slot: chemical oxygen demand (chem_oxygen_dem)","text":"

A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite

URI: MIXS:0000656

"},{"location":"chem_oxygen_dem/#inheritance","title":"Inheritance","text":""},{"location":"chem_oxygen_dem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_oxygen_dem/#properties","title":"Properties","text":""},{"location":"chem_oxygen_dem/#aliases","title":"Aliases","text":""},{"location":"chem_oxygen_dem/#examples","title":"Examples","text":"Value"},{"location":"chem_oxygen_dem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_oxygen_dem/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"chem_oxygen_dem/#schema-source","title":"Schema Source","text":""},{"location":"chem_oxygen_dem/#linkml-source","title":"LinkML Source","text":"
name: chem_oxygen_dem\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A measure of the capacity of water to consume oxygen during the decomposition\n  of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite\ntitle: chemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000656\nalias: chem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"chem_treat_method/","title":"Slot: chemical treatment method (chem_treat_method)","text":"

Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)

URI: MIXS:0000457

"},{"location":"chem_treat_method/#inheritance","title":"Inheritance","text":""},{"location":"chem_treat_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_treat_method/#properties","title":"Properties","text":""},{"location":"chem_treat_method/#aliases","title":"Aliases","text":""},{"location":"chem_treat_method/#examples","title":"Examples","text":"Value"},{"location":"chem_treat_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_treat_method/#annotations","title":"Annotations","text":"property value expected_value measurement value;frequency;duration;duration"},{"location":"chem_treat_method/#schema-source","title":"Schema Source","text":""},{"location":"chem_treat_method/#linkml-source","title":"LinkML Source","text":"
name: chem_treat_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;frequency;duration;duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Method of chemical administration(dose, frequency, duration, time elapsed\n  between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)\ntitle: chemical treatment method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\nslot_uri: MIXS:0000457\nalias: chem_treat_method\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"chem_treatment/","title":"Slot: chemical treatment (chem_treatment)","text":"

List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included

URI: MIXS:0001012

"},{"location":"chem_treatment/#inheritance","title":"Inheritance","text":""},{"location":"chem_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chem_treatment/#properties","title":"Properties","text":""},{"location":"chem_treatment/#aliases","title":"Aliases","text":""},{"location":"chem_treatment/#examples","title":"Examples","text":"Value ACCENT 1125;DOW;2010-11-17"},{"location":"chem_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chem_treatment/#annotations","title":"Annotations","text":"property value expected_value name;name;timestamp"},{"location":"chem_treatment/#schema-source","title":"Schema Source","text":""},{"location":"chem_treatment/#linkml-source","title":"LinkML Source","text":"
name: chem_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;name;timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of chemical compounds administered upstream the sampling location\n  where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n  demulsifiers, and other production chemicals etc.). The commercial name of the product\n  and name of the supplier should be provided. The date of administration should also\n  be included\ntitle: chemical treatment\nexamples:\n- value: ACCENT 1125;DOW;2010-11-17\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001012\nalias: chem_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"chemical_conversion_category/","title":"Slot: chemical_conversion_category","text":"

The type of chemical conversion process.

URI: nmdc:chemical_conversion_category

"},{"location":"chemical_conversion_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no"},{"location":"chemical_conversion_category/#properties","title":"Properties","text":""},{"location":"chemical_conversion_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chemical_conversion_category/#schema-source","title":"Schema Source","text":""},{"location":"chemical_conversion_category/#linkml-source","title":"LinkML Source","text":"
name: chemical_conversion_category\ndescription: The type of chemical conversion process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_conversion_category\ndomain_of:\n- ChemicalConversionProcess\nrange: ChemicalConversionCategoryEnum\n\n
"},{"location":"chemical_entity_set/","title":"Slot: chemical_entity_set","text":"

This property links a database object to the set of chemical entities within it.

URI: nmdc:chemical_entity_set

"},{"location":"chemical_entity_set/#inheritance","title":"Inheritance","text":""},{"location":"chemical_entity_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"chemical_entity_set/#properties","title":"Properties","text":""},{"location":"chemical_entity_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chemical_entity_set/#schema-source","title":"Schema Source","text":""},{"location":"chemical_entity_set/#linkml-source","title":"LinkML Source","text":"
name: chemical_entity_set\ndescription: This property links a database object to the set of chemical entities\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: chemical_entity_set\ndomain_of:\n- Database\nrange: ChemicalEntity\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"chemical_formula/","title":"Slot: chemical_formula","text":"

A generic grouping for molecular formulae and empirical formulae

URI: nmdc:chemical_formula

"},{"location":"chemical_formula/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"chemical_formula/#properties","title":"Properties","text":""},{"location":"chemical_formula/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chemical_formula/#schema-source","title":"Schema Source","text":""},{"location":"chemical_formula/#linkml-source","title":"LinkML Source","text":"
name: chemical_formula\ndescription: A generic grouping for molecular formulae and empirical formulae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_formula\ndomain_of:\n- ChemicalEntity\nrange: string\n\n
"},{"location":"chimera_check/","title":"Slot: chimera check software (chimera_check)","text":"

Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.

URI: MIXS:0000052

"},{"location":"chimera_check/#inheritance","title":"Inheritance","text":""},{"location":"chimera_check/#properties","title":"Properties","text":""},{"location":"chimera_check/#aliases","title":"Aliases","text":""},{"location":"chimera_check/#examples","title":"Examples","text":"Value uchime;v4.1;default parameters"},{"location":"chimera_check/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chimera_check/#annotations","title":"Annotations","text":"property value expected_value name and version of software, parameters used"},{"location":"chimera_check/#schema-source","title":"Schema Source","text":""},{"location":"chimera_check/#linkml-source","title":"LinkML Source","text":"
name: chimera_check\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name and version of software, parameters used\ndescription: Tool(s) used for chimera checking, including version number and parameters,\n  to discover and remove chimeric sequences. A chimeric sequence is comprised of two\n  or more phylogenetically distinct parent sequences.\ntitle: chimera check software\nexamples:\n- value: uchime;v4.1;default parameters\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chimera check software\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{software};{version};{parameters}'\nslot_uri: MIXS:0000052\nalias: chimera_check\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"chloride/","title":"Slot: chloride (chloride)","text":"

Concentration of chloride in the sample

URI: MIXS:0000429

"},{"location":"chloride/#inheritance","title":"Inheritance","text":""},{"location":"chloride/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chloride/#properties","title":"Properties","text":""},{"location":"chloride/#aliases","title":"Aliases","text":""},{"location":"chloride/#examples","title":"Examples","text":"Value 5000 milligram per liter"},{"location":"chloride/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chloride/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"chloride/#schema-source","title":"Schema Source","text":""},{"location":"chloride/#linkml-source","title":"LinkML Source","text":"
name: chloride\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of chloride in the sample\ntitle: chloride\nexamples:\n- value: 5000 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chloride\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000429\nalias: chloride\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"chlorophyll/","title":"Slot: chlorophyll (chlorophyll)","text":"

Concentration of chlorophyll

URI: MIXS:0000177

"},{"location":"chlorophyll/#inheritance","title":"Inheritance","text":""},{"location":"chlorophyll/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"chlorophyll/#properties","title":"Properties","text":""},{"location":"chlorophyll/#aliases","title":"Aliases","text":""},{"location":"chlorophyll/#examples","title":"Examples","text":"Value 5 milligram per cubic meter"},{"location":"chlorophyll/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chlorophyll/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"chlorophyll/#schema-source","title":"Schema Source","text":""},{"location":"chlorophyll/#linkml-source","title":"LinkML Source","text":"
name: chlorophyll\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter, microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of chlorophyll\ntitle: chlorophyll\nexamples:\n- value: 5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chlorophyll\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000177\nalias: chlorophyll\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"chromatographic_category/","title":"Slot: chromatographic_category","text":"

The type of chromatography used in a process.

URI: nmdc:chromatographic_category

"},{"location":"chromatographic_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no"},{"location":"chromatographic_category/#properties","title":"Properties","text":""},{"location":"chromatographic_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"chromatographic_category/#schema-source","title":"Schema Source","text":""},{"location":"chromatographic_category/#linkml-source","title":"LinkML Source","text":"
name: chromatographic_category\ndescription: The type of chromatography used in a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chromatographic_category\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: ChromatographicCategoryEnum\n\n
"},{"location":"climate_environment/","title":"Slot: climate environment (climate_environment)","text":"

Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates

URI: MIXS:0001040

"},{"location":"climate_environment/#inheritance","title":"Inheritance","text":""},{"location":"climate_environment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"climate_environment/#properties","title":"Properties","text":""},{"location":"climate_environment/#aliases","title":"Aliases","text":""},{"location":"climate_environment/#examples","title":"Examples","text":"Value tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"climate_environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"climate_environment/#annotations","title":"Annotations","text":"property value expected_value climate name;treatment interval and duration"},{"location":"climate_environment/#schema-source","title":"Schema Source","text":""},{"location":"climate_environment/#linkml-source","title":"LinkML Source","text":"
name: climate_environment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: climate name;treatment interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Treatment involving an exposure to a particular climate; treatment regimen\n  including how many times the treatment was repeated, how long each treatment lasted,\n  and the start and end time of the entire treatment; can include multiple climates\ntitle: climate environment\nexamples:\n- value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- climate environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001040\nalias: climate_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"collected_from/","title":"Slot: collected_from","text":"

The Site from which a Biosample was collected

URI: nmdc:collected_from

"},{"location":"collected_from/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"collected_from/#properties","title":"Properties","text":""},{"location":"collected_from/#comments","title":"Comments","text":""},{"location":"collected_from/#todos","title":"TODOs","text":""},{"location":"collected_from/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collected_from/#schema-source","title":"Schema Source","text":""},{"location":"collected_from/#linkml-source","title":"LinkML Source","text":"
name: collected_from\ndescription: The Site from which a Biosample was collected\ntodos:\n- add an OBO slot_uri ?\ncomments:\n- this illustrates implementing a Biosample relation with a (binary) slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: collected_from\ndomain_of:\n- Biosample\nrange: FieldResearchSite\n\n
"},{"location":"collecting_biosamples_from_site_set/","title":"Slot: collecting_biosamples_from_site_set","text":"

URI: nmdc:collecting_biosamples_from_site_set

"},{"location":"collecting_biosamples_from_site_set/#inheritance","title":"Inheritance","text":""},{"location":"collecting_biosamples_from_site_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"collecting_biosamples_from_site_set/#properties","title":"Properties","text":""},{"location":"collecting_biosamples_from_site_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collecting_biosamples_from_site_set/#schema-source","title":"Schema Source","text":""},{"location":"collecting_biosamples_from_site_set/#linkml-source","title":"LinkML Source","text":"
name: collecting_biosamples_from_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: collecting_biosamples_from_site_set\ndomain_of:\n- Database\nrange: CollectingBiosamplesFromSite\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"collection_date/","title":"Slot: collection date (collection_date)","text":"

The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant

URI: MIXS:0000011

"},{"location":"collection_date/#inheritance","title":"Inheritance","text":""},{"location":"collection_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_date/#properties","title":"Properties","text":""},{"location":"collection_date/#aliases","title":"Aliases","text":""},{"location":"collection_date/#examples","title":"Examples","text":"Value 2018-05-11T10:00:00+01:00; 2018-05-11"},{"location":"collection_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collection_date/#annotations","title":"Annotations","text":"property value expected_value date and time"},{"location":"collection_date/#schema-source","title":"Schema Source","text":""},{"location":"collection_date/#linkml-source","title":"LinkML Source","text":"
name: collection_date\nannotations:\n  expected_value:\n    tag: expected_value\n    value: date and time\ndescription: 'The time of sampling, either as an instance (single point in time) or\n  interval. In case no exact time is available, the date/time can be right truncated\n  i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n  2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\ntitle: collection date\nexamples:\n- value: 2018-05-11T10:00:00+01:00; 2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- collection date\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000011\nalias: collection_date\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"collection_date_inc/","title":"Slot: incubation collection date (collection_date_inc)","text":"

Date the incubation was harvested/collected/ended. Only relevant for incubation samples.

URI: nmdc:collection_date_inc

"},{"location":"collection_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_date_inc/#properties","title":"Properties","text":""},{"location":"collection_date_inc/#examples","title":"Examples","text":"Value 2021-04-15, 2021-04 and 2021 are all acceptable."},{"location":"collection_date_inc/#comments","title":"Comments","text":""},{"location":"collection_date_inc/#see-also","title":"See Also","text":""},{"location":"collection_date_inc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collection_date_inc/#schema-source","title":"Schema Source","text":""},{"location":"collection_date_inc/#linkml-source","title":"LinkML Source","text":"
name: collection_date_inc\ndescription: Date the incubation was harvested/collected/ended. Only relevant for\n  incubation samples.\ntitle: incubation collection date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n  date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n  all acceptable.\nexamples:\n- value: 2021-04-15, 2021-04 and 2021 are all acceptable.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 2\nstring_serialization: '{date, arbitrary precision}'\nalias: collection_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"collection_time/","title":"Slot: collection time, GMT (collection_time)","text":"

The time of sampling, either as an instance (single point) or interval.

URI: nmdc:collection_time

"},{"location":"collection_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time/#properties","title":"Properties","text":""},{"location":"collection_time/#examples","title":"Examples","text":"Value 13:33 or 13:33:55"},{"location":"collection_time/#comments","title":"Comments","text":""},{"location":"collection_time/#see-also","title":"See Also","text":""},{"location":"collection_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collection_time/#schema-source","title":"Schema Source","text":""},{"location":"collection_time/#linkml-source","title":"LinkML Source","text":"
name: collection_time\ndescription: The time of sampling, either as an instance (single point) or interval.\ntitle: collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n  only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 1\nstring_serialization: '{time, seconds optional}'\nalias: collection_time\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"collection_time_inc/","title":"Slot: incubation collection time, GMT (collection_time_inc)","text":"

Time the incubation was harvested/collected/ended. Only relevant for incubation samples.

URI: nmdc:collection_time_inc

"},{"location":"collection_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time_inc/#properties","title":"Properties","text":""},{"location":"collection_time_inc/#examples","title":"Examples","text":"Value 13:33 or 13:33:55"},{"location":"collection_time_inc/#comments","title":"Comments","text":""},{"location":"collection_time_inc/#see-also","title":"See Also","text":""},{"location":"collection_time_inc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"collection_time_inc/#schema-source","title":"Schema Source","text":""},{"location":"collection_time_inc/#linkml-source","title":"LinkML Source","text":"
name: collection_time_inc\ndescription: Time the incubation was harvested/collected/ended. Only relevant for\n  incubation samples.\ntitle: incubation collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n  only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 3\nstring_serialization: '{time, seconds optional}'\nalias: collection_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"community/","title":"Slot: community","text":"

URI: nmdc:community

"},{"location":"community/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"community/#properties","title":"Properties","text":""},{"location":"community/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"community/#schema-source","title":"Schema Source","text":""},{"location":"community/#linkml-source","title":"LinkML Source","text":"
name: community\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: community\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"completeness/","title":"Slot: completeness","text":"

URI: nmdc:completeness

"},{"location":"completeness/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"completeness/#properties","title":"Properties","text":""},{"location":"completeness/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"completeness/#schema-source","title":"Schema Source","text":""},{"location":"completeness/#linkml-source","title":"LinkML Source","text":"
name: completeness\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completeness\ndomain_of:\n- EukEval\n- MagBin\nrange: float\n\n
"},{"location":"completion_date/","title":"Slot: completion_date","text":"

URI: nmdc:completion_date

"},{"location":"completion_date/#properties","title":"Properties","text":""},{"location":"completion_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"completion_date/#schema-source","title":"Schema Source","text":""},{"location":"completion_date/#linkml-source","title":"LinkML Source","text":"
name: completion_date\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completion_date\nrange: string\n\n
"},{"location":"compression_type/","title":"Slot: compression_type","text":"

If provided, specifies the compression type

URI: nmdc:compression_type

"},{"location":"compression_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"compression_type/#properties","title":"Properties","text":""},{"location":"compression_type/#examples","title":"Examples","text":"Value gzip"},{"location":"compression_type/#todos","title":"TODOs","text":""},{"location":"compression_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"compression_type/#schema-source","title":"Schema Source","text":""},{"location":"compression_type/#linkml-source","title":"LinkML Source","text":"
name: compression_type\ndescription: If provided, specifies the compression type\ntodos:\n- consider setting the range to an enum\nexamples:\n- value: gzip\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: compression_type\ndomain_of:\n- DataObject\nrange: string\n\n
"},{"location":"concentration/","title":"Slot: concentration","text":"

The concentration of a substance used in a process

URI: nmdc:concentration

"},{"location":"concentration/#inheritance","title":"Inheritance","text":""},{"location":"concentration/#properties","title":"Properties","text":""},{"location":"concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"concentration/#schema-source","title":"Schema Source","text":""},{"location":"concentration/#linkml-source","title":"LinkML Source","text":"
name: concentration\ndescription: The concentration of a substance used in a process\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: concentration\nrange: QuantityValue\n\n
"},{"location":"conditionings/","title":"Slot: conditionings","text":"

Preliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized.

URI: nmdc:conditionings

"},{"location":"conditionings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"conditionings/#properties","title":"Properties","text":""},{"location":"conditionings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"conditionings/#schema-source","title":"Schema Source","text":""},{"location":"conditionings/#linkml-source","title":"LinkML Source","text":"
name: conditionings\ndescription: Preliminary treatment of either phase with a suitable solution of the\n  other phase (in the absence of main extractable solute(s)) so that when the subsequent\n  equilibration is carried out changes in the (volume) phase ratio or in the concentrations\n  of other components are minimized.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: conditionings\ndomain_of:\n- FiltrationProcess\nrange: string\nmultivalued: true\n\n
"},{"location":"conduc/","title":"Slot: conductivity (conduc)","text":"

Electrical conductivity of water

URI: MIXS:0000692

"},{"location":"conduc/#inheritance","title":"Inheritance","text":""},{"location":"conduc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"conduc/#properties","title":"Properties","text":""},{"location":"conduc/#aliases","title":"Aliases","text":""},{"location":"conduc/#examples","title":"Examples","text":"Value 10 milliSiemens per centimeter"},{"location":"conduc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"conduc/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"conduc/#schema-source","title":"Schema Source","text":""},{"location":"conduc/#linkml-source","title":"LinkML Source","text":"
name: conduc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milliSiemens per centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Electrical conductivity of water\ntitle: conductivity\nexamples:\n- value: 10 milliSiemens per centimeter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- conductivity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000692\nalias: conduc\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"configuration_set/","title":"Slot: configuration_set","text":"

This property links a database object to the set of configurations within it.

URI: nmdc:configuration_set

"},{"location":"configuration_set/#inheritance","title":"Inheritance","text":""},{"location":"configuration_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"configuration_set/#properties","title":"Properties","text":""},{"location":"configuration_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"configuration_set/#schema-source","title":"Schema Source","text":""},{"location":"configuration_set/#linkml-source","title":"LinkML Source","text":"
name: configuration_set\ndescription: This property links a database object to the set of configurations within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: configuration_set\ndomain_of:\n- Database\nrange: Configuration\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"contained_in/","title":"Slot: contained_in","text":"

A type of container.

URI: nmdc:contained_in

"},{"location":"contained_in/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot StorageProcess A planned process with the objective to preserve and protect material entitie... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no"},{"location":"contained_in/#properties","title":"Properties","text":""},{"location":"contained_in/#examples","title":"Examples","text":"Value test tube falcon tube whirlpak"},{"location":"contained_in/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"contained_in/#schema-source","title":"Schema Source","text":""},{"location":"contained_in/#linkml-source","title":"LinkML Source","text":"
name: contained_in\ndescription: A type of container.\nexamples:\n- value: test tube\n- value: falcon tube\n- value: whirlpak\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contained_in\ndomain_of:\n- SubSamplingProcess\n- StorageProcess\nrange: ContainerCategoryEnum\n\n
"},{"location":"container_size/","title":"Slot: container_size","text":"

The volume of the container an analyte is stored in or an activity takes place in

URI: nmdc:container_size

"},{"location":"container_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no FiltrationProcess The process of segregation of phases; e no"},{"location":"container_size/#properties","title":"Properties","text":""},{"location":"container_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"container_size/#schema-source","title":"Schema Source","text":""},{"location":"container_size/#linkml-source","title":"LinkML Source","text":"
name: container_size\ndescription: The volume of the container an analyte is stored in or an activity takes\n  place in\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: container_size\ndomain_of:\n- SubSamplingProcess\n- FiltrationProcess\nrange: QuantityValue\n\n
"},{"location":"contamination/","title":"Slot: contamination","text":"

URI: nmdc:contamination

"},{"location":"contamination/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"contamination/#properties","title":"Properties","text":""},{"location":"contamination/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"contamination/#schema-source","title":"Schema Source","text":""},{"location":"contamination/#linkml-source","title":"LinkML Source","text":"
name: contamination\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contamination\ndomain_of:\n- EukEval\n- MagBin\nrange: float\n\n
"},{"location":"contig_bp/","title":"Slot: contig_bp","text":"

Total size in bp of all contigs.

URI: nmdc:contig_bp

"},{"location":"contig_bp/#inheritance","title":"Inheritance","text":""},{"location":"contig_bp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"contig_bp/#properties","title":"Properties","text":""},{"location":"contig_bp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"contig_bp/#schema-source","title":"Schema Source","text":""},{"location":"contig_bp/#linkml-source","title":"LinkML Source","text":"
name: contig_bp\ndescription: Total size in bp of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contig_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"contigs/","title":"Slot: contigs","text":"

The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase

URI: nmdc:contigs

"},{"location":"contigs/#inheritance","title":"Inheritance","text":""},{"location":"contigs/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"contigs/#properties","title":"Properties","text":""},{"location":"contigs/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"contigs/#schema-source","title":"Schema Source","text":""},{"location":"contigs/#linkml-source","title":"LinkML Source","text":"
name: contigs\ndescription: The sum of the (length*log(length)) of all contigs, times some constant.  Increase\n  the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contigs\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"cool_syst_id/","title":"Slot: cooling system identifier (cool_syst_id)","text":"

The cooling system identifier

URI: MIXS:0000785

"},{"location":"cool_syst_id/#inheritance","title":"Inheritance","text":""},{"location":"cool_syst_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"cool_syst_id/#properties","title":"Properties","text":""},{"location":"cool_syst_id/#aliases","title":"Aliases","text":""},{"location":"cool_syst_id/#examples","title":"Examples","text":"Value 12345"},{"location":"cool_syst_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cool_syst_id/#annotations","title":"Annotations","text":"property value expected_value unique identifier"},{"location":"cool_syst_id/#schema-source","title":"Schema Source","text":""},{"location":"cool_syst_id/#linkml-source","title":"LinkML Source","text":"
name: cool_syst_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: unique identifier\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The cooling system identifier\ntitle: cooling system identifier\nexamples:\n- value: '12345'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- cooling system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000785\nalias: cool_syst_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"core_field/","title":"Slot: core_field","text":"

basic fields

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:core_field

"},{"location":"core_field/#inheritance","title":"Inheritance","text":""},{"location":"core_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"core_field/#properties","title":"Properties","text":""},{"location":"core_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"core_field/#schema-source","title":"Schema Source","text":""},{"location":"core_field/#linkml-source","title":"LinkML Source","text":"
name: core field\ndescription: basic fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: core_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"count/","title":"Slot: count","text":"

URI: nmdc:count

"},{"location":"count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"count/#properties","title":"Properties","text":""},{"location":"count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"count/#schema-source","title":"Schema Source","text":""},{"location":"count/#linkml-source","title":"LinkML Source","text":"
name: count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: count\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: integer\nrequired: true\n\n
"},{"location":"crop_rotation/","title":"Slot: history/crop rotation (crop_rotation)","text":"

Whether or not crop is rotated, and if yes, rotation schedule

URI: MIXS:0000318

"},{"location":"crop_rotation/#inheritance","title":"Inheritance","text":""},{"location":"crop_rotation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"crop_rotation/#properties","title":"Properties","text":""},{"location":"crop_rotation/#aliases","title":"Aliases","text":""},{"location":"crop_rotation/#examples","title":"Examples","text":"Value yes;R2/2017-01-01/2018-12-31/P6M"},{"location":"crop_rotation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"crop_rotation/#annotations","title":"Annotations","text":"property value expected_value crop rotation status;schedule"},{"location":"crop_rotation/#schema-source","title":"Schema Source","text":""},{"location":"crop_rotation/#linkml-source","title":"LinkML Source","text":"
name: crop_rotation\nannotations:\n  expected_value:\n    tag: expected_value\n    value: crop rotation status;schedule\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Whether or not crop is rotated, and if yes, rotation schedule\ntitle: history/crop rotation\nexamples:\n- value: yes;R2/2017-01-01/2018-12-31/P6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/crop rotation\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000318\nalias: crop_rotation\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ctg_l50/","title":"Slot: ctg_l50","text":"

Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.

URI: nmdc:ctg_l50

"},{"location":"ctg_l50/#inheritance","title":"Inheritance","text":""},{"location":"ctg_l50/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"ctg_l50/#properties","title":"Properties","text":""},{"location":"ctg_l50/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_l50/#schema-source","title":"Schema Source","text":""},{"location":"ctg_l50/#linkml-source","title":"LinkML Source","text":"
name: ctg_l50\ndescription: Given a set of contigs, the L50 is defined as the sequence length of\n  the shortest contig at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_l90/","title":"Slot: ctg_l90","text":"

The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.

URI: nmdc:ctg_l90

"},{"location":"ctg_l90/#inheritance","title":"Inheritance","text":""},{"location":"ctg_l90/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"ctg_l90/#properties","title":"Properties","text":""},{"location":"ctg_l90/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_l90/#schema-source","title":"Schema Source","text":""},{"location":"ctg_l90/#linkml-source","title":"LinkML Source","text":"
name: ctg_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n  length for which the collection of all contigs of that length or longer contains\n  at least 90% of the sum of the lengths of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_logsum/","title":"Slot: ctg_logsum","text":"

Maximum contig length.

URI: nmdc:ctg_logsum

"},{"location":"ctg_logsum/#inheritance","title":"Inheritance","text":""},{"location":"ctg_logsum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"ctg_logsum/#properties","title":"Properties","text":""},{"location":"ctg_logsum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_logsum/#schema-source","title":"Schema Source","text":""},{"location":"ctg_logsum/#linkml-source","title":"LinkML Source","text":"
name: ctg_logsum\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_max/","title":"Slot: ctg_max","text":"

Maximum contig length.

URI: nmdc:ctg_max

"},{"location":"ctg_max/#inheritance","title":"Inheritance","text":""},{"location":"ctg_max/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"ctg_max/#properties","title":"Properties","text":""},{"location":"ctg_max/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_max/#schema-source","title":"Schema Source","text":""},{"location":"ctg_max/#linkml-source","title":"LinkML Source","text":"
name: ctg_max\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_n50/","title":"Slot: ctg_n50","text":"

Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.

URI: nmdc:ctg_n50

"},{"location":"ctg_n50/#inheritance","title":"Inheritance","text":""},{"location":"ctg_n50/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"ctg_n50/#properties","title":"Properties","text":""},{"location":"ctg_n50/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_n50/#schema-source","title":"Schema Source","text":""},{"location":"ctg_n50/#linkml-source","title":"LinkML Source","text":"
name: ctg_n50\ndescription: Given a set of contigs, each with its own length, the N50 count is defined\n  as the smallest number_of_contigs whose length sum makes up half of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_n90/","title":"Slot: ctg_n90","text":"

Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.

URI: nmdc:ctg_n90

"},{"location":"ctg_n90/#inheritance","title":"Inheritance","text":""},{"location":"ctg_n90/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"ctg_n90/#properties","title":"Properties","text":""},{"location":"ctg_n90/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_n90/#schema-source","title":"Schema Source","text":""},{"location":"ctg_n90/#linkml-source","title":"LinkML Source","text":"
name: ctg_n90\ndescription: Given a set of contigs, each with its own length, the N90 count is defined\n  as the smallest number of contigs whose length sum makes up 90% of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"ctg_powsum/","title":"Slot: ctg_powsum","text":"

Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).

URI: nmdc:ctg_powsum

"},{"location":"ctg_powsum/#inheritance","title":"Inheritance","text":""},{"location":"ctg_powsum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"ctg_powsum/#properties","title":"Properties","text":""},{"location":"ctg_powsum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ctg_powsum/#schema-source","title":"Schema Source","text":""},{"location":"ctg_powsum/#linkml-source","title":"LinkML Source","text":"
name: ctg_powsum\ndescription: Powersum of all contigs is the same as logsum except that it uses the\n  sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"cult_root_med/","title":"Slot: culture rooting medium (cult_root_med)","text":"

Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.

URI: MIXS:0001041

"},{"location":"cult_root_med/#inheritance","title":"Inheritance","text":""},{"location":"cult_root_med/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"cult_root_med/#properties","title":"Properties","text":""},{"location":"cult_root_med/#aliases","title":"Aliases","text":""},{"location":"cult_root_med/#examples","title":"Examples","text":"Value http://himedialabs.com/TD/PT158.pdf"},{"location":"cult_root_med/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cult_root_med/#annotations","title":"Annotations","text":"property value expected_value name, PMID,DOI or url"},{"location":"cult_root_med/#schema-source","title":"Schema Source","text":""},{"location":"cult_root_med/#linkml-source","title":"LinkML Source","text":"
name: cult_root_med\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name, PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name or reference for the hydroponic or in vitro culture rooting medium;\n  can be the name of a commonly used medium or reference to a specific medium, e.g.\n  Murashige and Skoog medium. If the medium has not been formally published, use the\n  rooting medium descriptors.\ntitle: culture rooting medium\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- culture rooting medium\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001041\nalias: cult_root_med\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"cur_land_use/","title":"Slot: current land use (cur_land_use)","text":"

Present state of sample site

URI: MIXS:0001080

"},{"location":"cur_land_use/#inheritance","title":"Inheritance","text":""},{"location":"cur_land_use/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"cur_land_use/#properties","title":"Properties","text":""},{"location":"cur_land_use/#aliases","title":"Aliases","text":""},{"location":"cur_land_use/#examples","title":"Examples","text":"Value conifers"},{"location":"cur_land_use/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cur_land_use/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"cur_land_use/#schema-source","title":"Schema Source","text":""},{"location":"cur_land_use/#linkml-source","title":"LinkML Source","text":"
name: cur_land_use\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Present state of sample site\ntitle: current land use\nexamples:\n- value: conifers\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current land use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001080\nalias: cur_land_use\ndomain_of:\n- Biosample\nrange: cur_land_use_enum\nmultivalued: false\n\n
"},{"location":"cur_vegetation/","title":"Slot: current vegetation (cur_vegetation)","text":"

Vegetation classification from one or more standard classification systems, or agricultural crop

URI: MIXS:0000312

"},{"location":"cur_vegetation/#inheritance","title":"Inheritance","text":""},{"location":"cur_vegetation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no"},{"location":"cur_vegetation/#properties","title":"Properties","text":""},{"location":"cur_vegetation/#aliases","title":"Aliases","text":""},{"location":"cur_vegetation/#examples","title":"Examples","text":"Value"},{"location":"cur_vegetation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cur_vegetation/#annotations","title":"Annotations","text":"property value expected_value current vegetation type"},{"location":"cur_vegetation/#schema-source","title":"Schema Source","text":""},{"location":"cur_vegetation/#linkml-source","title":"LinkML Source","text":"
name: cur_vegetation\nannotations:\n  expected_value:\n    tag: expected_value\n    value: current vegetation type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Vegetation classification from one or more standard classification systems,\n  or agricultural crop\ntitle: current vegetation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000312\nalias: cur_vegetation\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"cur_vegetation_meth/","title":"Slot: current vegetation method (cur_vegetation_meth)","text":"

Reference or method used in vegetation classification

URI: MIXS:0000314

"},{"location":"cur_vegetation_meth/#inheritance","title":"Inheritance","text":""},{"location":"cur_vegetation_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"cur_vegetation_meth/#properties","title":"Properties","text":""},{"location":"cur_vegetation_meth/#aliases","title":"Aliases","text":""},{"location":"cur_vegetation_meth/#examples","title":"Examples","text":"Value"},{"location":"cur_vegetation_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"cur_vegetation_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"cur_vegetation_meth/#schema-source","title":"Schema Source","text":""},{"location":"cur_vegetation_meth/#linkml-source","title":"LinkML Source","text":"
name: cur_vegetation_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in vegetation classification\ntitle: current vegetation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000314\nalias: cur_vegetation_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"data_category/","title":"Slot: data_category","text":"

The category of the file, such as instrument data from data generation or processed data from a workflow execution.

URI: nmdc:data_category

"},{"location":"data_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_category/#properties","title":"Properties","text":""},{"location":"data_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"data_category/#schema-source","title":"Schema Source","text":""},{"location":"data_category/#linkml-source","title":"LinkML Source","text":"
name: data_category\ndescription: The category of the file, such as instrument data from data generation\n  or processed data from a workflow execution.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: data_category\ndomain_of:\n- DataObject\nrange: DataCategoryEnum\n\n
"},{"location":"data_generation_set/","title":"Slot: data_generation_set","text":"

This property links a database object to the set of data generations within it.

URI: nmdc:data_generation_set

"},{"location":"data_generation_set/#inheritance","title":"Inheritance","text":""},{"location":"data_generation_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"data_generation_set/#properties","title":"Properties","text":""},{"location":"data_generation_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"data_generation_set/#schema-source","title":"Schema Source","text":""},{"location":"data_generation_set/#linkml-source","title":"LinkML Source","text":"
name: data_generation_set\ndescription: This property links a database object to the set of data generations\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: data_generation_set\ndomain_of:\n- Database\nrange: DataGeneration\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"data_object_set/","title":"Slot: data_object_set","text":"

This property links a database object to the set of data objects within it.

URI: nmdc:data_object_set

"},{"location":"data_object_set/#inheritance","title":"Inheritance","text":""},{"location":"data_object_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"data_object_set/#properties","title":"Properties","text":""},{"location":"data_object_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"data_object_set/#schema-source","title":"Schema Source","text":""},{"location":"data_object_set/#linkml-source","title":"LinkML Source","text":"
name: data_object_set\ndescription: This property links a database object to the set of data objects within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: data_object_set\ndomain_of:\n- Database\nrange: DataObject\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"data_object_type/","title":"Slot: data_object_type","text":"

The type of file represented by the data object.

URI: nmdc:data_object_type

"},{"location":"data_object_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_object_type/#properties","title":"Properties","text":""},{"location":"data_object_type/#examples","title":"Examples","text":"Value FT ICR-MS Analysis Results GC-MS Metabolomics Results"},{"location":"data_object_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"data_object_type/#schema-source","title":"Schema Source","text":""},{"location":"data_object_type/#linkml-source","title":"LinkML Source","text":"
name: data_object_type\ndescription: The type of file represented by the data object.\nexamples:\n- value: FT ICR-MS Analysis Results\n- value: GC-MS Metabolomics Results\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: data_object_type\ndomain_of:\n- DataObject\nrange: FileTypeEnum\n\n
"},{"location":"date_created/","title":"Slot: date_created","text":"

from database class

URI: nmdc:date_created

"},{"location":"date_created/#properties","title":"Properties","text":""},{"location":"date_created/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"date_created/#schema-source","title":"Schema Source","text":""},{"location":"date_created/#linkml-source","title":"LinkML Source","text":"
name: date_created\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: date_created\nrange: string\n\n
"},{"location":"date_last_rain/","title":"Slot: date last rain (date_last_rain)","text":"

The date of the last time it rained

URI: MIXS:0000786

"},{"location":"date_last_rain/#inheritance","title":"Inheritance","text":""},{"location":"date_last_rain/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"date_last_rain/#properties","title":"Properties","text":""},{"location":"date_last_rain/#aliases","title":"Aliases","text":""},{"location":"date_last_rain/#examples","title":"Examples","text":"Value 2018-05-11:T14:30Z"},{"location":"date_last_rain/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"date_last_rain/#annotations","title":"Annotations","text":"property value expected_value timestamp"},{"location":"date_last_rain/#schema-source","title":"Schema Source","text":""},{"location":"date_last_rain/#linkml-source","title":"LinkML Source","text":"
name: date_last_rain\nannotations:\n  expected_value:\n    tag: expected_value\n    value: timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The date of the last time it rained\ntitle: date last rain\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- date last rain\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000786\nalias: date_last_rain\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"density/","title":"Slot: density (density)","text":"

Density of the sample, which is its mass per unit volume (aka volumetric mass density)

URI: MIXS:0000435

"},{"location":"density/#inheritance","title":"Inheritance","text":""},{"location":"density/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"density/#properties","title":"Properties","text":""},{"location":"density/#aliases","title":"Aliases","text":""},{"location":"density/#examples","title":"Examples","text":"Value 1000 kilogram per cubic meter"},{"location":"density/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"density/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"density/#schema-source","title":"Schema Source","text":""},{"location":"density/#linkml-source","title":"LinkML Source","text":"
name: density\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per cubic meter, gram per cubic centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Density of the sample, which is its mass per unit volume (aka volumetric\n  mass density)\ntitle: density\nexamples:\n- value: 1000 kilogram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000435\nalias: density\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"depos_env/","title":"Slot: depositional environment (depos_env)","text":"

Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000992

"},{"location":"depos_env/#inheritance","title":"Inheritance","text":""},{"location":"depos_env/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"depos_env/#properties","title":"Properties","text":""},{"location":"depos_env/#aliases","title":"Aliases","text":""},{"location":"depos_env/#examples","title":"Examples","text":"Value Continental - Alluvial"},{"location":"depos_env/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"depos_env/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"depos_env/#schema-source","title":"Schema Source","text":""},{"location":"depos_env/#linkml-source","title":"LinkML Source","text":"
name: depos_env\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n  If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: depositional environment\nexamples:\n- value: Continental - Alluvial\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000992\nalias: depos_env\ndomain_of:\n- Biosample\nrange: depos_env_enum\nmultivalued: false\n\n
"},{"location":"depth/","title":"Slot: depth (depth)","text":"

The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.

URI: MIXS:0000018

"},{"location":"depth/#inheritance","title":"Inheritance","text":""},{"location":"depth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"depth/#properties","title":"Properties","text":""},{"location":"depth/#aliases","title":"Aliases","text":""},{"location":"depth/#examples","title":"Examples","text":"Value 10 meter"},{"location":"depth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"depth/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"depth/#schema-source","title":"Schema Source","text":""},{"location":"depth/#linkml-source","title":"LinkML Source","text":"
name: depth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\ndescription: The vertical distance below local surface, e.g. for sediment or soil\n  samples depth is measured from sediment or soil surface, respectively. Depth can\n  be reported as an interval for subsurface samples.\ntitle: depth\nexamples:\n- value: 10 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000018\nalias: depth\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"description/","title":"Slot: description","text":"

a human-readable description of a thing

URI: dcterms:description

"},{"location":"description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no Site no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MaterialEntity no MetatranscriptomeAssembly no Configuration A set of parameters that define the actions of a process and is shared among ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DataObject An object that primarily consists of symbols that represent information yes PlannedProcess no EnvironmentalMaterialTerm no NamedThing a databased entity or concept/class no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no ProcessedSample no ChemicalEntity An atom or molecule that can be represented with a chemical formula no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no Instrument A material entity that is designed to perform a function in a scientific inve... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no GeneProduct A molecule encoded by a gene that has an evolved function no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Study A study summarizes the overall goal of a research initiative and outlines the... yes MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes CalibrationInformation A calibration object that is associated with a process no Extraction A material separation in which a desired component of an input material is se... no ImageValue An attribute value representing an image no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no OntologyClass no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes ProtocolExecution A PlannedProces that has PlannedProcess parts no Manifest no OrthologyGroup A set of genes or gene products in which all members are orthologous no Biosample Biological source material which can be characterized by an experiment no LibraryPreparation no"},{"location":"description/#properties","title":"Properties","text":""},{"location":"description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"description/#schema-source","title":"Schema Source","text":""},{"location":"description/#linkml-source","title":"LinkML Source","text":"
name: description\ndescription: a human-readable description of a thing\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: dcterms:description\nalias: description\ndomain_of:\n- ImageValue\n- NamedThing\nrange: string\n\n
"},{"location":"dew_point/","title":"Slot: dew point (dew_point)","text":"

The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.

URI: MIXS:0000129

"},{"location":"dew_point/#inheritance","title":"Inheritance","text":""},{"location":"dew_point/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dew_point/#properties","title":"Properties","text":""},{"location":"dew_point/#aliases","title":"Aliases","text":""},{"location":"dew_point/#examples","title":"Examples","text":"Value 22 degree Celsius"},{"location":"dew_point/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dew_point/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"dew_point/#schema-source","title":"Schema Source","text":""},{"location":"dew_point/#linkml-source","title":"LinkML Source","text":"
name: dew_point\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The temperature to which a given parcel of humid air must be cooled,\n  at constant barometric pressure, for water vapor to condense into water.\ntitle: dew point\nexamples:\n- value: 22 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000129\nalias: dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diether_lipids/","title":"Slot: diether lipids (diether_lipids)","text":"

Concentration of diether lipids; can include multiple types of diether lipids

URI: MIXS:0000178

"},{"location":"diether_lipids/#inheritance","title":"Inheritance","text":""},{"location":"diether_lipids/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diether_lipids/#properties","title":"Properties","text":""},{"location":"diether_lipids/#aliases","title":"Aliases","text":""},{"location":"diether_lipids/#examples","title":"Examples","text":"Value 0.2 nanogram per liter"},{"location":"diether_lipids/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diether_lipids/#annotations","title":"Annotations","text":"property value expected_value diether lipid name;measurement value"},{"location":"diether_lipids/#schema-source","title":"Schema Source","text":""},{"location":"diether_lipids/#linkml-source","title":"LinkML Source","text":"
name: diether_lipids\nannotations:\n  expected_value:\n    tag: expected_value\n    value: diether lipid name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: nanogram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of diether lipids; can include multiple types of diether\n  lipids\ntitle: diether lipids\nexamples:\n- value: 0.2 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- diether lipids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000178\nalias: diether_lipids\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"direct_infusion_category/","title":"Slot: direct_infusion_category","text":"

used when a processed sample is introduced into a mass spectrometer without chromatographic separation

URI: nmdc:direct_infusion_category

"},{"location":"direct_infusion_category/#properties","title":"Properties","text":""},{"location":"direct_infusion_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"direct_infusion_category/#schema-source","title":"Schema Source","text":""},{"location":"direct_infusion_category/#linkml-source","title":"LinkML Source","text":"
name: direct_infusion_category\ndescription: used when a processed sample is introduced into a mass spectrometer without\n  chromatographic separation\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: direct_infusion_category\nrange: DirectInfusionEnum\n\n
"},{"location":"display_order/","title":"Slot: display_order","text":"

When rendering information, this attribute to specify the order in which the information should be rendered.

URI: nmdc:display_order

"},{"location":"display_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ImageValue An attribute value representing an image no"},{"location":"display_order/#properties","title":"Properties","text":""},{"location":"display_order/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"display_order/#schema-source","title":"Schema Source","text":""},{"location":"display_order/#linkml-source","title":"LinkML Source","text":"
name: display_order\ndescription: When rendering information, this attribute to specify the order in which\n  the information should be rendered.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: display_order\ndomain_of:\n- ImageValue\nrange: integer\n\n
"},{"location":"diss_carb_dioxide/","title":"Slot: dissolved carbon dioxide (diss_carb_dioxide)","text":"

Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample

URI: MIXS:0000436

"},{"location":"diss_carb_dioxide/#inheritance","title":"Inheritance","text":""},{"location":"diss_carb_dioxide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_carb_dioxide/#properties","title":"Properties","text":""},{"location":"diss_carb_dioxide/#aliases","title":"Aliases","text":""},{"location":"diss_carb_dioxide/#examples","title":"Examples","text":"Value 5 milligram per liter"},{"location":"diss_carb_dioxide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_carb_dioxide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_carb_dioxide/#schema-source","title":"Schema Source","text":""},{"location":"diss_carb_dioxide/#linkml-source","title":"LinkML Source","text":"
name: diss_carb_dioxide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved carbon dioxide in the sample or liquid portion\n  of the sample\ntitle: dissolved carbon dioxide\nexamples:\n- value: 5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000436\nalias: diss_carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_hydrogen/","title":"Slot: dissolved hydrogen (diss_hydrogen)","text":"

Concentration of dissolved hydrogen

URI: MIXS:0000179

"},{"location":"diss_hydrogen/#inheritance","title":"Inheritance","text":""},{"location":"diss_hydrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_hydrogen/#properties","title":"Properties","text":""},{"location":"diss_hydrogen/#aliases","title":"Aliases","text":""},{"location":"diss_hydrogen/#examples","title":"Examples","text":"Value 0.3 micromole per liter"},{"location":"diss_hydrogen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_hydrogen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_hydrogen/#schema-source","title":"Schema Source","text":""},{"location":"diss_hydrogen/#linkml-source","title":"LinkML Source","text":"
name: diss_hydrogen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved hydrogen\ntitle: dissolved hydrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved hydrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000179\nalias: diss_hydrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_inorg_carb/","title":"Slot: dissolved inorganic carbon (diss_inorg_carb)","text":"

Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter

URI: MIXS:0000434

"},{"location":"diss_inorg_carb/#inheritance","title":"Inheritance","text":""},{"location":"diss_inorg_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_inorg_carb/#properties","title":"Properties","text":""},{"location":"diss_inorg_carb/#aliases","title":"Aliases","text":""},{"location":"diss_inorg_carb/#examples","title":"Examples","text":"Value 2059 micromole per kilogram"},{"location":"diss_inorg_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_inorg_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_inorg_carb/#schema-source","title":"Schema Source","text":""},{"location":"diss_inorg_carb/#linkml-source","title":"LinkML Source","text":"
name: diss_inorg_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Dissolved inorganic carbon concentration in the sample, typically measured\n  after filtering the sample using a 0.45 micrometer filter\ntitle: dissolved inorganic carbon\nexamples:\n- value: 2059 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000434\nalias: diss_inorg_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_inorg_nitro/","title":"Slot: dissolved inorganic nitrogen (diss_inorg_nitro)","text":"

Concentration of dissolved inorganic nitrogen

URI: MIXS:0000698

"},{"location":"diss_inorg_nitro/#inheritance","title":"Inheritance","text":""},{"location":"diss_inorg_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_inorg_nitro/#properties","title":"Properties","text":""},{"location":"diss_inorg_nitro/#aliases","title":"Aliases","text":""},{"location":"diss_inorg_nitro/#examples","title":"Examples","text":"Value 761 micromole per liter"},{"location":"diss_inorg_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_inorg_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_inorg_nitro/#schema-source","title":"Schema Source","text":""},{"location":"diss_inorg_nitro/#linkml-source","title":"LinkML Source","text":"
name: diss_inorg_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved inorganic nitrogen\ntitle: dissolved inorganic nitrogen\nexamples:\n- value: 761 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000698\nalias: diss_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_inorg_phosp/","title":"Slot: dissolved inorganic phosphorus (diss_inorg_phosp)","text":"

Concentration of dissolved inorganic phosphorus in the sample

URI: MIXS:0000106

"},{"location":"diss_inorg_phosp/#inheritance","title":"Inheritance","text":""},{"location":"diss_inorg_phosp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_inorg_phosp/#properties","title":"Properties","text":""},{"location":"diss_inorg_phosp/#aliases","title":"Aliases","text":""},{"location":"diss_inorg_phosp/#examples","title":"Examples","text":"Value 56.5 micromole per liter"},{"location":"diss_inorg_phosp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_inorg_phosp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_inorg_phosp/#schema-source","title":"Schema Source","text":""},{"location":"diss_inorg_phosp/#linkml-source","title":"LinkML Source","text":"
name: diss_inorg_phosp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved inorganic phosphorus in the sample\ntitle: dissolved inorganic phosphorus\nexamples:\n- value: 56.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000106\nalias: diss_inorg_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_iron/","title":"Slot: dissolved iron (diss_iron)","text":"

Concentration of dissolved iron in the sample

URI: MIXS:0000139

"},{"location":"diss_iron/#inheritance","title":"Inheritance","text":""},{"location":"diss_iron/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_iron/#properties","title":"Properties","text":""},{"location":"diss_iron/#aliases","title":"Aliases","text":""},{"location":"diss_iron/#examples","title":"Examples","text":"Value"},{"location":"diss_iron/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_iron/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_iron/#schema-source","title":"Schema Source","text":""},{"location":"diss_iron/#linkml-source","title":"LinkML Source","text":"
name: diss_iron\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved iron in the sample\ntitle: dissolved iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000139\nalias: diss_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_org_carb/","title":"Slot: dissolved organic carbon (diss_org_carb)","text":"

Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid

URI: MIXS:0000433

"},{"location":"diss_org_carb/#inheritance","title":"Inheritance","text":""},{"location":"diss_org_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_org_carb/#properties","title":"Properties","text":""},{"location":"diss_org_carb/#aliases","title":"Aliases","text":""},{"location":"diss_org_carb/#examples","title":"Examples","text":"Value 197 micromole per liter"},{"location":"diss_org_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_org_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_org_carb/#schema-source","title":"Schema Source","text":""},{"location":"diss_org_carb/#linkml-source","title":"LinkML Source","text":"
name: diss_org_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved organic carbon in the sample, liquid portion\n  of the sample, or aqueous phase of the fluid\ntitle: dissolved organic carbon\nexamples:\n- value: 197 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000433\nalias: diss_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_org_nitro/","title":"Slot: dissolved organic nitrogen (diss_org_nitro)","text":"

Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2

URI: MIXS:0000162

"},{"location":"diss_org_nitro/#inheritance","title":"Inheritance","text":""},{"location":"diss_org_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_org_nitro/#properties","title":"Properties","text":""},{"location":"diss_org_nitro/#aliases","title":"Aliases","text":""},{"location":"diss_org_nitro/#examples","title":"Examples","text":"Value 0.05 micromole per liter"},{"location":"diss_org_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_org_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_org_nitro/#schema-source","title":"Schema Source","text":""},{"location":"diss_org_nitro/#linkml-source","title":"LinkML Source","text":"
name: diss_org_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Dissolved organic nitrogen concentration measured as; total dissolved\n  nitrogen - NH4 - NO3 - NO2\ntitle: dissolved organic nitrogen\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000162\nalias: diss_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_oxygen/","title":"Slot: dissolved oxygen (diss_oxygen)","text":"

Concentration of dissolved oxygen

URI: MIXS:0000119

"},{"location":"diss_oxygen/#inheritance","title":"Inheritance","text":""},{"location":"diss_oxygen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_oxygen/#properties","title":"Properties","text":""},{"location":"diss_oxygen/#aliases","title":"Aliases","text":""},{"location":"diss_oxygen/#examples","title":"Examples","text":"Value 175 micromole per kilogram"},{"location":"diss_oxygen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_oxygen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_oxygen/#schema-source","title":"Schema Source","text":""},{"location":"diss_oxygen/#linkml-source","title":"LinkML Source","text":"
name: diss_oxygen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per kilogram, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved oxygen\ntitle: dissolved oxygen\nexamples:\n- value: 175 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000119\nalias: diss_oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"diss_oxygen_fluid/","title":"Slot: dissolved oxygen in fluids (diss_oxygen_fluid)","text":"

Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).

URI: MIXS:0000438

"},{"location":"diss_oxygen_fluid/#inheritance","title":"Inheritance","text":""},{"location":"diss_oxygen_fluid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"diss_oxygen_fluid/#properties","title":"Properties","text":""},{"location":"diss_oxygen_fluid/#aliases","title":"Aliases","text":""},{"location":"diss_oxygen_fluid/#examples","title":"Examples","text":"Value"},{"location":"diss_oxygen_fluid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"diss_oxygen_fluid/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"diss_oxygen_fluid/#schema-source","title":"Schema Source","text":""},{"location":"diss_oxygen_fluid/#linkml-source","title":"LinkML Source","text":"
name: diss_oxygen_fluid\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per kilogram, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of dissolved oxygen in the oil field produced fluids as\n  it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\ntitle: dissolved oxygen in fluids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen in fluids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000438\nalias: diss_oxygen_fluid\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"dna_absorb1/","title":"Slot: DNA absorbance 260/280 (dna_absorb1)","text":"

260/280 measurement of DNA sample purity

URI: nmdc:dna_absorb1

"},{"location":"dna_absorb1/#inheritance","title":"Inheritance","text":""},{"location":"dna_absorb1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no ProcessedSample no"},{"location":"dna_absorb1/#properties","title":"Properties","text":""},{"location":"dna_absorb1/#examples","title":"Examples","text":"Value 2.02"},{"location":"dna_absorb1/#comments","title":"Comments","text":""},{"location":"dna_absorb1/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_absorb1/#schema-source","title":"Schema Source","text":""},{"location":"dna_absorb1/#linkml-source","title":"LinkML Source","text":"
name: dna_absorb1\ndescription: 260/280 measurement of DNA sample purity\ntitle: DNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nis_a: biomaterial_purity\nalias: dna_absorb1\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\n
"},{"location":"dna_absorb2/","title":"Slot: DNA absorbance 260/230 (dna_absorb2)","text":"

260/230 measurement of DNA sample purity

URI: nmdc:dna_absorb2

"},{"location":"dna_absorb2/#inheritance","title":"Inheritance","text":""},{"location":"dna_absorb2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_absorb2/#properties","title":"Properties","text":""},{"location":"dna_absorb2/#examples","title":"Examples","text":"Value 2.02"},{"location":"dna_absorb2/#comments","title":"Comments","text":""},{"location":"dna_absorb2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_absorb2/#schema-source","title":"Schema Source","text":""},{"location":"dna_absorb2/#linkml-source","title":"LinkML Source","text":"
name: dna_absorb2\ndescription: 260/230 measurement of DNA sample purity\ntitle: DNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nis_a: biomaterial_purity\nalias: dna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\n
"},{"location":"dna_collect_site/","title":"Slot: DNA collection site (dna_collect_site)","text":"

Provide information on the site your DNA sample was collected from

URI: nmdc:dna_collect_site

"},{"location":"dna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_collect_site/#properties","title":"Properties","text":""},{"location":"dna_collect_site/#examples","title":"Examples","text":"Value untreated pond water"},{"location":"dna_collect_site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_collect_site/#schema-source","title":"Schema Source","text":""},{"location":"dna_collect_site/#linkml-source","title":"LinkML Source","text":"
name: dna_collect_site\ndescription: Provide information on the site your DNA sample was collected from\ntitle: DNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: dna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_concentration/","title":"Slot: DNA concentration in ng/ul (dna_concentration)","text":"

URI: nmdc:dna_concentration

"},{"location":"dna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no ProcessedSample no"},{"location":"dna_concentration/#properties","title":"Properties","text":""},{"location":"dna_concentration/#examples","title":"Examples","text":"Value 100"},{"location":"dna_concentration/#comments","title":"Comments","text":""},{"location":"dna_concentration/#see-also","title":"See Also","text":""},{"location":"dna_concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_concentration/#schema-source","title":"Schema Source","text":""},{"location":"dna_concentration/#linkml-source","title":"LinkML Source","text":"
name: dna_concentration\ntitle: DNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n  a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nalias: dna_concentration\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\n
"},{"location":"dna_cont_type/","title":"Slot: DNA container type (dna_cont_type)","text":"

Tube or plate (96-well)

URI: nmdc:dna_cont_type

"},{"location":"dna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_type/#properties","title":"Properties","text":""},{"location":"dna_cont_type/#examples","title":"Examples","text":"Value plate"},{"location":"dna_cont_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_cont_type/#schema-source","title":"Schema Source","text":""},{"location":"dna_cont_type/#linkml-source","title":"LinkML Source","text":"
name: dna_cont_type\ndescription: Tube or plate (96-well)\ntitle: DNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: dna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: JgiContTypeEnum\nrecommended: true\n\n
"},{"location":"dna_cont_well/","title":"Slot: DNA plate position (dna_cont_well)","text":"

URI: nmdc:dna_cont_well

"},{"location":"dna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_well/#properties","title":"Properties","text":""},{"location":"dna_cont_well/#examples","title":"Examples","text":"Value B2"},{"location":"dna_cont_well/#comments","title":"Comments","text":""},{"location":"dna_cont_well/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_cont_well/#schema-source","title":"Schema Source","text":""},{"location":"dna_cont_well/#linkml-source","title":"LinkML Source","text":"
name: dna_cont_well\ntitle: DNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n  validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: dna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\npattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n\n
"},{"location":"dna_container_id/","title":"Slot: DNA container label (dna_container_id)","text":"

URI: nmdc:dna_container_id

"},{"location":"dna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_container_id/#properties","title":"Properties","text":""},{"location":"dna_container_id/#examples","title":"Examples","text":"Value Pond_MT_041618"},{"location":"dna_container_id/#comments","title":"Comments","text":""},{"location":"dna_container_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_container_id/#schema-source","title":"Schema Source","text":""},{"location":"dna_container_id/#linkml-source","title":"LinkML Source","text":"
name: dna_container_id\ntitle: DNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n  plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: dna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_dnase/","title":"Slot: DNase treatment DNA (dna_dnase)","text":"

URI: nmdc:dna_dnase

"},{"location":"dna_dnase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_dnase/#properties","title":"Properties","text":""},{"location":"dna_dnase/#examples","title":"Examples","text":"Value no"},{"location":"dna_dnase/#comments","title":"Comments","text":""},{"location":"dna_dnase/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_dnase/#schema-source","title":"Schema Source","text":""},{"location":"dna_dnase/#linkml-source","title":"LinkML Source","text":"
name: dna_dnase\ntitle: DNase treatment DNA\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nalias: dna_dnase\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: YesNoEnum\nrecommended: true\n\n
"},{"location":"dna_isolate_meth/","title":"Slot: DNA isolation method (dna_isolate_meth)","text":"

Describe the method/protocol/kit used to extract DNA/RNA.

URI: nmdc:dna_isolate_meth

"},{"location":"dna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_isolate_meth/#properties","title":"Properties","text":""},{"location":"dna_isolate_meth/#aliases","title":"Aliases","text":""},{"location":"dna_isolate_meth/#examples","title":"Examples","text":"Value phenol/chloroform extraction"},{"location":"dna_isolate_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_isolate_meth/#schema-source","title":"Schema Source","text":""},{"location":"dna_isolate_meth/#linkml-source","title":"LinkML Source","text":"
name: dna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: DNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Sample Isolation Method\nrank: 16\nstring_serialization: '{text}'\nalias: dna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_organisms/","title":"Slot: DNA expected organisms (dna_organisms)","text":"

List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.

URI: nmdc:dna_organisms

"},{"location":"dna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_organisms/#properties","title":"Properties","text":""},{"location":"dna_organisms/#examples","title":"Examples","text":"Value expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)"},{"location":"dna_organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_organisms/#schema-source","title":"Schema Source","text":""},{"location":"dna_organisms/#linkml-source","title":"LinkML Source","text":"
name: dna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n  as estimated % of the organism in that culture.\ntitle: DNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: dna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_project_contact/","title":"Slot: DNA seq project contact (dna_project_contact)","text":"

URI: nmdc:dna_project_contact

"},{"location":"dna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_project_contact/#properties","title":"Properties","text":""},{"location":"dna_project_contact/#examples","title":"Examples","text":"Value John Jones"},{"location":"dna_project_contact/#comments","title":"Comments","text":""},{"location":"dna_project_contact/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_project_contact/#schema-source","title":"Schema Source","text":""},{"location":"dna_project_contact/#linkml-source","title":"LinkML Source","text":"
name: dna_project_contact\ntitle: DNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: dna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_samp_id/","title":"Slot: DNA sample ID (dna_samp_id)","text":"

URI: nmdc:dna_samp_id

"},{"location":"dna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_samp_id/#properties","title":"Properties","text":""},{"location":"dna_samp_id/#examples","title":"Examples","text":"Value 187654"},{"location":"dna_samp_id/#comments","title":"Comments","text":""},{"location":"dna_samp_id/#todos","title":"TODOs","text":""},{"location":"dna_samp_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_samp_id/#schema-source","title":"Schema Source","text":""},{"location":"dna_samp_id/#linkml-source","title":"LinkML Source","text":"
name: dna_samp_id\ntitle: DNA sample ID\ntodos:\n- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n  have two identifiers. How to force uniqueness? Moot because that column will be\n  prefilled?\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: dna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_sample_format/","title":"Slot: DNA sample format (dna_sample_format)","text":"

Solution in which the DNA sample has been suspended

URI: nmdc:dna_sample_format

"},{"location":"dna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_format/#properties","title":"Properties","text":""},{"location":"dna_sample_format/#examples","title":"Examples","text":"Value Water"},{"location":"dna_sample_format/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_sample_format/#schema-source","title":"Schema Source","text":""},{"location":"dna_sample_format/#linkml-source","title":"LinkML Source","text":"
name: dna_sample_format\ndescription: Solution in which the DNA sample has been suspended\ntitle: DNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: dna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: DNASampleFormatEnum\nrecommended: true\n\n
"},{"location":"dna_sample_name/","title":"Slot: DNA sample name (dna_sample_name)","text":"

Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.

URI: nmdc:dna_sample_name

"},{"location":"dna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_name/#properties","title":"Properties","text":""},{"location":"dna_sample_name/#examples","title":"Examples","text":"Value JGI_pond_041618"},{"location":"dna_sample_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_sample_name/#schema-source","title":"Schema Source","text":""},{"location":"dna_sample_name/#linkml-source","title":"LinkML Source","text":"
name: dna_sample_name\ndescription: Give the DNA sample a name that is meaningful to you. Sample names must\n  be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: DNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: dna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_seq_project/","title":"Slot: DNA seq project ID (dna_seq_project)","text":"

URI: nmdc:dna_seq_project

"},{"location":"dna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project/#properties","title":"Properties","text":""},{"location":"dna_seq_project/#aliases","title":"Aliases","text":""},{"location":"dna_seq_project/#examples","title":"Examples","text":"Value 1191234"},{"location":"dna_seq_project/#comments","title":"Comments","text":""},{"location":"dna_seq_project/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_seq_project/#schema-source","title":"Schema Source","text":""},{"location":"dna_seq_project/#linkml-source","title":"LinkML Source","text":"
name: dna_seq_project\ntitle: DNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Seq Project ID\nrank: 1\nstring_serialization: '{text}'\nalias: dna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_seq_project_name/","title":"Slot: DNA seq project name (dna_seq_project_name)","text":"

URI: nmdc:dna_seq_project_name

"},{"location":"dna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_name/#properties","title":"Properties","text":""},{"location":"dna_seq_project_name/#examples","title":"Examples","text":"Value JGI Pond metagenomics"},{"location":"dna_seq_project_name/#comments","title":"Comments","text":""},{"location":"dna_seq_project_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_seq_project_name/#schema-source","title":"Schema Source","text":""},{"location":"dna_seq_project_name/#linkml-source","title":"LinkML Source","text":"
name: dna_seq_project_name\ntitle: DNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: JGI Pond metagenomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: dna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_seq_project_pi/","title":"Slot: DNA seq project PI (dna_seq_project_pi)","text":"

URI: nmdc:dna_seq_project_pi

"},{"location":"dna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_pi/#properties","title":"Properties","text":""},{"location":"dna_seq_project_pi/#examples","title":"Examples","text":"Value Jane Johnson"},{"location":"dna_seq_project_pi/#comments","title":"Comments","text":""},{"location":"dna_seq_project_pi/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_seq_project_pi/#schema-source","title":"Schema Source","text":""},{"location":"dna_seq_project_pi/#linkml-source","title":"LinkML Source","text":"
name: dna_seq_project_pi\ntitle: DNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: dna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"dna_volume/","title":"Slot: DNA volume in ul (dna_volume)","text":"

URI: nmdc:dna_volume

"},{"location":"dna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_volume/#properties","title":"Properties","text":""},{"location":"dna_volume/#examples","title":"Examples","text":"Value 25"},{"location":"dna_volume/#comments","title":"Comments","text":""},{"location":"dna_volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dna_volume/#schema-source","title":"Schema Source","text":""},{"location":"dna_volume/#linkml-source","title":"LinkML Source","text":"
name: dna_volume\ntitle: DNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n  accepts values < 25, but JGI may refuse to process them unless permission has been\n  granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: dna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\n
"},{"location":"dnase_rna/","title":"Slot: DNase treated (dnase_rna)","text":"

URI: nmdc:dnase_rna

"},{"location":"dnase_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dnase_rna/#properties","title":"Properties","text":""},{"location":"dnase_rna/#aliases","title":"Aliases","text":""},{"location":"dnase_rna/#examples","title":"Examples","text":"Value no"},{"location":"dnase_rna/#comments","title":"Comments","text":""},{"location":"dnase_rna/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"dnase_rna/#schema-source","title":"Schema Source","text":""},{"location":"dnase_rna/#linkml-source","title":"LinkML Source","text":"
name: dnase_rna\ntitle: DNase treated\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Was Sample DNAse treated?\nrank: 13\nalias: dnase_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: YesNoEnum\nrecommended: true\n\n
"},{"location":"doi_category/","title":"Slot: doi_category","text":"

The resource type the corresponding doi resolves to.

URI: nmdc:doi_category

"},{"location":"doi_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_category/#properties","title":"Properties","text":""},{"location":"doi_category/#examples","title":"Examples","text":"Value dataset_doi"},{"location":"doi_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"doi_category/#schema-source","title":"Schema Source","text":""},{"location":"doi_category/#linkml-source","title":"LinkML Source","text":"
name: doi_category\ndescription: The resource type the corresponding doi resolves to.\nexamples:\n- value: dataset_doi\n  description: The corresponding DOI is a dataset resource type.\nin_subset:\n- data_portal_subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: doi_category\ndomain_of:\n- Doi\nrange: DoiCategoryEnum\nrequired: true\n\n
"},{"location":"doi_provider/","title":"Slot: doi_provider","text":"

The authority, or organization, the DOI is associated with.

URI: nmdc:doi_provider

"},{"location":"doi_provider/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_provider/#properties","title":"Properties","text":""},{"location":"doi_provider/#examples","title":"Examples","text":"Value ess_dive"},{"location":"doi_provider/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"doi_provider/#schema-source","title":"Schema Source","text":""},{"location":"doi_provider/#linkml-source","title":"LinkML Source","text":"
name: doi_provider\ndescription: The authority, or organization, the DOI is associated with.\nexamples:\n- value: ess_dive\n  description: The corresponding DOI is associated with ESS-DIVE.\nin_subset:\n- data_portal_subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C74932\nrank: 1000\nalias: doi_provider\ndomain_of:\n- Doi\nrange: DoiProviderEnum\n\n
"},{"location":"doi_value/","title":"Slot: doi_value","text":"

A digital object identifier, which is intended to persistantly identify some resource on the web.

URI: nmdc:doi_value

"},{"location":"doi_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_value/#properties","title":"Properties","text":""},{"location":"doi_value/#aliases","title":"Aliases","text":""},{"location":"doi_value/#examples","title":"Examples","text":"Value doi:10.46936/10.25585/60000880"},{"location":"doi_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"doi_value/#schema-source","title":"Schema Source","text":""},{"location":"doi_value/#linkml-source","title":"LinkML Source","text":"
name: doi_value\ndescription: A digital object identifier, which is intended to persistantly identify\n  some resource on the web.\nexamples:\n- value: doi:10.46936/10.25585/60000880\n  description: The DOI links to an electronic document.\nin_subset:\n- data_portal_subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOI\n- digital object identifier\nexact_mappings:\n- OBI:0002110\nnarrow_mappings:\n- edam.data:1188\nrank: 1000\nalias: doi_value\ndomain_of:\n- Doi\nrange: uriorcurie\nrequired: true\npattern: ^doi:10.\\d{2,9}/.*$\n\n
"},{"location":"door_comp_type/","title":"Slot: door type, composite (door_comp_type)","text":"

The composite type of the door

URI: MIXS:0000795

"},{"location":"door_comp_type/#inheritance","title":"Inheritance","text":""},{"location":"door_comp_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_comp_type/#properties","title":"Properties","text":""},{"location":"door_comp_type/#aliases","title":"Aliases","text":""},{"location":"door_comp_type/#examples","title":"Examples","text":"Value revolving"},{"location":"door_comp_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_comp_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_comp_type/#schema-source","title":"Schema Source","text":""},{"location":"door_comp_type/#linkml-source","title":"LinkML Source","text":"
name: door_comp_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The composite type of the door\ntitle: door type, composite\nexamples:\n- value: revolving\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, composite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000795\nalias: door_comp_type\ndomain_of:\n- Biosample\nrange: door_comp_type_enum\nmultivalued: false\n\n
"},{"location":"door_cond/","title":"Slot: door condition (door_cond)","text":"

The phsical condition of the door

URI: MIXS:0000788

"},{"location":"door_cond/#inheritance","title":"Inheritance","text":""},{"location":"door_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_cond/#properties","title":"Properties","text":""},{"location":"door_cond/#aliases","title":"Aliases","text":""},{"location":"door_cond/#examples","title":"Examples","text":"Value new"},{"location":"door_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_cond/#schema-source","title":"Schema Source","text":""},{"location":"door_cond/#linkml-source","title":"LinkML Source","text":"
name: door_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The phsical condition of the door\ntitle: door condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000788\nalias: door_cond\ndomain_of:\n- Biosample\nrange: door_cond_enum\nmultivalued: false\n\n
"},{"location":"door_direct/","title":"Slot: door direction of opening (door_direct)","text":"

The direction the door opens

URI: MIXS:0000789

"},{"location":"door_direct/#inheritance","title":"Inheritance","text":""},{"location":"door_direct/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_direct/#properties","title":"Properties","text":""},{"location":"door_direct/#aliases","title":"Aliases","text":""},{"location":"door_direct/#examples","title":"Examples","text":"Value inward"},{"location":"door_direct/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_direct/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_direct/#schema-source","title":"Schema Source","text":""},{"location":"door_direct/#linkml-source","title":"LinkML Source","text":"
name: door_direct\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The direction the door opens\ntitle: door direction of opening\nexamples:\n- value: inward\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door direction of opening\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000789\nalias: door_direct\ndomain_of:\n- Biosample\nrange: door_direct_enum\nmultivalued: false\n\n
"},{"location":"door_loc/","title":"Slot: door location (door_loc)","text":"

The relative location of the door in the room

URI: MIXS:0000790

"},{"location":"door_loc/#inheritance","title":"Inheritance","text":""},{"location":"door_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_loc/#properties","title":"Properties","text":""},{"location":"door_loc/#aliases","title":"Aliases","text":""},{"location":"door_loc/#examples","title":"Examples","text":"Value north"},{"location":"door_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_loc/#schema-source","title":"Schema Source","text":""},{"location":"door_loc/#linkml-source","title":"LinkML Source","text":"
name: door_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The relative location of the door in the room\ntitle: door location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000790\nalias: door_loc\ndomain_of:\n- Biosample\nrange: door_loc_enum\nmultivalued: false\n\n
"},{"location":"door_mat/","title":"Slot: door material (door_mat)","text":"

The material the door is composed of

URI: MIXS:0000791

"},{"location":"door_mat/#inheritance","title":"Inheritance","text":""},{"location":"door_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_mat/#properties","title":"Properties","text":""},{"location":"door_mat/#aliases","title":"Aliases","text":""},{"location":"door_mat/#examples","title":"Examples","text":"Value wood"},{"location":"door_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_mat/#schema-source","title":"Schema Source","text":""},{"location":"door_mat/#linkml-source","title":"LinkML Source","text":"
name: door_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The material the door is composed of\ntitle: door material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000791\nalias: door_mat\ndomain_of:\n- Biosample\nrange: door_mat_enum\nmultivalued: false\n\n
"},{"location":"door_move/","title":"Slot: door movement (door_move)","text":"

The type of movement of the door

URI: MIXS:0000792

"},{"location":"door_move/#inheritance","title":"Inheritance","text":""},{"location":"door_move/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_move/#properties","title":"Properties","text":""},{"location":"door_move/#aliases","title":"Aliases","text":""},{"location":"door_move/#examples","title":"Examples","text":"Value swinging"},{"location":"door_move/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_move/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_move/#schema-source","title":"Schema Source","text":""},{"location":"door_move/#linkml-source","title":"LinkML Source","text":"
name: door_move\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of movement of the door\ntitle: door movement\nexamples:\n- value: swinging\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door movement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000792\nalias: door_move\ndomain_of:\n- Biosample\nrange: door_move_enum\nmultivalued: false\n\n
"},{"location":"door_size/","title":"Slot: door area or size (door_size)","text":"

The size of the door

URI: MIXS:0000158

"},{"location":"door_size/#inheritance","title":"Inheritance","text":""},{"location":"door_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_size/#properties","title":"Properties","text":""},{"location":"door_size/#aliases","title":"Aliases","text":""},{"location":"door_size/#examples","title":"Examples","text":"Value 2.5 square meter"},{"location":"door_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_size/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"door_size/#schema-source","title":"Schema Source","text":""},{"location":"door_size/#linkml-source","title":"LinkML Source","text":"
name: door_size\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The size of the door\ntitle: door area or size\nexamples:\n- value: 2.5 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door area or size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000158\nalias: door_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"door_type/","title":"Slot: door type (door_type)","text":"

The type of door material

URI: MIXS:0000794

"},{"location":"door_type/#inheritance","title":"Inheritance","text":""},{"location":"door_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_type/#properties","title":"Properties","text":""},{"location":"door_type/#aliases","title":"Aliases","text":""},{"location":"door_type/#examples","title":"Examples","text":"Value wooden"},{"location":"door_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_type/#schema-source","title":"Schema Source","text":""},{"location":"door_type/#linkml-source","title":"LinkML Source","text":"
name: door_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of door material\ntitle: door type\nexamples:\n- value: wooden\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000794\nalias: door_type\ndomain_of:\n- Biosample\nrange: door_type_enum\nmultivalued: false\n\n
"},{"location":"door_type_metal/","title":"Slot: door type, metal (door_type_metal)","text":"

The type of metal door

URI: MIXS:0000796

"},{"location":"door_type_metal/#inheritance","title":"Inheritance","text":""},{"location":"door_type_metal/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_type_metal/#properties","title":"Properties","text":""},{"location":"door_type_metal/#aliases","title":"Aliases","text":""},{"location":"door_type_metal/#examples","title":"Examples","text":"Value hollow"},{"location":"door_type_metal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_type_metal/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_type_metal/#schema-source","title":"Schema Source","text":""},{"location":"door_type_metal/#linkml-source","title":"LinkML Source","text":"
name: door_type_metal\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of metal door\ntitle: door type, metal\nexamples:\n- value: hollow\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, metal\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000796\nalias: door_type_metal\ndomain_of:\n- Biosample\nrange: door_type_metal_enum\nmultivalued: false\n\n
"},{"location":"door_type_wood/","title":"Slot: door type, wood (door_type_wood)","text":"

The type of wood door

URI: MIXS:0000797

"},{"location":"door_type_wood/#inheritance","title":"Inheritance","text":""},{"location":"door_type_wood/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_type_wood/#properties","title":"Properties","text":""},{"location":"door_type_wood/#aliases","title":"Aliases","text":""},{"location":"door_type_wood/#examples","title":"Examples","text":"Value battened"},{"location":"door_type_wood/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_type_wood/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_type_wood/#schema-source","title":"Schema Source","text":""},{"location":"door_type_wood/#linkml-source","title":"LinkML Source","text":"
name: door_type_wood\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of wood door\ntitle: door type, wood\nexamples:\n- value: battened\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, wood\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000797\nalias: door_type_wood\ndomain_of:\n- Biosample\nrange: door_type_wood_enum\nmultivalued: false\n\n
"},{"location":"door_water_mold/","title":"Slot: door signs of water/mold (door_water_mold)","text":"

Signs of the presence of mold or mildew on a door

URI: MIXS:0000793

"},{"location":"door_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"door_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"door_water_mold/#properties","title":"Properties","text":""},{"location":"door_water_mold/#aliases","title":"Aliases","text":""},{"location":"door_water_mold/#examples","title":"Examples","text":"Value presence of mold visible"},{"location":"door_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"door_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"door_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"door_water_mold/#linkml-source","title":"LinkML Source","text":"
name: door_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on a door\ntitle: door signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000793\nalias: door_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"down_par/","title":"Slot: downward PAR (down_par)","text":"

Visible waveband radiance and irradiance measurements in the water column

URI: MIXS:0000703

"},{"location":"down_par/#inheritance","title":"Inheritance","text":""},{"location":"down_par/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"down_par/#properties","title":"Properties","text":""},{"location":"down_par/#aliases","title":"Aliases","text":""},{"location":"down_par/#examples","title":"Examples","text":"Value 28.71 microEinstein per square meter per second"},{"location":"down_par/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"down_par/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"down_par/#schema-source","title":"Schema Source","text":""},{"location":"down_par/#linkml-source","title":"LinkML Source","text":"
name: down_par\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microEinstein per square meter per second, microEinstein per square centimeter\n      per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Visible waveband radiance and irradiance measurements in the water column\ntitle: downward PAR\nexamples:\n- value: 28.71 microEinstein per square meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- downward PAR\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000703\nalias: down_par\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"drainage_class/","title":"Slot: drainage classification (drainage_class)","text":"

Drainage classification from a standard system such as the USDA system

URI: MIXS:0001085

"},{"location":"drainage_class/#inheritance","title":"Inheritance","text":""},{"location":"drainage_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"drainage_class/#properties","title":"Properties","text":""},{"location":"drainage_class/#aliases","title":"Aliases","text":""},{"location":"drainage_class/#examples","title":"Examples","text":"Value well"},{"location":"drainage_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drainage_class/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"drainage_class/#schema-source","title":"Schema Source","text":""},{"location":"drainage_class/#linkml-source","title":"LinkML Source","text":"
name: drainage_class\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Drainage classification from a standard system such as the USDA system\ntitle: drainage classification\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drainage classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001085\nalias: drainage_class\ndomain_of:\n- Biosample\nrange: drainage_class_enum\nmultivalued: false\n\n
"},{"location":"drawings/","title":"Slot: drawings (drawings)","text":"

The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents

URI: MIXS:0000798

"},{"location":"drawings/#inheritance","title":"Inheritance","text":""},{"location":"drawings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"drawings/#properties","title":"Properties","text":""},{"location":"drawings/#aliases","title":"Aliases","text":""},{"location":"drawings/#examples","title":"Examples","text":"Value sketch"},{"location":"drawings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"drawings/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"drawings/#schema-source","title":"Schema Source","text":""},{"location":"drawings/#linkml-source","title":"LinkML Source","text":"
name: drawings\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The buildings architectural drawings; if design is chosen, indicate phase-conceptual,\n  schematic, design development, and construction documents\ntitle: drawings\nexamples:\n- value: sketch\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drawings\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000798\nalias: drawings\ndomain_of:\n- Biosample\nrange: drawings_enum\nmultivalued: false\n\n
"},{"location":"duration/","title":"Slot: duration","text":"

The elapsed time of an activity.

URI: nmdc:duration

"},{"location":"duration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no"},{"location":"duration/#properties","title":"Properties","text":""},{"location":"duration/#examples","title":"Examples","text":"Value JsonObj(has_numeric_value=2, has_unit='hours')"},{"location":"duration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"duration/#schema-source","title":"Schema Source","text":""},{"location":"duration/#linkml-source","title":"LinkML Source","text":"
name: duration\ndescription: The elapsed time of an activity.\nexamples:\n- value: JsonObj(has_numeric_value=2, has_unit='hours')\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: duration\ndomain_of:\n- MixingProcess\n- DissolvingProcess\n- ChemicalConversionProcess\n- MobilePhaseSegment\nrange: QuantityValue\n\n
"},{"location":"ecosystem/","title":"Slot: ecosystem","text":"

An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.

URI: nmdc:ecosystem

"},{"location":"ecosystem/#inheritance","title":"Inheritance","text":""},{"location":"ecosystem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ecosystem/#properties","title":"Properties","text":""},{"location":"ecosystem/#comments","title":"Comments","text":""},{"location":"ecosystem/#see-also","title":"See Also","text":""},{"location":"ecosystem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem/#linkml-source","title":"LinkML Source","text":"
name: ecosystem\ndescription: An ecosystem is a combination of a physical environment (abiotic factors)\n  and all the organisms (biotic factors) that interact with this environment. Ecosystem\n  is in position 1/5 in a GOLD path.\ncomments:\n- The abiotic factors play a profound role on the type and composition of organisms\n  in a given environment. The GOLD Ecosystem at the top of the five-level classification\n  system is aimed at capturing the broader environment from which an organism or environmental\n  sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated,\n  and Engineered. They represent samples collected from a natural environment or from\n  another organism or from engineered environments like bioreactors respectively.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"ecosystem_category/","title":"Slot: ecosystem_category","text":"

Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.

URI: nmdc:ecosystem_category

"},{"location":"ecosystem_category/#inheritance","title":"Inheritance","text":""},{"location":"ecosystem_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ecosystem_category/#properties","title":"Properties","text":""},{"location":"ecosystem_category/#comments","title":"Comments","text":""},{"location":"ecosystem_category/#see-also","title":"See Also","text":""},{"location":"ecosystem_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem_category/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem_category/#linkml-source","title":"LinkML Source","text":"
name: ecosystem_category\ndescription: Ecosystem categories represent divisions within the ecosystem based on\n  specific characteristics of the environment from where an organism or sample is\n  isolated. Ecosystem category is in position 2/5 in a GOLD path.\ncomments:\n- The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n  Ecosystem categories for Host-associated samples can be individual hosts or phyla\n  and for engineered samples it may be manipulated environments like bioreactors,\n  solid waste etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_category\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"ecosystem_path_id/","title":"Slot: ecosystem_path_id","text":"

A unique id representing the GOLD classifiers associated with a sample.

URI: nmdc:ecosystem_path_id

"},{"location":"ecosystem_path_id/#properties","title":"Properties","text":""},{"location":"ecosystem_path_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem_path_id/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem_path_id/#linkml-source","title":"LinkML Source","text":"
name: ecosystem_path_id\ndescription: A unique id representing the GOLD classifiers associated with a sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ecosystem_path_id\nrange: string\n\n
"},{"location":"ecosystem_subtype/","title":"Slot: ecosystem_subtype","text":"

Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.

URI: nmdc:ecosystem_subtype

"},{"location":"ecosystem_subtype/#inheritance","title":"Inheritance","text":""},{"location":"ecosystem_subtype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ecosystem_subtype/#properties","title":"Properties","text":""},{"location":"ecosystem_subtype/#comments","title":"Comments","text":""},{"location":"ecosystem_subtype/#see-also","title":"See Also","text":""},{"location":"ecosystem_subtype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem_subtype/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem_subtype/#linkml-source","title":"LinkML Source","text":"
name: ecosystem_subtype\ndescription: Ecosystem subtypes represent further subdivision of Ecosystem types into\n  more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.\ncomments:\n- Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for\n  example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem\n  subtype category.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_subtype\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"ecosystem_type/","title":"Slot: ecosystem_type","text":"

Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.

URI: nmdc:ecosystem_type

"},{"location":"ecosystem_type/#inheritance","title":"Inheritance","text":""},{"location":"ecosystem_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ecosystem_type/#properties","title":"Properties","text":""},{"location":"ecosystem_type/#comments","title":"Comments","text":""},{"location":"ecosystem_type/#see-also","title":"See Also","text":""},{"location":"ecosystem_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ecosystem_type/#schema-source","title":"Schema Source","text":""},{"location":"ecosystem_type/#linkml-source","title":"LinkML Source","text":"
name: ecosystem_type\ndescription: Ecosystem types represent things having common characteristics within\n  the Ecosystem Category. These common characteristics based grouping is still broad\n  but specific to the characteristics of a given environment. Ecosystem type is in\n  position 3/5 in a GOLD path.\ncomments:\n- The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n  or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air\n  as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n  type can represent Respiratory system, Digestive system, Roots etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_type\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"efficiency_percent/","title":"Slot: efficiency percent (efficiency_percent)","text":"

Percentage of volatile solids removed from the anaerobic digestor

URI: MIXS:0000657

"},{"location":"efficiency_percent/#inheritance","title":"Inheritance","text":""},{"location":"efficiency_percent/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"efficiency_percent/#properties","title":"Properties","text":""},{"location":"efficiency_percent/#aliases","title":"Aliases","text":""},{"location":"efficiency_percent/#examples","title":"Examples","text":"Value"},{"location":"efficiency_percent/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"efficiency_percent/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"efficiency_percent/#schema-source","title":"Schema Source","text":""},{"location":"efficiency_percent/#linkml-source","title":"LinkML Source","text":"
name: efficiency_percent\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Percentage of volatile solids removed from the anaerobic digestor\ntitle: efficiency percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- efficiency percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000657\nalias: efficiency_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"elev/","title":"Slot: elevation (elev)","text":"

Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.

URI: MIXS:0000093

"},{"location":"elev/#inheritance","title":"Inheritance","text":""},{"location":"elev/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no"},{"location":"elev/#properties","title":"Properties","text":""},{"location":"elev/#aliases","title":"Aliases","text":""},{"location":"elev/#examples","title":"Examples","text":"Value 100 meter"},{"location":"elev/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"elev/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"elev/#schema-source","title":"Schema Source","text":""},{"location":"elev/#linkml-source","title":"LinkML Source","text":"
name: elev\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\ndescription: Elevation of the sampling site is its height above a fixed reference\n  point, most commonly the mean sea level. Elevation is mainly used when referring\n  to points on the earth's surface, while altitude is used for points above the surface,\n  such as an aircraft in flight or a spacecraft in orbit.\ntitle: elevation\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevation\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000093\nalias: elev\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: float\nmultivalued: false\n\n
"},{"location":"elevator/","title":"Slot: elevator count (elevator)","text":"

The number of elevators within the built structure

URI: MIXS:0000799

"},{"location":"elevator/#inheritance","title":"Inheritance","text":""},{"location":"elevator/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"elevator/#properties","title":"Properties","text":""},{"location":"elevator/#aliases","title":"Aliases","text":""},{"location":"elevator/#examples","title":"Examples","text":"Value 2"},{"location":"elevator/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"elevator/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"elevator/#schema-source","title":"Schema Source","text":""},{"location":"elevator/#linkml-source","title":"LinkML Source","text":"
name: elevator\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of elevators within the built structure\ntitle: elevator count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000799\nalias: elevator\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"eluent_introduction_category/","title":"Slot: eluent_introduction_category","text":"

A high-level categorization for how the processed sample is introduced into a mass spectrometer.

URI: nmdc:eluent_introduction_category

"},{"location":"eluent_introduction_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"eluent_introduction_category/#properties","title":"Properties","text":""},{"location":"eluent_introduction_category/#examples","title":"Examples","text":"Value liquid_chromatography direct_infusion_syringe"},{"location":"eluent_introduction_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"eluent_introduction_category/#schema-source","title":"Schema Source","text":""},{"location":"eluent_introduction_category/#linkml-source","title":"LinkML Source","text":"
name: eluent_introduction_category\ndescription: A high-level categorization for how the processed sample is introduced\n  into a mass spectrometer.\nexamples:\n- value: liquid_chromatography\n- value: direct_infusion_syringe\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: eluent_introduction_category\ndomain_of:\n- MassSpectrometry\nrange: EluentIntroductionCategoryEnum\n\n
"},{"location":"email/","title":"Slot: email","text":"

An email address for an entity such as a person. This should be the primary email address used.

URI: schema:email

"},{"location":"email/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"email/#properties","title":"Properties","text":""},{"location":"email/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"email/#schema-source","title":"Schema Source","text":""},{"location":"email/#linkml-source","title":"LinkML Source","text":"
name: email\ndescription: An email address for an entity such as a person. This should be the primary\n  email address used.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: schema:email\nalias: email\ndomain_of:\n- PersonValue\nrange: string\n\n
"},{"location":"embargoed/","title":"Slot: embargoed","text":"

If true, the data are embargoed and not available for public access.

URI: nmdc:embargoed

"},{"location":"embargoed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"embargoed/#properties","title":"Properties","text":""},{"location":"embargoed/#todos","title":"TODOs","text":""},{"location":"embargoed/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"embargoed/#schema-source","title":"Schema Source","text":""},{"location":"embargoed/#linkml-source","title":"LinkML Source","text":"
name: embargoed\ndescription: If true, the data are embargoed and not available for public access.\ntodos:\n- make this required?\n- first apply to Biosample\n- try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n- applying to a Study may not be granular enough\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: embargoed\ndomain_of:\n- Biosample\nrange: boolean\nrecommended: true\n\n
"},{"location":"emsl_biosample_identifiers/","title":"Slot: EMSL Biosample Identifiers (emsl_biosample_identifiers)","text":"

A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.

URI: nmdc:emsl_biosample_identifiers

"},{"location":"emsl_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"emsl_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"emsl_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"emsl_biosample_identifiers/#todos","title":"TODOs","text":""},{"location":"emsl_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emsl_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"emsl_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: emsl_biosample_identifiers\ndescription: A list of identifiers for the biosample from the EMSL database.  This\n  is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n  EMSL NEXUS database.\ntitle: EMSL Biosample Identifiers\ntodos:\n- removed \"planned\" once NEXUS is online\n- determine real expansion for emsl prefix\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- emsl_identifiers\nalias: emsl_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"emsl_identifiers/","title":"Slot: emsl_identifiers","text":"

URI: nmdc:emsl_identifiers

"},{"location":"emsl_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain emsl_project_identifiers Identifiers that link a NMDC study to the EMSL user facility website hosting ... None Study emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database None Biosample"},{"location":"emsl_identifiers/#properties","title":"Properties","text":""},{"location":"emsl_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emsl_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"emsl_identifiers/#linkml-source","title":"LinkML Source","text":"
name: emsl_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: emsl_identifiers\nrange: string\n\n
"},{"location":"emsl_project_identifiers/","title":"Slot: EMSL Project Identifiers (emsl_project_identifiers)","text":"

Identifiers that link a NMDC study to the EMSL user facility website hosting the project description of an EMSL user project

URI: nmdc:emsl_project_identifiers

"},{"location":"emsl_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"emsl_project_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"emsl_project_identifiers/#properties","title":"Properties","text":""},{"location":"emsl_project_identifiers/#examples","title":"Examples","text":"Value emsl.project:60141"},{"location":"emsl_project_identifiers/#todos","title":"TODOs","text":""},{"location":"emsl_project_identifiers/#see-also","title":"See Also","text":""},{"location":"emsl_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emsl_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"emsl_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: emsl_project_identifiers\ndescription: Identifiers that link a NMDC study to the EMSL user facility website\n  hosting the project description of an EMSL user project\ntitle: EMSL Project Identifiers\ntodos:\n- elaborate on description\nnotes:\n- these identifiers are all currently 5 digits long but that could change in the future\nexamples:\n- value: emsl.project:60141\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-schema/issues/927#issuecomment-1802136437\nrank: 1000\nis_a: study_identifiers\nmixins:\n- emsl_identifiers\nalias: emsl_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^emsl\\.project:[0-9]{5}$\n\n
"},{"location":"emsl_store_temp/","title":"Slot: EMSL sample storage temperature, deg. C (emsl_store_temp)","text":"

The temperature at which the sample should be stored upon delivery to EMSL

URI: nmdc:emsl_store_temp

"},{"location":"emsl_store_temp/#properties","title":"Properties","text":""},{"location":"emsl_store_temp/#examples","title":"Examples","text":"Value -80"},{"location":"emsl_store_temp/#comments","title":"Comments","text":""},{"location":"emsl_store_temp/#todos","title":"TODOs","text":""},{"location":"emsl_store_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emsl_store_temp/#schema-source","title":"Schema Source","text":""},{"location":"emsl_store_temp/#linkml-source","title":"LinkML Source","text":"
name: emsl_store_temp\ndescription: The temperature at which the sample should be stored upon delivery to\n  EMSL\ntitle: EMSL sample storage temperature, deg. C\ntodos:\n- add 'see_alsos' with link to NEXUS info\ncomments:\n- Enter a temperature in celsius. Numeric portion only.\nexamples:\n- value: '-80'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{float}'\nalias: emsl_store_temp\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"emulsions/","title":"Slot: emulsions (emulsions)","text":"

Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types

URI: MIXS:0000660

"},{"location":"emulsions/#inheritance","title":"Inheritance","text":""},{"location":"emulsions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"emulsions/#properties","title":"Properties","text":""},{"location":"emulsions/#aliases","title":"Aliases","text":""},{"location":"emulsions/#examples","title":"Examples","text":"Value"},{"location":"emulsions/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"emulsions/#annotations","title":"Annotations","text":"property value expected_value emulsion name;measurement value"},{"location":"emulsions/#schema-source","title":"Schema Source","text":""},{"location":"emulsions/#linkml-source","title":"LinkML Source","text":"
name: emulsions\nannotations:\n  expected_value:\n    tag: expected_value\n    value: emulsion name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Amount or concentration of substances such as paints, adhesives, mayonnaise,\n  hair colorants, emulsified oils, etc.; can include multiple emulsion types\ntitle: emulsions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- emulsions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000660\nalias: emulsions\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"encodes/","title":"Slot: encodes","text":"

The gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA

URI: nmdc:encodes

"},{"location":"encodes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"encodes/#properties","title":"Properties","text":""},{"location":"encodes/#todos","title":"TODOs","text":""},{"location":"encodes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"encodes/#schema-source","title":"Schema Source","text":""},{"location":"encodes/#linkml-source","title":"LinkML Source","text":"
name: encodes\ndescription: The gene product encoded by this feature. Typically this is used for\n  a CDS feature or gene feature which will encode a protein. It can also be used by\n  a nc transcript ot gene feature that encoded a ncRNA\ntodos:\n- If we revert Reaction back into the schema, that would be a reasonable domain for\n  this slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: encodes\ndomain_of:\n- GenomeFeature\nrange: GeneProduct\n\n
"},{"location":"end/","title":"Slot: end","text":"

The end of the feature in positive 1-based integer coordinates

URI: nmdc:end

"},{"location":"end/#inheritance","title":"Inheritance","text":""},{"location":"end/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"end/#properties","title":"Properties","text":""},{"location":"end/#comments","title":"Comments","text":""},{"location":"end/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"end/#schema-source","title":"Schema Source","text":""},{"location":"end/#linkml-source","title":"LinkML Source","text":"
name: end\ndescription: The end of the feature in positive 1-based integer coordinates\ncomments:\n- '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n  feature,  end = the position of the end + the length of the landmark feature.\"'\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:end_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: end\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\n
"},{"location":"end_date/","title":"Slot: end_date","text":"

The date on which any process or activity was ended

URI: nmdc:end_date

"},{"location":"end_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeAssembly no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no PlannedProcess no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ProtocolExecution A PlannedProces that has PlannedProcess parts no LibraryPreparation no"},{"location":"end_date/#properties","title":"Properties","text":""},{"location":"end_date/#comments","title":"Comments","text":""},{"location":"end_date/#todos","title":"TODOs","text":""},{"location":"end_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"end_date/#schema-source","title":"Schema Source","text":""},{"location":"end_date/#linkml-source","title":"LinkML Source","text":"
name: end_date\ndescription: The date on which any process or activity was ended\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n  can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: end_date\ndomain_of:\n- PlannedProcess\nrange: string\n\n
"},{"location":"ended_at_time/","title":"Slot: ended_at_time","text":"

URI: nmdc:ended_at_time

"},{"location":"ended_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetatranscriptomeAssembly no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetabolomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetaproteomicsAnalysis no"},{"location":"ended_at_time/#properties","title":"Properties","text":""},{"location":"ended_at_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ended_at_time/#schema-source","title":"Schema Source","text":""},{"location":"ended_at_time/#linkml-source","title":"LinkML Source","text":"
name: ended_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n  It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:endedAtTime\nrank: 1000\nalias: ended_at_time\ndomain_of:\n- WorkflowExecution\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\n
"},{"location":"env_broad_scale/","title":"Slot: broad-scale environmental context (env_broad_scale)","text":"

Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS

URI: MIXS:0000012

"},{"location":"env_broad_scale/#inheritance","title":"Inheritance","text":""},{"location":"env_broad_scale/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"env_broad_scale/#properties","title":"Properties","text":""},{"location":"env_broad_scale/#aliases","title":"Aliases","text":""},{"location":"env_broad_scale/#examples","title":"Examples","text":"Value oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean"},{"location":"env_broad_scale/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"env_broad_scale/#annotations","title":"Annotations","text":"property value expected_value The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes."},{"location":"env_broad_scale/#schema-source","title":"Schema Source","text":""},{"location":"env_broad_scale/#linkml-source","title":"LinkML Source","text":"
name: env_broad_scale\nannotations:\n  expected_value:\n    tag: expected_value\n    value: The major environment type(s) where the sample was collected. Recommend\n      subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one\n      or more pipes.\n  tooltip:\n    tag: tooltip\n    value: The biome or major environmental system where the sample or specimen originated.\n      Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment\n      Ontology (ENVO). For host-associated or plant-associated samples, use terms\n      from the UBERON or Plant Ontology to describe the broad anatomical or morphological\n      context\ndescription: 'Report the major environmental system the sample or specimen came from.\n  The system(s) identified should have a coarse spatial grain, to provide the general\n  environmental context of where the sampling was done (e.g. in the desert or a rainforest).\n  We recommend using subclasses of EnvO\u2019s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.\n  EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\ntitle: broad-scale environmental context\nexamples:\n- value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample\n    from the photic zone in middle of the Atlantic Ocean\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- broad-scale environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000012\nalias: env_broad_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"env_local_scale/","title":"Slot: local environmental context (env_local_scale)","text":"

Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.

URI: MIXS:0000013

"},{"location":"env_local_scale/#inheritance","title":"Inheritance","text":""},{"location":"env_local_scale/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"env_local_scale/#properties","title":"Properties","text":""},{"location":"env_local_scale/#aliases","title":"Aliases","text":""},{"location":"env_local_scale/#examples","title":"Examples","text":"Value litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]"},{"location":"env_local_scale/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"env_local_scale/#annotations","title":"Annotations","text":"property value expected_value Environmental entities having causal influences upon the entity at time of sampling."},{"location":"env_local_scale/#schema-source","title":"Schema Source","text":""},{"location":"env_local_scale/#linkml-source","title":"LinkML Source","text":"
name: env_local_scale\nannotations:\n  expected_value:\n    tag: expected_value\n    value: Environmental entities having causal influences upon the entity at time\n      of sampling.\n  tooltip:\n    tag: tooltip\n    value: The specific environmental entities or features near the sample or specimen\n      that significantly influence its characteristics or composition. These entities\n      are typically smaller in scale than the broad environmental context. Values\n      for this field should be countable, material nouns and must be chosen from subclasses\n      of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO).\n      For host-associated or plant-associated samples, use terms from the UBERON or\n      Plant Ontology to describe specific anatomical structures or plant parts.\ndescription: 'Report the entity or entities which are in the sample or specimen\u2019s\n  local vicinity and which you believe have significant causal influences on your\n  sample or specimen. We recommend using EnvO terms which are of smaller spatial grain\n  than your entry for env_broad_scale. Terms, such as anatomical sites, from other\n  OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in\n  this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\ntitle: local environmental context\nexamples:\n- value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from various\n    vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer\n    [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer\n    [ENVO:01000336].'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- local environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000013\nalias: env_local_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"env_medium/","title":"Slot: environmental medium (env_medium)","text":"

Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).

URI: MIXS:0000014

"},{"location":"env_medium/#inheritance","title":"Inheritance","text":""},{"location":"env_medium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"env_medium/#properties","title":"Properties","text":""},{"location":"env_medium/#aliases","title":"Aliases","text":""},{"location":"env_medium/#examples","title":"Examples","text":"Value soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]"},{"location":"env_medium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"env_medium/#annotations","title":"Annotations","text":"property value expected_value The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]."},{"location":"env_medium/#schema-source","title":"Schema Source","text":""},{"location":"env_medium/#linkml-source","title":"LinkML Source","text":"
name: env_medium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: The material displaced by the entity at time of sampling. Recommend subclasses\n      of environmental material [ENVO:00010483].\n  tooltip:\n    tag: tooltip\n    value: The predominant environmental material or substrate that directly surrounds\n      or hosts the sample or specimen at the time of sampling. Choose values from\n      subclasses of the 'environmental material' class [ENVO:00010483] in the Environment\n      Ontology (ENVO). Values for this field should be measurable or mass material\n      nouns, representing continuous environmental materials. For host-associated\n      or plant-associated samples, use terms from the UBERON or Plant Ontology to\n      indicate a tissue, organ, or plant structure\ndescription: 'Report the environmental material(s) immediately surrounding the sample\n  or specimen at the time of sampling. We recommend using subclasses of ''environmental\n  material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about\n  how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n  . Terms from other OBO ontologies are permissible as long as they reference mass/volume\n  nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree,\n  a leaf, a table top).'\ntitle: environmental medium\nexamples:\n- value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the\n    Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck\n    on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental medium\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000014\nalias: env_medium\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"env_package/","title":"Slot: env_package","text":"

MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported

URI: nmdc:env_package

"},{"location":"env_package/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"env_package/#properties","title":"Properties","text":""},{"location":"env_package/#aliases","title":"Aliases","text":""},{"location":"env_package/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"env_package/#schema-source","title":"Schema Source","text":""},{"location":"env_package/#linkml-source","title":"LinkML Source","text":"
name: env_package\ndescription: MIxS extension for reporting of measurements and observations obtained\n  from one or more of the environments where the sample was obtained. All environmental\n  packages listed here are further defined in separate subtables. By giving the name\n  of the environmental package, a selection of fields can be made from the subtables\n  and can be reported\nnotes:\n- no longer in MIxS as of 6.0?\nin_subset:\n- mixs extension\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental package\nrank: 1000\nalias: env_package\ndomain_of:\n- Biosample\nrange: TextValue\n\n
"},{"location":"environment_field/","title":"Slot: environment_field","text":"

field describing environmental aspect of a sample

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:environment_field

"},{"location":"environment_field/#inheritance","title":"Inheritance","text":""},{"location":"environment_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"environment_field/#properties","title":"Properties","text":""},{"location":"environment_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"environment_field/#schema-source","title":"Schema Source","text":""},{"location":"environment_field/#linkml-source","title":"LinkML Source","text":"
name: environment field\ndescription: field describing environmental aspect of a sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: environment_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"escalator/","title":"Slot: escalator count (escalator)","text":"

The number of escalators within the built structure

URI: MIXS:0000800

"},{"location":"escalator/#inheritance","title":"Inheritance","text":""},{"location":"escalator/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"escalator/#properties","title":"Properties","text":""},{"location":"escalator/#aliases","title":"Aliases","text":""},{"location":"escalator/#examples","title":"Examples","text":"Value 4"},{"location":"escalator/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"escalator/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"escalator/#schema-source","title":"Schema Source","text":""},{"location":"escalator/#linkml-source","title":"LinkML Source","text":"
name: escalator\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of escalators within the built structure\ntitle: escalator count\nexamples:\n- value: '4'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- escalator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000800\nalias: escalator\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ethylbenzene/","title":"Slot: ethylbenzene (ethylbenzene)","text":"

Concentration of ethylbenzene in the sample

URI: MIXS:0000155

"},{"location":"ethylbenzene/#inheritance","title":"Inheritance","text":""},{"location":"ethylbenzene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ethylbenzene/#properties","title":"Properties","text":""},{"location":"ethylbenzene/#aliases","title":"Aliases","text":""},{"location":"ethylbenzene/#examples","title":"Examples","text":"Value"},{"location":"ethylbenzene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ethylbenzene/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ethylbenzene/#schema-source","title":"Schema Source","text":""},{"location":"ethylbenzene/#linkml-source","title":"LinkML Source","text":"
name: ethylbenzene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of ethylbenzene in the sample\ntitle: ethylbenzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ethylbenzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000155\nalias: ethylbenzene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"etl_software_version/","title":"Slot: etl_software_version","text":"

from database class

URI: nmdc:etl_software_version

"},{"location":"etl_software_version/#properties","title":"Properties","text":""},{"location":"etl_software_version/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"etl_software_version/#schema-source","title":"Schema Source","text":""},{"location":"etl_software_version/#linkml-source","title":"LinkML Source","text":"
name: etl_software_version\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: etl_software_version\nrange: string\n\n
"},{"location":"eukaryotic_evaluation/","title":"Slot: eukaryotic_evaluation","text":"

Contains results from evaluating if a Metagenome-Assembled Genome is of eukaryotic lineage.

URI: nmdc:eukaryotic_evaluation

"},{"location":"eukaryotic_evaluation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"eukaryotic_evaluation/#properties","title":"Properties","text":""},{"location":"eukaryotic_evaluation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"eukaryotic_evaluation/#schema-source","title":"Schema Source","text":""},{"location":"eukaryotic_evaluation/#linkml-source","title":"LinkML Source","text":"
name: eukaryotic_evaluation\ndescription: Contains results from evaluating if a Metagenome-Assembled Genome is\n  of eukaryotic lineage.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: eukaryotic_evaluation\ndomain_of:\n- MagBin\nrange: EukEval\n\n
"},{"location":"execution_resource/","title":"Slot: execution_resource","text":"

The computing resource or facility where the workflow was executed.

URI: nmdc:execution_resource

"},{"location":"execution_resource/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetatranscriptomeAssembly no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetabolomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetaproteomicsAnalysis no"},{"location":"execution_resource/#properties","title":"Properties","text":""},{"location":"execution_resource/#examples","title":"Examples","text":"Value NERSC-Cori"},{"location":"execution_resource/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"execution_resource/#schema-source","title":"Schema Source","text":""},{"location":"execution_resource/#linkml-source","title":"LinkML Source","text":"
name: execution_resource\ndescription: The computing resource or facility where the workflow was executed.\nexamples:\n- value: NERSC-Cori\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: execution_resource\ndomain_of:\n- WorkflowExecution\nrange: ExecutionResourceEnum\n\n
"},{"location":"exp_duct/","title":"Slot: exposed ductwork (exp_duct)","text":"

The amount of exposed ductwork in the room

URI: MIXS:0000144

"},{"location":"exp_duct/#inheritance","title":"Inheritance","text":""},{"location":"exp_duct/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"exp_duct/#properties","title":"Properties","text":""},{"location":"exp_duct/#aliases","title":"Aliases","text":""},{"location":"exp_duct/#examples","title":"Examples","text":"Value"},{"location":"exp_duct/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"exp_duct/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"exp_duct/#schema-source","title":"Schema Source","text":""},{"location":"exp_duct/#linkml-source","title":"LinkML Source","text":"
name: exp_duct\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The amount of exposed ductwork in the room\ntitle: exposed ductwork\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed ductwork\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000144\nalias: exp_duct\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"exp_pipe/","title":"Slot: exposed pipes (exp_pipe)","text":"

The number of exposed pipes in the room

URI: MIXS:0000220

"},{"location":"exp_pipe/#inheritance","title":"Inheritance","text":""},{"location":"exp_pipe/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"exp_pipe/#properties","title":"Properties","text":""},{"location":"exp_pipe/#aliases","title":"Aliases","text":""},{"location":"exp_pipe/#examples","title":"Examples","text":"Value"},{"location":"exp_pipe/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"exp_pipe/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"exp_pipe/#schema-source","title":"Schema Source","text":""},{"location":"exp_pipe/#linkml-source","title":"LinkML Source","text":"
name: exp_pipe\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of exposed pipes in the room\ntitle: exposed pipes\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed pipes\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000220\nalias: exp_pipe\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"experimental_factor/","title":"Slot: experimental factor (experimental_factor)","text":"

Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI

URI: MIXS:0000008

"},{"location":"experimental_factor/#inheritance","title":"Inheritance","text":""},{"location":"experimental_factor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"experimental_factor/#properties","title":"Properties","text":""},{"location":"experimental_factor/#aliases","title":"Aliases","text":""},{"location":"experimental_factor/#examples","title":"Examples","text":"Value time series design [EFO:EFO_0001779]"},{"location":"experimental_factor/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"experimental_factor/#annotations","title":"Annotations","text":"property value expected_value text or EFO and/or OBI"},{"location":"experimental_factor/#schema-source","title":"Schema Source","text":""},{"location":"experimental_factor/#linkml-source","title":"LinkML Source","text":"
name: experimental_factor\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text or EFO and/or OBI\ndescription: Experimental factors are essentially the variable aspects of an experiment\n  design which can be used to describe an experiment, or set of experiments, in an\n  increasingly detailed manner. This field accepts ontology terms from Experimental\n  Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a\n  browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n  for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\ntitle: experimental factor\nexamples:\n- value: time series design [EFO:EFO_0001779]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- experimental factor\nrank: 1000\nis_a: investigation field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000008\nalias: experimental_factor\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"experimental_factor_other/","title":"Slot: experimental factor- other (experimental_factor_other)","text":"

Other details about your sample that you feel can't be accurately represented in the available columns.

URI: nmdc:experimental_factor_other

"},{"location":"experimental_factor_other/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"experimental_factor_other/#properties","title":"Properties","text":""},{"location":"experimental_factor_other/#examples","title":"Examples","text":"Value experimental treatment: value"},{"location":"experimental_factor_other/#comments","title":"Comments","text":""},{"location":"experimental_factor_other/#see-also","title":"See Also","text":""},{"location":"experimental_factor_other/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"experimental_factor_other/#schema-source","title":"Schema Source","text":""},{"location":"experimental_factor_other/#linkml-source","title":"LinkML Source","text":"
name: experimental_factor_other\ndescription: Other details about your sample that you feel can't be accurately represented\n  in the available columns.\ntitle: experimental factor- other\ncomments:\n- This slot accepts open-ended text about your sample.\n- We recommend using key:value pairs.\n- Provided pairs will be considered for inclusion as future slots/terms in this data\n  collection template.\nexamples:\n- value: 'experimental treatment: value'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000008\n- MIXS:0000300\nrank: 7\nstring_serialization: '{text}'\nalias: experimental_factor_other\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"ext_door/","title":"Slot: exterior door count (ext_door)","text":"

The number of exterior doors in the built structure

URI: MIXS:0000170

"},{"location":"ext_door/#inheritance","title":"Inheritance","text":""},{"location":"ext_door/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ext_door/#properties","title":"Properties","text":""},{"location":"ext_door/#aliases","title":"Aliases","text":""},{"location":"ext_door/#examples","title":"Examples","text":"Value"},{"location":"ext_door/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ext_door/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"ext_door/#schema-source","title":"Schema Source","text":""},{"location":"ext_door/#linkml-source","title":"LinkML Source","text":"
name: ext_door\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of exterior doors in the built structure\ntitle: exterior door count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exterior door count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000170\nalias: ext_door\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ext_wall_orient/","title":"Slot: orientations of exterior wall (ext_wall_orient)","text":"

The orientation of the exterior wall

URI: MIXS:0000817

"},{"location":"ext_wall_orient/#inheritance","title":"Inheritance","text":""},{"location":"ext_wall_orient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ext_wall_orient/#properties","title":"Properties","text":""},{"location":"ext_wall_orient/#aliases","title":"Aliases","text":""},{"location":"ext_wall_orient/#examples","title":"Examples","text":"Value northwest"},{"location":"ext_wall_orient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ext_wall_orient/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ext_wall_orient/#schema-source","title":"Schema Source","text":""},{"location":"ext_wall_orient/#linkml-source","title":"LinkML Source","text":"
name: ext_wall_orient\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The orientation of the exterior wall\ntitle: orientations of exterior wall\nexamples:\n- value: northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior wall\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000817\nalias: ext_wall_orient\ndomain_of:\n- Biosample\nrange: ext_wall_orient_enum\nmultivalued: false\n\n
"},{"location":"ext_window_orient/","title":"Slot: orientations of exterior window (ext_window_orient)","text":"

The compass direction the exterior window of the room is facing

URI: MIXS:0000818

"},{"location":"ext_window_orient/#inheritance","title":"Inheritance","text":""},{"location":"ext_window_orient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ext_window_orient/#properties","title":"Properties","text":""},{"location":"ext_window_orient/#aliases","title":"Aliases","text":""},{"location":"ext_window_orient/#examples","title":"Examples","text":"Value southwest"},{"location":"ext_window_orient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ext_window_orient/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"ext_window_orient/#schema-source","title":"Schema Source","text":""},{"location":"ext_window_orient/#linkml-source","title":"LinkML Source","text":"
name: ext_window_orient\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The compass direction the exterior window of the room is facing\ntitle: orientations of exterior window\nexamples:\n- value: southwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior window\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000818\nalias: ext_window_orient\ndomain_of:\n- Biosample\nrange: ext_window_orient_enum\nmultivalued: false\n\n
"},{"location":"external_database_identifiers/","title":"Slot: external_database_identifiers","text":"

Link to corresponding identifier in external database

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:external_database_identifiers

"},{"location":"external_database_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"external_database_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProcessedSample no"},{"location":"external_database_identifiers/#properties","title":"Properties","text":""},{"location":"external_database_identifiers/#comments","title":"Comments","text":""},{"location":"external_database_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"external_database_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"external_database_identifiers/#linkml-source","title":"LinkML Source","text":"
name: external_database_identifiers\ndescription: Link to corresponding identifier in external database\nnotes:\n- had tried ranges of external identifier and string\ncomments:\n- The value of this field is always a registered CURIE\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- skos:closeMatch\nrank: 1000\nis_a: alternative_identifiers\nabstract: true\nalias: external_database_identifiers\ndomain_of:\n- ProcessedSample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"extraction_targets/","title":"Slot: extraction_targets","text":"

Provides the target biomolecule that has been separated from a sample during an extraction process.

URI: nmdc:extraction_targets

"},{"location":"extraction_targets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"extraction_targets/#properties","title":"Properties","text":""},{"location":"extraction_targets/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"extraction_targets/#schema-source","title":"Schema Source","text":""},{"location":"extraction_targets/#linkml-source","title":"LinkML Source","text":"
name: extraction_targets\ndescription: Provides the target biomolecule that has been separated from a sample\n  during an extraction process.\nnotes:\n- todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)\nfrom_schema: https://w3id.org/nmdc/nmdc\nnarrow_mappings:\n- NCIT:C177560\n- MIXS:0000037\nrank: 1000\nalias: extraction_targets\ndomain_of:\n- Extraction\nrange: ExtractionTargetEnum\nmultivalued: true\n\n
"},{"location":"extreme_event/","title":"Slot: history/extreme events (extreme_event)","text":"

Unusual physical events that may have affected microbial populations

URI: MIXS:0000320

"},{"location":"extreme_event/#inheritance","title":"Inheritance","text":""},{"location":"extreme_event/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"extreme_event/#properties","title":"Properties","text":""},{"location":"extreme_event/#aliases","title":"Aliases","text":""},{"location":"extreme_event/#examples","title":"Examples","text":"Value"},{"location":"extreme_event/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"extreme_event/#annotations","title":"Annotations","text":"property value expected_value date"},{"location":"extreme_event/#schema-source","title":"Schema Source","text":""},{"location":"extreme_event/#linkml-source","title":"LinkML Source","text":"
name: extreme_event\nannotations:\n  expected_value:\n    tag: expected_value\n    value: date\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Unusual physical events that may have affected microbial populations\ntitle: history/extreme events\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/extreme events\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000320\nalias: extreme_event\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"fao_class/","title":"Slot: soil_taxonomic/FAO classification (fao_class)","text":"

Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups

URI: MIXS:0001083

"},{"location":"fao_class/#inheritance","title":"Inheritance","text":""},{"location":"fao_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fao_class/#properties","title":"Properties","text":""},{"location":"fao_class/#aliases","title":"Aliases","text":""},{"location":"fao_class/#examples","title":"Examples","text":"Value Luvisols"},{"location":"fao_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fao_class/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"fao_class/#schema-source","title":"Schema Source","text":""},{"location":"fao_class/#linkml-source","title":"LinkML Source","text":"
name: fao_class\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Soil classification from the FAO World Reference Database for Soil Resources.\n  The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\ntitle: soil_taxonomic/FAO classification\nexamples:\n- value: Luvisols\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/FAO classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001083\nalias: fao_class\ndomain_of:\n- Biosample\nrange: fao_class_enum\nmultivalued: false\n\n
"},{"location":"feature_category/","title":"Slot: feature_category","text":"

A Sequence Ontology term that describes the category of a feature

URI: nmdc:feature_category

"},{"location":"feature_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e no GenomeFeature A feature localized to an interval along a genome no"},{"location":"feature_category/#properties","title":"Properties","text":""},{"location":"feature_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"feature_category/#schema-source","title":"Schema Source","text":""},{"location":"feature_category/#linkml-source","title":"LinkML Source","text":"
name: feature_category\ndescription: A Sequence Ontology term that describes the category of a feature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_category\ndomain_of:\n- GenomeFeature\n- FunctionalAnnotation\nrange: ControlledIdentifiedTermValue\n\n
"},{"location":"feature_type/","title":"Slot: feature_type","text":"

TODO: Yuri to write

URI: nmdc:feature_type

"},{"location":"feature_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"feature_type/#properties","title":"Properties","text":""},{"location":"feature_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"feature_type/#schema-source","title":"Schema Source","text":""},{"location":"feature_type/#linkml-source","title":"LinkML Source","text":"
name: feature_type\ndescription: 'TODO: Yuri to write'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_type\ndomain_of:\n- GenomeFeature\nrange: string\n\n
"},{"location":"fertilizer_regm/","title":"Slot: fertilizer regimen (fertilizer_regm)","text":"

Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens

URI: MIXS:0000556

"},{"location":"fertilizer_regm/#inheritance","title":"Inheritance","text":""},{"location":"fertilizer_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fertilizer_regm/#properties","title":"Properties","text":""},{"location":"fertilizer_regm/#aliases","title":"Aliases","text":""},{"location":"fertilizer_regm/#examples","title":"Examples","text":"Value urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M"},{"location":"fertilizer_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fertilizer_regm/#annotations","title":"Annotations","text":"property value expected_value fertilizer name;fertilizer amount;treatment interval and duration"},{"location":"fertilizer_regm/#schema-source","title":"Schema Source","text":""},{"location":"fertilizer_regm/#linkml-source","title":"LinkML Source","text":"
name: fertilizer_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: fertilizer name;fertilizer amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving the use of fertilizers; should\n  include the name of fertilizer, amount administered, treatment regimen including\n  how many times the treatment was repeated, how long each treatment lasted, and the\n  start and end time of the entire treatment; can include multiple fertilizer regimens\ntitle: fertilizer regimen\nexamples:\n- value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fertilizer regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000556\nalias: fertilizer_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"field/","title":"Slot: field name (field)","text":"

Name of the hydrocarbon field (e.g. Albacora)

URI: MIXS:0000291

"},{"location":"field/#inheritance","title":"Inheritance","text":""},{"location":"field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"field/#properties","title":"Properties","text":""},{"location":"field/#aliases","title":"Aliases","text":""},{"location":"field/#examples","title":"Examples","text":"Value"},{"location":"field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"field/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"field/#schema-source","title":"Schema Source","text":""},{"location":"field/#linkml-source","title":"LinkML Source","text":"
name: field\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of the hydrocarbon field (e.g. Albacora)\ntitle: field name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- field name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000291\nalias: field\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"field_research_site_set/","title":"Slot: field_research_site_set","text":"

URI: nmdc:field_research_site_set

"},{"location":"field_research_site_set/#inheritance","title":"Inheritance","text":""},{"location":"field_research_site_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"field_research_site_set/#properties","title":"Properties","text":""},{"location":"field_research_site_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"field_research_site_set/#schema-source","title":"Schema Source","text":""},{"location":"field_research_site_set/#linkml-source","title":"LinkML Source","text":"
name: field_research_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: field_research_site_set\ndomain_of:\n- Database\nrange: FieldResearchSite\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"file_size_bytes/","title":"Slot: file_size_bytes","text":"

Size of the file in bytes

URI: nmdc:file_size_bytes

"},{"location":"file_size_bytes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"file_size_bytes/#properties","title":"Properties","text":""},{"location":"file_size_bytes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"file_size_bytes/#schema-source","title":"Schema Source","text":""},{"location":"file_size_bytes/#linkml-source","title":"LinkML Source","text":"
name: file_size_bytes\ndescription: Size of the file in bytes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: file_size_bytes\ndomain_of:\n- DataObject\nrange: bytes\n\n
"},{"location":"filter_material/","title":"Slot: filter_material","text":"

A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained.

URI: nmdc:filter_material

"},{"location":"filter_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filter_material/#properties","title":"Properties","text":""},{"location":"filter_material/#comments","title":"Comments","text":""},{"location":"filter_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filter_material/#schema-source","title":"Schema Source","text":""},{"location":"filter_material/#linkml-source","title":"LinkML Source","text":"
name: filter_material\ndescription: A porous material on which solid particles present in air or other fluid\n  which flows through it are largely caught and retained.\ncomments:\n- 'Filters are made with a variety of materials: cellulose and derivatives, glass\n  fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous or\n  be made so by mechanical or other means. Membrane/ceramic filters are prepared with\n  highly controlled pore size in a sheet of suitable material such as polyfluoroethylene,\n  polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement.\n  The pores constitute 80\u201385% of the filter volume commonly and several pore sizes\n  are available for air sampling (0.45\u22120.8 \u03bcm are commonly employed).'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filter_material\ndomain_of:\n- FiltrationProcess\nrange: string\n\n
"},{"location":"filter_method/","title":"Slot: filter method (filter_method)","text":"

Type of filter used or how the sample was filtered

URI: nmdc:filter_method

"},{"location":"filter_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"filter_method/#properties","title":"Properties","text":""},{"location":"filter_method/#examples","title":"Examples","text":"Value C18 Basix PES, 13-100-106 FisherSci"},{"location":"filter_method/#comments","title":"Comments","text":""},{"location":"filter_method/#see-also","title":"See Also","text":""},{"location":"filter_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filter_method/#schema-source","title":"Schema Source","text":""},{"location":"filter_method/#linkml-source","title":"LinkML Source","text":"
name: filter_method\ndescription: Type of filter used or how the sample was filtered\ntitle: filter method\ncomments:\n- describe the filter or provide a catalog number and manufacturer\nexamples:\n- value: C18\n- value: Basix PES, 13-100-106 FisherSci\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000765\nrank: 6\nstring_serialization: '{text}'\nalias: filter_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"filter_pore_size/","title":"Slot: filter_pore_size","text":"

A quantitative or qualitative measurement of the physical dimensions of the pores in a material.

URI: nmdc:filter_pore_size

"},{"location":"filter_pore_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filter_pore_size/#properties","title":"Properties","text":""},{"location":"filter_pore_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filter_pore_size/#schema-source","title":"Schema Source","text":""},{"location":"filter_pore_size/#linkml-source","title":"LinkML Source","text":"
name: filter_pore_size\ndescription: A quantitative or qualitative measurement of the physical dimensions\n  of the pores in a material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filter_pore_size\ndomain_of:\n- FiltrationProcess\nrange: QuantityValue\n\n
"},{"location":"filter_type/","title":"Slot: filter type (filter_type)","text":"

A device which removes solid particulates or airborne molecular contaminants

URI: MIXS:0000765

"},{"location":"filter_type/#inheritance","title":"Inheritance","text":""},{"location":"filter_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"filter_type/#properties","title":"Properties","text":""},{"location":"filter_type/#aliases","title":"Aliases","text":""},{"location":"filter_type/#examples","title":"Examples","text":"Value HEPA"},{"location":"filter_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filter_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"filter_type/#schema-source","title":"Schema Source","text":""},{"location":"filter_type/#linkml-source","title":"LinkML Source","text":"
name: filter_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: A device which removes solid particulates or airborne molecular contaminants\ntitle: filter type\nexamples:\n- value: HEPA\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- filter type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000765\nalias: filter_type\ndomain_of:\n- Biosample\nrange: filter_type_enum\nmultivalued: true\n\n
"},{"location":"filtration_category/","title":"Slot: filtration_category","text":"

The type of conditioning applied to a filter, device, etc.

URI: nmdc:filtration_category

"},{"location":"filtration_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filtration_category/#properties","title":"Properties","text":""},{"location":"filtration_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"filtration_category/#schema-source","title":"Schema Source","text":""},{"location":"filtration_category/#linkml-source","title":"LinkML Source","text":"
name: filtration_category\ndescription: The type of conditioning applied to a filter, device, etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filtration_category\ndomain_of:\n- FiltrationProcess\nrange: string\n\n
"},{"location":"final_concentration/","title":"Slot: final_concentration","text":"

When solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in the combination

URI: nmdc:final_concentration

"},{"location":"final_concentration/#inheritance","title":"Inheritance","text":""},{"location":"final_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"final_concentration/#properties","title":"Properties","text":""},{"location":"final_concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"final_concentration/#schema-source","title":"Schema Source","text":""},{"location":"final_concentration/#linkml-source","title":"LinkML Source","text":"
name: final_concentration\ndescription: When solutions A (containing substance X) and B are combined together,\n  this slot captures the concentration of X in the combination\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: concentration\nalias: final_concentration\ndomain_of:\n- PortionOfSubstance\nrange: QuantityValue\n\n
"},{"location":"fire/","title":"Slot: history/fire (fire)","text":"

Historical and/or physical evidence of fire

URI: MIXS:0001086

"},{"location":"fire/#inheritance","title":"Inheritance","text":""},{"location":"fire/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"fire/#properties","title":"Properties","text":""},{"location":"fire/#aliases","title":"Aliases","text":""},{"location":"fire/#examples","title":"Examples","text":"Value"},{"location":"fire/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fire/#annotations","title":"Annotations","text":"property value expected_value date"},{"location":"fire/#schema-source","title":"Schema Source","text":""},{"location":"fire/#linkml-source","title":"LinkML Source","text":"
name: fire\nannotations:\n  expected_value:\n    tag: expected_value\n    value: date\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Historical and/or physical evidence of fire\ntitle: history/fire\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/fire\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001086\nalias: fire\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"fireplace_type/","title":"Slot: fireplace type (fireplace_type)","text":"

A firebox with chimney

URI: MIXS:0000802

"},{"location":"fireplace_type/#inheritance","title":"Inheritance","text":""},{"location":"fireplace_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fireplace_type/#properties","title":"Properties","text":""},{"location":"fireplace_type/#aliases","title":"Aliases","text":""},{"location":"fireplace_type/#examples","title":"Examples","text":"Value wood burning"},{"location":"fireplace_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fireplace_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"fireplace_type/#schema-source","title":"Schema Source","text":""},{"location":"fireplace_type/#linkml-source","title":"LinkML Source","text":"
name: fireplace_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A firebox with chimney\ntitle: fireplace type\nexamples:\n- value: wood burning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fireplace type\nrank: 1000\nis_a: core field\nstring_serialization: '[gas burning|wood burning]'\nslot_uri: MIXS:0000802\nalias: fireplace_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"flooding/","title":"Slot: history/flooding (flooding)","text":"

Historical and/or physical evidence of flooding

URI: MIXS:0000319

"},{"location":"flooding/#inheritance","title":"Inheritance","text":""},{"location":"flooding/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"flooding/#properties","title":"Properties","text":""},{"location":"flooding/#aliases","title":"Aliases","text":""},{"location":"flooding/#examples","title":"Examples","text":"Value"},{"location":"flooding/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"flooding/#annotations","title":"Annotations","text":"property value expected_value date"},{"location":"flooding/#schema-source","title":"Schema Source","text":""},{"location":"flooding/#linkml-source","title":"LinkML Source","text":"
name: flooding\nannotations:\n  expected_value:\n    tag: expected_value\n    value: date\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Historical and/or physical evidence of flooding\ntitle: history/flooding\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/flooding\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000319\nalias: flooding\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"floor_age/","title":"Slot: floor age (floor_age)","text":"

The time period since installment of the carpet or flooring

URI: MIXS:0000164

"},{"location":"floor_age/#inheritance","title":"Inheritance","text":""},{"location":"floor_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_age/#properties","title":"Properties","text":""},{"location":"floor_age/#aliases","title":"Aliases","text":""},{"location":"floor_age/#examples","title":"Examples","text":"Value"},{"location":"floor_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_age/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"floor_age/#schema-source","title":"Schema Source","text":""},{"location":"floor_age/#linkml-source","title":"LinkML Source","text":"
name: floor_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: years, weeks, days\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The time period since installment of the carpet or flooring\ntitle: floor age\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000164\nalias: floor_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"floor_area/","title":"Slot: floor area (floor_area)","text":"

The area of the floor space within the room

URI: MIXS:0000165

"},{"location":"floor_area/#inheritance","title":"Inheritance","text":""},{"location":"floor_area/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_area/#properties","title":"Properties","text":""},{"location":"floor_area/#aliases","title":"Aliases","text":""},{"location":"floor_area/#examples","title":"Examples","text":"Value"},{"location":"floor_area/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_area/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"floor_area/#schema-source","title":"Schema Source","text":""},{"location":"floor_area/#linkml-source","title":"LinkML Source","text":"
name: floor_area\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The area of the floor space within the room\ntitle: floor area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000165\nalias: floor_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"floor_cond/","title":"Slot: floor condition (floor_cond)","text":"

The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas

URI: MIXS:0000803

"},{"location":"floor_cond/#inheritance","title":"Inheritance","text":""},{"location":"floor_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_cond/#properties","title":"Properties","text":""},{"location":"floor_cond/#aliases","title":"Aliases","text":""},{"location":"floor_cond/#examples","title":"Examples","text":"Value new"},{"location":"floor_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"floor_cond/#schema-source","title":"Schema Source","text":""},{"location":"floor_cond/#linkml-source","title":"LinkML Source","text":"
name: floor_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the floor at the time of sampling; photos or\n  video preferred; use drawings to indicate location of damaged areas\ntitle: floor condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000803\nalias: floor_cond\ndomain_of:\n- Biosample\nrange: floor_cond_enum\nmultivalued: false\n\n
"},{"location":"floor_count/","title":"Slot: floor count (floor_count)","text":"

The number of floors in the building, including basements and mechanical penthouse

URI: MIXS:0000225

"},{"location":"floor_count/#inheritance","title":"Inheritance","text":""},{"location":"floor_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_count/#properties","title":"Properties","text":""},{"location":"floor_count/#aliases","title":"Aliases","text":""},{"location":"floor_count/#examples","title":"Examples","text":"Value"},{"location":"floor_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"floor_count/#schema-source","title":"Schema Source","text":""},{"location":"floor_count/#linkml-source","title":"LinkML Source","text":"
name: floor_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of floors in the building, including basements and mechanical\n  penthouse\ntitle: floor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000225\nalias: floor_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"floor_finish_mat/","title":"Slot: floor finish material (floor_finish_mat)","text":"

The floor covering type; the finished surface that is walked on

URI: MIXS:0000804

"},{"location":"floor_finish_mat/#inheritance","title":"Inheritance","text":""},{"location":"floor_finish_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_finish_mat/#properties","title":"Properties","text":""},{"location":"floor_finish_mat/#aliases","title":"Aliases","text":""},{"location":"floor_finish_mat/#examples","title":"Examples","text":"Value carpet"},{"location":"floor_finish_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_finish_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"floor_finish_mat/#schema-source","title":"Schema Source","text":""},{"location":"floor_finish_mat/#linkml-source","title":"LinkML Source","text":"
name: floor_finish_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The floor covering type; the finished surface that is walked on\ntitle: floor finish material\nexamples:\n- value: carpet\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000804\nalias: floor_finish_mat\ndomain_of:\n- Biosample\nrange: floor_finish_mat_enum\nmultivalued: false\n\n
"},{"location":"floor_struc/","title":"Slot: floor structure (floor_struc)","text":"

Refers to the structural elements and subfloor upon which the finish flooring is installed

URI: MIXS:0000806

"},{"location":"floor_struc/#inheritance","title":"Inheritance","text":""},{"location":"floor_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_struc/#properties","title":"Properties","text":""},{"location":"floor_struc/#aliases","title":"Aliases","text":""},{"location":"floor_struc/#examples","title":"Examples","text":"Value concrete"},{"location":"floor_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"floor_struc/#schema-source","title":"Schema Source","text":""},{"location":"floor_struc/#linkml-source","title":"LinkML Source","text":"
name: floor_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Refers to the structural elements and subfloor upon which the finish\n  flooring is installed\ntitle: floor structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000806\nalias: floor_struc\ndomain_of:\n- Biosample\nrange: floor_struc_enum\nmultivalued: false\n\n
"},{"location":"floor_thermal_mass/","title":"Slot: floor thermal mass (floor_thermal_mass)","text":"

The ability of the floor to provide inertia against temperature fluctuations

URI: MIXS:0000166

"},{"location":"floor_thermal_mass/#inheritance","title":"Inheritance","text":""},{"location":"floor_thermal_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_thermal_mass/#properties","title":"Properties","text":""},{"location":"floor_thermal_mass/#aliases","title":"Aliases","text":""},{"location":"floor_thermal_mass/#examples","title":"Examples","text":"Value"},{"location":"floor_thermal_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_thermal_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"floor_thermal_mass/#schema-source","title":"Schema Source","text":""},{"location":"floor_thermal_mass/#linkml-source","title":"LinkML Source","text":"
name: floor_thermal_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: joule per degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The ability of the floor to provide inertia against temperature fluctuations\ntitle: floor thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000166\nalias: floor_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"floor_water_mold/","title":"Slot: floor signs of water/mold (floor_water_mold)","text":"

Signs of the presence of mold or mildew in a room

URI: MIXS:0000805

"},{"location":"floor_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"floor_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"floor_water_mold/#properties","title":"Properties","text":""},{"location":"floor_water_mold/#aliases","title":"Aliases","text":""},{"location":"floor_water_mold/#examples","title":"Examples","text":"Value ceiling discoloration"},{"location":"floor_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"floor_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"floor_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"floor_water_mold/#linkml-source","title":"LinkML Source","text":"
name: floor_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew in a room\ntitle: floor signs of water/mold\nexamples:\n- value: ceiling discoloration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor signs of water/mold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000805\nalias: floor_water_mold\ndomain_of:\n- Biosample\nrange: floor_water_mold_enum\nmultivalued: false\n\n
"},{"location":"fluor/","title":"Slot: fluorescence (fluor)","text":"

Raw or converted fluorescence of water

URI: MIXS:0000704

"},{"location":"fluor/#inheritance","title":"Inheritance","text":""},{"location":"fluor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fluor/#properties","title":"Properties","text":""},{"location":"fluor/#aliases","title":"Aliases","text":""},{"location":"fluor/#examples","title":"Examples","text":"Value 2.5 volts"},{"location":"fluor/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fluor/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"fluor/#schema-source","title":"Schema Source","text":""},{"location":"fluor/#linkml-source","title":"LinkML Source","text":"
name: fluor\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram chlorophyll a per cubic meter, volts\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Raw or converted fluorescence of water\ntitle: fluorescence\nexamples:\n- value: 2.5 volts\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fluorescence\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000704\nalias: fluor\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"freq_clean/","title":"Slot: frequency of cleaning (freq_clean)","text":"

The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.

URI: MIXS:0000226

"},{"location":"freq_clean/#inheritance","title":"Inheritance","text":""},{"location":"freq_clean/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"freq_clean/#properties","title":"Properties","text":""},{"location":"freq_clean/#aliases","title":"Aliases","text":""},{"location":"freq_clean/#examples","title":"Examples","text":"Value"},{"location":"freq_clean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"freq_clean/#annotations","title":"Annotations","text":"property value expected_value enumeration or {text}"},{"location":"freq_clean/#schema-source","title":"Schema Source","text":""},{"location":"freq_clean/#linkml-source","title":"LinkML Source","text":"
name: freq_clean\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration or {text}\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of times the sample location is cleaned. Frequency of cleaning\n  might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\ntitle: frequency of cleaning\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cleaning\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000226\nalias: freq_clean\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"freq_cook/","title":"Slot: frequency of cooking (freq_cook)","text":"

The number of times a meal is cooked per week

URI: MIXS:0000227

"},{"location":"freq_cook/#inheritance","title":"Inheritance","text":""},{"location":"freq_cook/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"freq_cook/#properties","title":"Properties","text":""},{"location":"freq_cook/#aliases","title":"Aliases","text":""},{"location":"freq_cook/#examples","title":"Examples","text":"Value"},{"location":"freq_cook/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"freq_cook/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"freq_cook/#schema-source","title":"Schema Source","text":""},{"location":"freq_cook/#linkml-source","title":"LinkML Source","text":"
name: freq_cook\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of times a meal is cooked per week\ntitle: frequency of cooking\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cooking\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000227\nalias: freq_cook\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"functional_annotation_agg/","title":"Slot: functional_annotation_agg","text":"

URI: nmdc:functional_annotation_agg

"},{"location":"functional_annotation_agg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"functional_annotation_agg/#properties","title":"Properties","text":""},{"location":"functional_annotation_agg/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"functional_annotation_agg/#schema-source","title":"Schema Source","text":""},{"location":"functional_annotation_agg/#linkml-source","title":"LinkML Source","text":"
name: functional_annotation_agg\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: functional_annotation_agg\ndomain_of:\n- Database\nrange: FunctionalAnnotationAggMember\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"functional_annotation_set/","title":"Slot: functional_annotation_set","text":"

This property links a database object to the set of all functional annotations

URI: nmdc:functional_annotation_set

"},{"location":"functional_annotation_set/#inheritance","title":"Inheritance","text":""},{"location":"functional_annotation_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"functional_annotation_set/#properties","title":"Properties","text":""},{"location":"functional_annotation_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"functional_annotation_set/#schema-source","title":"Schema Source","text":""},{"location":"functional_annotation_set/#linkml-source","title":"LinkML Source","text":"
name: functional_annotation_set\ndescription: This property links a database object to the set of all functional annotations\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: functional_annotation_set\ndomain_of:\n- Database\nrange: FunctionalAnnotation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"funding_sources/","title":"Slot: funding_sources","text":"

A list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants.

URI: nmdc:funding_sources

"},{"location":"funding_sources/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"funding_sources/#properties","title":"Properties","text":""},{"location":"funding_sources/#examples","title":"Examples","text":"Value National Sciences Foundation Dimensions of Biodiversity (award no. 1342701) U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract DE-AC05-00OR2275"},{"location":"funding_sources/#comments","title":"Comments","text":""},{"location":"funding_sources/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"funding_sources/#schema-source","title":"Schema Source","text":""},{"location":"funding_sources/#linkml-source","title":"LinkML Source","text":"
name: funding_sources\ndescription: A list of organizations, along with the award numbers, that underwrite\n  financial support for projects of a particular type. Typically, they process applications\n  and award funds to the chosen qualified applicants.\ncomments:\n- Include only the name of the funding organization and the award or contract number.\nexamples:\n- value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n- value: U.S. Department of Energy, Office of Science, Office of Biological and Environmental\n    Research (BER) under contract DE-AC05-00OR2275\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C39409\nrank: 1000\nalias: funding_sources\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\n
"},{"location":"fungicide_regm/","title":"Slot: fungicide regimen (fungicide_regm)","text":"

Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens

URI: MIXS:0000557

"},{"location":"fungicide_regm/#inheritance","title":"Inheritance","text":""},{"location":"fungicide_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"fungicide_regm/#properties","title":"Properties","text":""},{"location":"fungicide_regm/#aliases","title":"Aliases","text":""},{"location":"fungicide_regm/#examples","title":"Examples","text":"Value bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"fungicide_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"fungicide_regm/#annotations","title":"Annotations","text":"property value expected_value fungicide name;fungicide amount;treatment interval and duration"},{"location":"fungicide_regm/#schema-source","title":"Schema Source","text":""},{"location":"fungicide_regm/#linkml-source","title":"LinkML Source","text":"
name: fungicide_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: fungicide name;fungicide amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of fungicides; should include\n  the name of fungicide, amount administered, treatment regimen including how many\n  times the treatment was repeated, how long each treatment lasted, and the start\n  and end time of the entire treatment; can include multiple fungicide regimens\ntitle: fungicide regimen\nexamples:\n- value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fungicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000557\nalias: fungicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"furniture/","title":"Slot: furniture (furniture)","text":"

The types of furniture present in the sampled room

URI: MIXS:0000807

"},{"location":"furniture/#inheritance","title":"Inheritance","text":""},{"location":"furniture/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"furniture/#properties","title":"Properties","text":""},{"location":"furniture/#aliases","title":"Aliases","text":""},{"location":"furniture/#examples","title":"Examples","text":"Value chair"},{"location":"furniture/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"furniture/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"furniture/#schema-source","title":"Schema Source","text":""},{"location":"furniture/#linkml-source","title":"LinkML Source","text":"
name: furniture\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The types of furniture present in the sampled room\ntitle: furniture\nexamples:\n- value: chair\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- furniture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000807\nalias: furniture\ndomain_of:\n- Biosample\nrange: furniture_enum\nmultivalued: false\n\n
"},{"location":"gap_pct/","title":"Slot: gap_pct","text":"

The gap size percentage of all scaffolds.

URI: nmdc:gap_pct

"},{"location":"gap_pct/#inheritance","title":"Inheritance","text":""},{"location":"gap_pct/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"gap_pct/#properties","title":"Properties","text":""},{"location":"gap_pct/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gap_pct/#schema-source","title":"Schema Source","text":""},{"location":"gap_pct/#linkml-source","title":"LinkML Source","text":"
name: gap_pct\ndescription: The gap size percentage of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gap_pct\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"gaseous_environment/","title":"Slot: gaseous environment (gaseous_environment)","text":"

Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens

URI: MIXS:0000558

"},{"location":"gaseous_environment/#inheritance","title":"Inheritance","text":""},{"location":"gaseous_environment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"gaseous_environment/#properties","title":"Properties","text":""},{"location":"gaseous_environment/#aliases","title":"Aliases","text":""},{"location":"gaseous_environment/#examples","title":"Examples","text":"Value nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"gaseous_environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gaseous_environment/#annotations","title":"Annotations","text":"property value expected_value gaseous compound name;gaseous compound amount;treatment interval and duration"},{"location":"gaseous_environment/#schema-source","title":"Schema Source","text":""},{"location":"gaseous_environment/#linkml-source","title":"LinkML Source","text":"
name: gaseous_environment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gaseous compound name;gaseous compound amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Use of conditions with differing gaseous environments; should include\n  the name of gaseous compound, amount administered, treatment duration, interval\n  and total experimental duration; can include multiple gaseous environment regimens\ntitle: gaseous environment\nexamples:\n- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000558\nalias: gaseous_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gaseous_substances/","title":"Slot: gaseous substances (gaseous_substances)","text":"

Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances

URI: MIXS:0000661

"},{"location":"gaseous_substances/#inheritance","title":"Inheritance","text":""},{"location":"gaseous_substances/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"gaseous_substances/#properties","title":"Properties","text":""},{"location":"gaseous_substances/#aliases","title":"Aliases","text":""},{"location":"gaseous_substances/#examples","title":"Examples","text":"Value"},{"location":"gaseous_substances/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gaseous_substances/#annotations","title":"Annotations","text":"property value expected_value gaseous substance name;measurement value"},{"location":"gaseous_substances/#schema-source","title":"Schema Source","text":""},{"location":"gaseous_substances/#linkml-source","title":"LinkML Source","text":"
name: gaseous_substances\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gaseous substance name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Amount or concentration of substances such as hydrogen sulfide, carbon\n  dioxide, methane, etc.; can include multiple substances\ntitle: gaseous substances\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous substances\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000661\nalias: gaseous_substances\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gc_avg/","title":"Slot: gc_avg","text":"

Average of GC content of all contigs.

URI: nmdc:gc_avg

"},{"location":"gc_avg/#inheritance","title":"Inheritance","text":""},{"location":"gc_avg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"gc_avg/#properties","title":"Properties","text":""},{"location":"gc_avg/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gc_avg/#schema-source","title":"Schema Source","text":""},{"location":"gc_avg/#linkml-source","title":"LinkML Source","text":"
name: gc_avg\ndescription: Average of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_avg\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"gc_std/","title":"Slot: gc_std","text":"

Standard deviation of GC content of all contigs.

URI: nmdc:gc_std

"},{"location":"gc_std/#inheritance","title":"Inheritance","text":""},{"location":"gc_std/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"gc_std/#properties","title":"Properties","text":""},{"location":"gc_std/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gc_std/#schema-source","title":"Schema Source","text":""},{"location":"gc_std/#linkml-source","title":"LinkML Source","text":"
name: gc_std\ndescription: Standard deviation of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_std\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"gender_restroom/","title":"Slot: gender of restroom (gender_restroom)","text":"

The gender type of the restroom

URI: MIXS:0000808

"},{"location":"gender_restroom/#inheritance","title":"Inheritance","text":""},{"location":"gender_restroom/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"gender_restroom/#properties","title":"Properties","text":""},{"location":"gender_restroom/#aliases","title":"Aliases","text":""},{"location":"gender_restroom/#examples","title":"Examples","text":"Value male"},{"location":"gender_restroom/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gender_restroom/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"gender_restroom/#schema-source","title":"Schema Source","text":""},{"location":"gender_restroom/#linkml-source","title":"LinkML Source","text":"
name: gender_restroom\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The gender type of the restroom\ntitle: gender of restroom\nexamples:\n- value: male\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gender of restroom\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000808\nalias: gender_restroom\ndomain_of:\n- Biosample\nrange: gender_restroom_enum\nmultivalued: false\n\n
"},{"location":"gene_count/","title":"Slot: gene_count","text":"

URI: nmdc:gene_count

"},{"location":"gene_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gene_count/#properties","title":"Properties","text":""},{"location":"gene_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_count/#schema-source","title":"Schema Source","text":""},{"location":"gene_count/#linkml-source","title":"LinkML Source","text":"
name: gene_count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_count\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"gene_function_id/","title":"Slot: gene_function_id","text":"

The identifier for the gene function.

URI: nmdc:gene_function_id

"},{"location":"gene_function_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"gene_function_id/#properties","title":"Properties","text":""},{"location":"gene_function_id/#examples","title":"Examples","text":"Value KEGG.ORTHOLOGY:K00627"},{"location":"gene_function_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gene_function_id/#schema-source","title":"Schema Source","text":""},{"location":"gene_function_id/#linkml-source","title":"LinkML Source","text":"
name: gene_function_id\ndescription: The identifier for the gene function.\nexamples:\n- value: KEGG.ORTHOLOGY:K00627\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_function_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: uriorcurie\nrequired: true\n\n
"},{"location":"genetic_mod/","title":"Slot: genetic modification (genetic_mod)","text":"

Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection

URI: MIXS:0000859

"},{"location":"genetic_mod/#inheritance","title":"Inheritance","text":""},{"location":"genetic_mod/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"genetic_mod/#properties","title":"Properties","text":""},{"location":"genetic_mod/#aliases","title":"Aliases","text":""},{"location":"genetic_mod/#examples","title":"Examples","text":"Value aox1A transgenic"},{"location":"genetic_mod/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"genetic_mod/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url or free text"},{"location":"genetic_mod/#schema-source","title":"Schema Source","text":""},{"location":"genetic_mod/#linkml-source","title":"LinkML Source","text":"
name: genetic_mod\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url or free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Genetic modifications of the genome of an organism, which may occur naturally\n  by spontaneous mutation, or be introduced by some experimental means, e.g. specification\n  of a transgene or the gene knocked-out or details of transient transfection\ntitle: genetic modification\nexamples:\n- value: aox1A transgenic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- genetic modification\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000859\nalias: genetic_mod\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"genome_feature_set/","title":"Slot: genome_feature_set","text":"

This property links a database object to the set of all features

URI: nmdc:genome_feature_set

"},{"location":"genome_feature_set/#inheritance","title":"Inheritance","text":""},{"location":"genome_feature_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"genome_feature_set/#properties","title":"Properties","text":""},{"location":"genome_feature_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"genome_feature_set/#schema-source","title":"Schema Source","text":""},{"location":"genome_feature_set/#linkml-source","title":"LinkML Source","text":"
name: genome_feature_set\ndescription: This property links a database object to the set of all features\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: genome_feature_set\ndomain_of:\n- Database\nrange: GenomeFeature\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"geo_loc_name/","title":"Slot: geographic location (country and/or sea,region) (geo_loc_name)","text":"

The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)

URI: MIXS:0000010

"},{"location":"geo_loc_name/#inheritance","title":"Inheritance","text":""},{"location":"geo_loc_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no"},{"location":"geo_loc_name/#properties","title":"Properties","text":""},{"location":"geo_loc_name/#aliases","title":"Aliases","text":""},{"location":"geo_loc_name/#examples","title":"Examples","text":"Value USA: Maryland, Bethesda"},{"location":"geo_loc_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"geo_loc_name/#annotations","title":"Annotations","text":"property value expected_value country or sea name (INSDC or GAZ): region(GAZ), specific location name"},{"location":"geo_loc_name/#schema-source","title":"Schema Source","text":""},{"location":"geo_loc_name/#linkml-source","title":"LinkML Source","text":"
name: geo_loc_name\nannotations:\n  expected_value:\n    tag: expected_value\n    value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location name'\ndescription: The geographical origin of the sample as defined by the country or sea\n  name followed by specific region name. Country or sea names should be chosen from\n  the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)\ntitle: geographic location (country and/or sea,region)\nexamples:\n- value: 'USA: Maryland, Bethesda'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (country and/or sea,region)\nrank: 1000\nis_a: environment field\nstring_serialization: '{term}: {term}, {text}'\nslot_uri: MIXS:0000010\nalias: geo_loc_name\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"gff_coordinate/","title":"Slot: gff_coordinate","text":"

A positive 1-based integer coordinate indicating start or end

URI: nmdc:gff_coordinate

"},{"location":"gff_coordinate/#inheritance","title":"Inheritance","text":""},{"location":"gff_coordinate/#properties","title":"Properties","text":""},{"location":"gff_coordinate/#comments","title":"Comments","text":""},{"location":"gff_coordinate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gff_coordinate/#schema-source","title":"Schema Source","text":""},{"location":"gff_coordinate/#linkml-source","title":"LinkML Source","text":"
name: gff_coordinate\ndescription: A positive 1-based integer coordinate indicating start or end\ncomments:\n- For features that cross the origin of a circular feature (e.g. most bacterial genomes,\n  plasmids, and some viral genomes), the requirement for start to be less than or\n  equal to end is satisfied by making end = the position of the end + the length of\n  the landmark feature.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gff_coordinate\nrange: integer\nminimum_value: 1\n\n
"},{"location":"git_url/","title":"Slot: git_url","text":"

The url that points to the exact github location of a workflow.

URI: nmdc:git_url

"},{"location":"git_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetatranscriptomeAssembly no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetabolomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetaproteomicsAnalysis no"},{"location":"git_url/#properties","title":"Properties","text":""},{"location":"git_url/#examples","title":"Examples","text":"Value https://github.com/microbiomedata/mg_annotation/releases/tag/0.1 https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py"},{"location":"git_url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"git_url/#schema-source","title":"Schema Source","text":""},{"location":"git_url/#linkml-source","title":"LinkML Source","text":"
name: git_url\ndescription: The url that points to the exact github location of a workflow.\nexamples:\n- value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n- value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: git_url\ndomain_of:\n- WorkflowExecution\nrange: string\n\n
"},{"location":"glucosidase_act/","title":"Slot: glucosidase activity (glucosidase_act)","text":"

Measurement of glucosidase activity

URI: MIXS:0000137

"},{"location":"glucosidase_act/#inheritance","title":"Inheritance","text":""},{"location":"glucosidase_act/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"glucosidase_act/#properties","title":"Properties","text":""},{"location":"glucosidase_act/#aliases","title":"Aliases","text":""},{"location":"glucosidase_act/#examples","title":"Examples","text":"Value 5 mol per liter per hour"},{"location":"glucosidase_act/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"glucosidase_act/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"glucosidase_act/#schema-source","title":"Schema Source","text":""},{"location":"glucosidase_act/#linkml-source","title":"LinkML Source","text":"
name: glucosidase_act\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mol per liter per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of glucosidase activity\ntitle: glucosidase activity\nexamples:\n- value: 5 mol per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- glucosidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000137\nalias: glucosidase_act\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"gnps_identifiers/","title":"Slot: gnps_identifiers","text":"

URI: nmdc:gnps_identifiers

"},{"location":"gnps_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... None Study"},{"location":"gnps_identifiers/#properties","title":"Properties","text":""},{"location":"gnps_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gnps_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gnps_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gnps_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: gnps_identifiers\nrange: string\n\n
"},{"location":"gnps_task_identifiers/","title":"Slot: GNPS task identifiers (gnps_task_identifiers)","text":"

identifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results

URI: nmdc:gnps_task_identifiers

"},{"location":"gnps_task_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gnps_task_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"gnps_task_identifiers/#properties","title":"Properties","text":""},{"location":"gnps_task_identifiers/#examples","title":"Examples","text":"Value gnps.task:4b848c342a4f4abc871bdf8a09a60807"},{"location":"gnps_task_identifiers/#comments","title":"Comments","text":""},{"location":"gnps_task_identifiers/#see-also","title":"See Also","text":""},{"location":"gnps_task_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gnps_task_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gnps_task_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gnps_task_identifiers\ndescription: identifiers that link a NMDC study to a web-based report about metabolomics\n  analysis progress and results\ntitle: GNPS task identifiers\ncomments:\n- this could be considered a related identifier, as the metabolomics progress and\n  results aren't a study per se\n- this identifier was registered with bioregistry but not identifiers.org\nexamples:\n- value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysis/\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gnps_identifiers\nalias: gnps_task_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^gnps\\.task:[a-f0-9]+$\n\n
"},{"location":"gold_analysis_project_identifiers/","title":"Slot: gold_analysis_project_identifiers","text":"

identifiers for corresponding analysis projects in GOLD

URI: nmdc:gold_analysis_project_identifiers

"},{"location":"gold_analysis_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gold_analysis_project_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAnnotation yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes"},{"location":"gold_analysis_project_identifiers/#properties","title":"Properties","text":""},{"location":"gold_analysis_project_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/gold:Ga0526289"},{"location":"gold_analysis_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_analysis_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_analysis_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_analysis_project_identifiers\ndescription: identifiers for corresponding analysis projects in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Ga0526289\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- gold_identifiers\nalias: gold_analysis_project_identifiers\ndomain_of:\n- MetagenomeAnnotation\n- MetatranscriptomeAnnotation\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Ga[0-9]+$\n\n
"},{"location":"gold_biosample_identifiers/","title":"Slot: gold_biosample_identifiers","text":"

identifiers for corresponding sample in GOLD

URI: nmdc:gold_biosample_identifiers

"},{"location":"gold_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gold_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"gold_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"gold_biosample_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/gold:Gb0312930"},{"location":"gold_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_biosample_identifiers\ndescription: identifiers for corresponding sample in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gb0312930\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- gold_identifiers\nalias: gold_biosample_identifiers\ndomain_of:\n- Biosample\nrange: uriorcurie\nmultivalued: true\npattern: ^gold:Gb[0-9]+$\n\n
"},{"location":"gold_identifiers/","title":"Slot: gold_identifiers","text":"

URI: nmdc:gold_identifiers

"},{"location":"gold_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gold_study_identifiers identifiers for corresponding project(s) in GOLD None Study gold_biosample_identifiers identifiers for corresponding sample in GOLD uriorcurie Biosample gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD None NucleotideSequencing gold_analysis_project_identifiers identifiers for corresponding analysis projects in GOLD None MetatranscriptomeAnnotation, MetagenomeAnnotation"},{"location":"gold_identifiers/#properties","title":"Properties","text":""},{"location":"gold_identifiers/#see-also","title":"See Also","text":""},{"location":"gold_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: gold_identifiers\nrange: string\n\n
"},{"location":"gold_path_field/","title":"Slot: gold_path_field","text":"

This is a grouping for any of the gold path fields

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:gold_path_field

"},{"location":"gold_path_field/#inheritance","title":"Inheritance","text":""},{"location":"gold_path_field/#properties","title":"Properties","text":""},{"location":"gold_path_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_path_field/#annotations","title":"Annotations","text":"property value tooltip GOLD Ecosystem Classification paths describe the surroundings from which an environmental sample or an organism is collected."},{"location":"gold_path_field/#schema-source","title":"Schema Source","text":""},{"location":"gold_path_field/#linkml-source","title":"LinkML Source","text":"
name: gold_path_field\nannotations:\n  tooltip:\n    tag: tooltip\n    value: GOLD Ecosystem Classification paths describe the surroundings from which\n      an environmental sample or an organism is collected.\n    annotations:\n      source:\n        tag: source\n        value: https://gold.jgi.doe.gov/ecosystem_classification\ndescription: This is a grouping for any of the gold path fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: gold_path_field\nrange: string\n\n
"},{"location":"gold_sequencing_project_identifiers/","title":"Slot: gold_sequencing_project_identifiers","text":"

identifiers for corresponding sequencing project in GOLD

URI: nmdc:gold_sequencing_project_identifiers

"},{"location":"gold_sequencing_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gold_sequencing_project_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"gold_sequencing_project_identifiers/#properties","title":"Properties","text":""},{"location":"gold_sequencing_project_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/gold:Gp0108335"},{"location":"gold_sequencing_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_sequencing_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_sequencing_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_sequencing_project_identifiers\ndescription: identifiers for corresponding sequencing project in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gp0108335\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: omics_processing_identifiers\nmixins:\n- gold_identifiers\nalias: gold_sequencing_project_identifiers\ndomain_of:\n- NucleotideSequencing\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Gp[0-9]+$\n\n
"},{"location":"gold_study_identifiers/","title":"Slot: GOLD Study Identifiers (gold_study_identifiers)","text":"

identifiers for corresponding project(s) in GOLD

URI: nmdc:gold_study_identifiers

"},{"location":"gold_study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"gold_study_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"gold_study_identifiers/#properties","title":"Properties","text":""},{"location":"gold_study_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/gold:Gs0110115"},{"location":"gold_study_identifiers/#comments","title":"Comments","text":""},{"location":"gold_study_identifiers/#see-also","title":"See Also","text":""},{"location":"gold_study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gold_study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"gold_study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: gold_study_identifiers\ndescription: identifiers for corresponding project(s) in GOLD\ntitle: GOLD Study Identifiers\ncomments:\n- uses the prefix GS (but possibly in a different case)\nexamples:\n- value: https://bioregistry.io/gold:Gs0110115\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/studies\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gold_identifiers\nalias: gold_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Gs[0-9]+$\n\n
"},{"location":"gravidity/","title":"Slot: gravidity (gravidity)","text":"

Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used

URI: MIXS:0000875

"},{"location":"gravidity/#inheritance","title":"Inheritance","text":""},{"location":"gravidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"gravidity/#properties","title":"Properties","text":""},{"location":"gravidity/#aliases","title":"Aliases","text":""},{"location":"gravidity/#examples","title":"Examples","text":"Value yes;due date:2018-05-11"},{"location":"gravidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gravidity/#annotations","title":"Annotations","text":"property value expected_value gravidity status;timestamp"},{"location":"gravidity/#schema-source","title":"Schema Source","text":""},{"location":"gravidity/#linkml-source","title":"LinkML Source","text":"
name: gravidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gravidity status;timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Whether or not subject is gravid, and if yes date due or date post-conception,\n  specifying which is used\ntitle: gravidity\nexamples:\n- value: yes;due date:2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravidity\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{timestamp}'\nslot_uri: MIXS:0000875\nalias: gravidity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"gravity/","title":"Slot: gravity (gravity)","text":"

Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments

URI: MIXS:0000559

"},{"location":"gravity/#inheritance","title":"Inheritance","text":""},{"location":"gravity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"gravity/#properties","title":"Properties","text":""},{"location":"gravity/#aliases","title":"Aliases","text":""},{"location":"gravity/#examples","title":"Examples","text":"Value 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"gravity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gravity/#annotations","title":"Annotations","text":"property value expected_value gravity factor value;treatment interval and duration"},{"location":"gravity/#schema-source","title":"Schema Source","text":""},{"location":"gravity/#linkml-source","title":"LinkML Source","text":"
name: gravity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gravity factor value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: meter per square second, g\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of gravity factor to study\n  various types of responses in presence, absence or modified levels of gravity; treatment\n  regimen including how many times the treatment was repeated, how long each treatment\n  lasted, and the start and end time of the entire treatment; can include multiple\n  treatments\ntitle: gravity\nexamples:\n- value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000559\nalias: gravity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"growth_facil/","title":"Slot: growth facility (growth_facil)","text":"

Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research

URI: MIXS:0001043

"},{"location":"growth_facil/#inheritance","title":"Inheritance","text":""},{"location":"growth_facil/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"growth_facil/#properties","title":"Properties","text":""},{"location":"growth_facil/#aliases","title":"Aliases","text":""},{"location":"growth_facil/#examples","title":"Examples","text":"Value Growth chamber [CO_715:0000189]"},{"location":"growth_facil/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"growth_facil/#annotations","title":"Annotations","text":"property value expected_value free text or CO"},{"location":"growth_facil/#schema-source","title":"Schema Source","text":""},{"location":"growth_facil/#linkml-source","title":"LinkML Source","text":"
name: growth_facil\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text or CO\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n  growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n  use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\ntitle: growth facility\nexamples:\n- value: Growth chamber [CO_715:0000189]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth facility\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{termLabel} {[termID]}'\nslot_uri: MIXS:0001043\nalias: growth_facil\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"growth_habit/","title":"Slot: growth habit (growth_habit)","text":"

Characteristic shape, appearance or growth form of a plant species

URI: MIXS:0001044

"},{"location":"growth_habit/#inheritance","title":"Inheritance","text":""},{"location":"growth_habit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"growth_habit/#properties","title":"Properties","text":""},{"location":"growth_habit/#aliases","title":"Aliases","text":""},{"location":"growth_habit/#examples","title":"Examples","text":"Value spreading"},{"location":"growth_habit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"growth_habit/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"growth_habit/#schema-source","title":"Schema Source","text":""},{"location":"growth_habit/#linkml-source","title":"LinkML Source","text":"
name: growth_habit\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Characteristic shape, appearance or growth form of a plant species\ntitle: growth habit\nexamples:\n- value: spreading\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth habit\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001044\nalias: growth_habit\ndomain_of:\n- Biosample\nrange: growth_habit_enum\nmultivalued: false\n\n
"},{"location":"growth_hormone_regm/","title":"Slot: growth hormone regimen (growth_hormone_regm)","text":"

Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens

URI: MIXS:0000560

"},{"location":"growth_hormone_regm/#inheritance","title":"Inheritance","text":""},{"location":"growth_hormone_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"growth_hormone_regm/#properties","title":"Properties","text":""},{"location":"growth_hormone_regm/#aliases","title":"Aliases","text":""},{"location":"growth_hormone_regm/#examples","title":"Examples","text":"Value abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"growth_hormone_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"growth_hormone_regm/#annotations","title":"Annotations","text":"property value expected_value growth hormone name;growth hormone amount;treatment interval and duration"},{"location":"growth_hormone_regm/#schema-source","title":"Schema Source","text":""},{"location":"growth_hormone_regm/#linkml-source","title":"LinkML Source","text":"
name: growth_hormone_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: growth hormone name;growth hormone amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of growth hormones; should\n  include the name of growth hormone, amount administered, treatment regimen including\n  how many times the treatment was repeated, how long each treatment lasted, and the\n  start and end time of the entire treatment; can include multiple growth hormone\n  regimens\ntitle: growth hormone regimen\nexamples:\n- value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth hormone regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000560\nalias: growth_hormone_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"gtdbtk_class/","title":"Slot: gtdbtk_class","text":"

URI: nmdc:gtdbtk_class

"},{"location":"gtdbtk_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_class/#properties","title":"Properties","text":""},{"location":"gtdbtk_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_class/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_class/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_class\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_domain/","title":"Slot: gtdbtk_domain","text":"

URI: nmdc:gtdbtk_domain

"},{"location":"gtdbtk_domain/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_domain/#properties","title":"Properties","text":""},{"location":"gtdbtk_domain/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_domain/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_domain/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_domain\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_domain\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_family/","title":"Slot: gtdbtk_family","text":"

URI: nmdc:gtdbtk_family

"},{"location":"gtdbtk_family/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_family/#properties","title":"Properties","text":""},{"location":"gtdbtk_family/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_family/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_family/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_family\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_family\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_genus/","title":"Slot: gtdbtk_genus","text":"

URI: nmdc:gtdbtk_genus

"},{"location":"gtdbtk_genus/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_genus/#properties","title":"Properties","text":""},{"location":"gtdbtk_genus/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_genus/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_genus/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_genus\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_genus\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_order/","title":"Slot: gtdbtk_order","text":"

URI: nmdc:gtdbtk_order

"},{"location":"gtdbtk_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_order/#properties","title":"Properties","text":""},{"location":"gtdbtk_order/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_order/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_order/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_order\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_order\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_phylum/","title":"Slot: gtdbtk_phylum","text":"

URI: nmdc:gtdbtk_phylum

"},{"location":"gtdbtk_phylum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_phylum/#properties","title":"Properties","text":""},{"location":"gtdbtk_phylum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_phylum/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_phylum/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_phylum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_phylum\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"gtdbtk_species/","title":"Slot: gtdbtk_species","text":"

URI: nmdc:gtdbtk_species

"},{"location":"gtdbtk_species/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_species/#properties","title":"Properties","text":""},{"location":"gtdbtk_species/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"gtdbtk_species/#schema-source","title":"Schema Source","text":""},{"location":"gtdbtk_species/#linkml-source","title":"LinkML Source","text":"
name: gtdbtk_species\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_species\ndomain_of:\n- MagBin\nrange: string\n\n
"},{"location":"habitat/","title":"Slot: habitat","text":"

URI: nmdc:habitat

"},{"location":"habitat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no"},{"location":"habitat/#properties","title":"Properties","text":""},{"location":"habitat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"habitat/#schema-source","title":"Schema Source","text":""},{"location":"habitat/#linkml-source","title":"LinkML Source","text":"
name: habitat\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: habitat\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: string\n\n
"},{"location":"hall_count/","title":"Slot: hallway/corridor count (hall_count)","text":"

The total count of hallways and cooridors in the built structure

URI: MIXS:0000228

"},{"location":"hall_count/#inheritance","title":"Inheritance","text":""},{"location":"hall_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hall_count/#properties","title":"Properties","text":""},{"location":"hall_count/#aliases","title":"Aliases","text":""},{"location":"hall_count/#examples","title":"Examples","text":"Value"},{"location":"hall_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hall_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"hall_count/#schema-source","title":"Schema Source","text":""},{"location":"hall_count/#linkml-source","title":"LinkML Source","text":"
name: hall_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The total count of hallways and cooridors in the built structure\ntitle: hallway/corridor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hallway/corridor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000228\nalias: hall_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"handidness/","title":"Slot: handidness (handidness)","text":"

The handidness of the individual sampled

URI: MIXS:0000809

"},{"location":"handidness/#inheritance","title":"Inheritance","text":""},{"location":"handidness/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"handidness/#properties","title":"Properties","text":""},{"location":"handidness/#aliases","title":"Aliases","text":""},{"location":"handidness/#examples","title":"Examples","text":"Value right handedness"},{"location":"handidness/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"handidness/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"handidness/#schema-source","title":"Schema Source","text":""},{"location":"handidness/#linkml-source","title":"LinkML Source","text":"
name: handidness\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The handidness of the individual sampled\ntitle: handidness\nexamples:\n- value: right handedness\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- handidness\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000809\nalias: handidness\ndomain_of:\n- Biosample\nrange: handidness_enum\nmultivalued: false\n\n
"},{"location":"has_boolean_value/","title":"Slot: has_boolean_value","text":"

Links a quantity value to a boolean

URI: nmdc:has_boolean_value

"},{"location":"has_boolean_value/#properties","title":"Properties","text":""},{"location":"has_boolean_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_boolean_value/#schema-source","title":"Schema Source","text":""},{"location":"has_boolean_value/#linkml-source","title":"LinkML Source","text":"
name: has_boolean_value\ndescription: Links a quantity value to a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_boolean_value\nrange: boolean\n\n
"},{"location":"has_calibration/","title":"Slot: has_calibration","text":"

a calibration instance associated with a process

URI: nmdc:has_calibration

"},{"location":"has_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes NomAnalysis no MetabolomicsAnalysis no"},{"location":"has_calibration/#properties","title":"Properties","text":""},{"location":"has_calibration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_calibration/#schema-source","title":"Schema Source","text":""},{"location":"has_calibration/#linkml-source","title":"LinkML Source","text":"
name: has_calibration\ndescription: a calibration instance associated with a process\nnotes:\n- 'has_calibration slot will be removed from all WorkflowExecution classes but remain\n  on the MassSpectrometry class after an ingest of the appropriate set has occurred.  Once\n  this has occurred, this slot''s range can be updated to CalibrationInformation and\n  class/slot definitions can move to nmdc.yaml.   See PR #29 in Berkeley schema.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_calibration\ndomain_of:\n- MassSpectrometry\n- MetabolomicsAnalysis\n- NomAnalysis\nrange: string\nany_of:\n- range: CalibrationInformation\n- range: string\n\n
"},{"location":"has_chromatography_configuration/","title":"Slot: has_chromatography_configuration","text":"

The identifier of the associated ChromatographyConfiguration, providing information about how a sample was introduced into the mass spectrometer.

URI: nmdc:has_chromatography_configuration

"},{"location":"has_chromatography_configuration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"has_chromatography_configuration/#properties","title":"Properties","text":""},{"location":"has_chromatography_configuration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_chromatography_configuration/#schema-source","title":"Schema Source","text":""},{"location":"has_chromatography_configuration/#linkml-source","title":"LinkML Source","text":"
name: has_chromatography_configuration\ndescription: The identifier of the associated ChromatographyConfiguration, providing\n  information about how a sample was introduced into the mass spectrometer.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_chromatography_configuration\ndomain_of:\n- MassSpectrometry\nrange: ChromatographyConfiguration\n\n
"},{"location":"has_credit_associations/","title":"Slot: has_credit_associations","text":"

This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study

URI: prov:qualifiedAssociation

"},{"location":"has_credit_associations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"has_credit_associations/#properties","title":"Properties","text":""},{"location":"has_credit_associations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_credit_associations/#annotations","title":"Annotations","text":"property value tooltip Other researchers associated with this study."},{"location":"has_credit_associations/#schema-source","title":"Schema Source","text":""},{"location":"has_credit_associations/#linkml-source","title":"LinkML Source","text":"
name: has_credit_associations\nannotations:\n  tooltip:\n    tag: tooltip\n    value: Other researchers associated with this study.\ndescription: 'This slot links a study to a credit association.  The credit association\n  will be linked to a person value and to a CRediT Contributor Roles term. Overall\n  semantics: person should get credit X for their participation in the study'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: prov:qualifiedAssociation\nalias: has_credit_associations\ndomain_of:\n- Study\nrange: CreditAssociation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"has_failure_categorization/","title":"Slot: has_failure_categorization","text":"

URI: nmdc:has_failure_categorization

"},{"location":"has_failure_categorization/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeAssembly no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no PlannedProcess no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ProtocolExecution A PlannedProces that has PlannedProcess parts no LibraryPreparation no"},{"location":"has_failure_categorization/#properties","title":"Properties","text":""},{"location":"has_failure_categorization/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_failure_categorization/#schema-source","title":"Schema Source","text":""},{"location":"has_failure_categorization/#linkml-source","title":"LinkML Source","text":"
name: has_failure_categorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_failure_categorization\ndomain_of:\n- PlannedProcess\nrange: FailureCategorization\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"has_function/","title":"Slot: has_function","text":"

URI: nmdc:has_function

"},{"location":"has_function/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e yes"},{"location":"has_function/#properties","title":"Properties","text":""},{"location":"has_function/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_function/#schema-source","title":"Schema Source","text":""},{"location":"has_function/#linkml-source","title":"LinkML Source","text":"
name: has_function\nnotes:\n- the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm,\n- but is actually taking string arguments in MongoDB,\n- and those are frequently fulltext, not CURIEs. MAM 2021-06-23\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_function\ndomain_of:\n- FunctionalAnnotation\nrange: string\npattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n\n
"},{"location":"has_input/","title":"Slot: has_input","text":"

An input to a process.

URI: nmdc:has_input

"},{"location":"has_input/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow yes MetatranscriptomeAnnotation yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MetatranscriptomeAssembly no StorageProcess A planned process with the objective to preserve and protect material entitie... yes ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no PlannedProcess no MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis yes NomAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... yes Pooling physical combination of several instances of like material yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e yes MetabolomicsAnalysis no ProtocolExecution A PlannedProces that has PlannedProcess parts yes LibraryPreparation yes"},{"location":"has_input/#properties","title":"Properties","text":""},{"location":"has_input/#aliases","title":"Aliases","text":""},{"location":"has_input/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_input/#schema-source","title":"Schema Source","text":""},{"location":"has_input/#linkml-source","title":"LinkML Source","text":"
name: has_input\ndescription: An input to a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- input\nrank: 1000\nalias: has_input\ndomain_of:\n- PlannedProcess\nrange: NamedThing\nmultivalued: true\n\n
"},{"location":"has_mass_spectrometry_configuration/","title":"Slot: has_mass_spectrometry_configuration","text":"

The identifier of the associated MassSpectrometryConfiguration.

URI: nmdc:has_mass_spectrometry_configuration

"},{"location":"has_mass_spectrometry_configuration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"has_mass_spectrometry_configuration/#properties","title":"Properties","text":""},{"location":"has_mass_spectrometry_configuration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_mass_spectrometry_configuration/#schema-source","title":"Schema Source","text":""},{"location":"has_mass_spectrometry_configuration/#linkml-source","title":"LinkML Source","text":"
name: has_mass_spectrometry_configuration\ndescription: The identifier of the associated MassSpectrometryConfiguration.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_mass_spectrometry_configuration\ndomain_of:\n- MassSpectrometry\nrange: MassSpectrometryConfiguration\n\n
"},{"location":"has_maximum_numeric_value/","title":"Slot: has_maximum_numeric_value","text":"

The maximum value part, expressed as number, of the quantity value when the value covers a range.

URI: nmdc:has_maximum_numeric_value

"},{"location":"has_maximum_numeric_value/#inheritance","title":"Inheritance","text":""},{"location":"has_maximum_numeric_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e no"},{"location":"has_maximum_numeric_value/#properties","title":"Properties","text":""},{"location":"has_maximum_numeric_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_maximum_numeric_value/#schema-source","title":"Schema Source","text":""},{"location":"has_maximum_numeric_value/#linkml-source","title":"LinkML Source","text":"
name: has_maximum_numeric_value\ndescription: The maximum value part, expressed as number, of the quantity value when\n  the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_maximum_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\n
"},{"location":"has_metabolite_identifications/","title":"Slot: has_metabolite_identifications","text":"

URI: nmdc:has_metabolite_identifications

"},{"location":"has_metabolite_identifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysis no"},{"location":"has_metabolite_identifications/#properties","title":"Properties","text":""},{"location":"has_metabolite_identifications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_metabolite_identifications/#schema-source","title":"Schema Source","text":""},{"location":"has_metabolite_identifications/#linkml-source","title":"LinkML Source","text":"
name: has_metabolite_identifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_metabolite_identifications\ndomain_of:\n- MetabolomicsAnalysis\nrange: MetaboliteIdentification\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"has_minimum_numeric_value/","title":"Slot: has_minimum_numeric_value","text":"

The minimum value part, expressed as number, of the quantity value when the value covers a range.

URI: nmdc:has_minimum_numeric_value

"},{"location":"has_minimum_numeric_value/#inheritance","title":"Inheritance","text":""},{"location":"has_minimum_numeric_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e no"},{"location":"has_minimum_numeric_value/#properties","title":"Properties","text":""},{"location":"has_minimum_numeric_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_minimum_numeric_value/#schema-source","title":"Schema Source","text":""},{"location":"has_minimum_numeric_value/#linkml-source","title":"LinkML Source","text":"
name: has_minimum_numeric_value\ndescription: The minimum value part, expressed as number, of the quantity value when\n  the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_minimum_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\n
"},{"location":"has_numeric_value/","title":"Slot: has_numeric_value","text":"

Links a quantity value to a number

URI: nmdc:has_numeric_value

"},{"location":"has_numeric_value/#inheritance","title":"Inheritance","text":""},{"location":"has_numeric_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e yes"},{"location":"has_numeric_value/#properties","title":"Properties","text":""},{"location":"has_numeric_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_numeric_value/#schema-source","title":"Schema Source","text":""},{"location":"has_numeric_value/#linkml-source","title":"LinkML Source","text":"
name: has_numeric_value\ndescription: Links a quantity value to a number\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- qud:quantityValue\n- schema:value\nrank: 1000\nalias: has_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\n
"},{"location":"has_output/","title":"Slot: has_output","text":"

An output from a process.

URI: nmdc:has_output

"},{"location":"has_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow yes MetatranscriptomeAnnotation yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MetatranscriptomeAssembly no StorageProcess A planned process with the objective to preserve and protect material entitie... yes ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no PlannedProcess no MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... yes Pooling physical combination of several instances of like material yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e yes MetabolomicsAnalysis no ProtocolExecution A PlannedProces that has PlannedProcess parts yes LibraryPreparation yes"},{"location":"has_output/#properties","title":"Properties","text":""},{"location":"has_output/#aliases","title":"Aliases","text":""},{"location":"has_output/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_output/#schema-source","title":"Schema Source","text":""},{"location":"has_output/#linkml-source","title":"LinkML Source","text":"
name: has_output\ndescription: An output from a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- output\nrank: 1000\nalias: has_output\ndomain_of:\n- PlannedProcess\nrange: NamedThing\nmultivalued: true\n\n
"},{"location":"has_peptide_quantifications/","title":"Slot: has_peptide_quantifications","text":"

URI: nmdc:has_peptide_quantifications

"},{"location":"has_peptide_quantifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no"},{"location":"has_peptide_quantifications/#properties","title":"Properties","text":""},{"location":"has_peptide_quantifications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_peptide_quantifications/#schema-source","title":"Schema Source","text":""},{"location":"has_peptide_quantifications/#linkml-source","title":"LinkML Source","text":"
name: has_peptide_quantifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_peptide_quantifications\ndomain_of:\n- MetaproteomicsAnalysis\nrange: PeptideQuantification\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"has_process_parts/","title":"Slot: has_process_parts","text":"

A list of process parts that make up a protocol.

URI: nmdc:has_process_parts

"},{"location":"has_process_parts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProtocolExecution A PlannedProces that has PlannedProcess parts yes"},{"location":"has_process_parts/#properties","title":"Properties","text":""},{"location":"has_process_parts/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_process_parts/#schema-source","title":"Schema Source","text":""},{"location":"has_process_parts/#linkml-source","title":"LinkML Source","text":"
name: has_process_parts\ndescription: A list of process parts that make up a protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: has_process_parts\ndomain_of:\n- ProtocolExecution\nrange: PlannedProcess\nrequired: true\nmultivalued: true\n\n
"},{"location":"has_raw_value/","title":"Slot: has_raw_value","text":"

The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"

URI: nmdc:has_raw_value

"},{"location":"has_raw_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e yes TextValue A basic string value no PersonValue An attribute value representing a person yes ImageValue An attribute value representing an image no AttributeValue The value for any value of a attribute for a sample no ControlledTermValue A controlled term or class from an ontology no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no GeolocationValue A normalized value for a location on the earth's surface yes TimestampValue A value that is a timestamp no"},{"location":"has_raw_value/#properties","title":"Properties","text":""},{"location":"has_raw_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_raw_value/#schema-source","title":"Schema Source","text":""},{"location":"has_raw_value/#linkml-source","title":"LinkML Source","text":"
name: has_raw_value\ndescription: The value that was specified for an annotation in raw form, i.e. a string.\n  E.g. \"2 cm\" or \"2-4 cm\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_raw_value\ndomain_of:\n- AttributeValue\nrange: string\n\n
"},{"location":"has_unit/","title":"Slot: has_unit","text":"

Links a QuantityValue to a unit

URI: nmdc:has_unit

"},{"location":"has_unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e yes"},{"location":"has_unit/#properties","title":"Properties","text":""},{"location":"has_unit/#aliases","title":"Aliases","text":""},{"location":"has_unit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"has_unit/#schema-source","title":"Schema Source","text":""},{"location":"has_unit/#linkml-source","title":"LinkML Source","text":"
name: has_unit\ndescription: Links a QuantityValue to a unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- scale\nmappings:\n- qud:unit\n- schema:unitCode\nrank: 1000\nalias: has_unit\ndomain_of:\n- QuantityValue\nrange: unit\n\n
"},{"location":"hc_produced/","title":"Slot: hydrocarbon type produced (hc_produced)","text":"

Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000989

"},{"location":"hc_produced/#inheritance","title":"Inheritance","text":""},{"location":"hc_produced/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hc_produced/#properties","title":"Properties","text":""},{"location":"hc_produced/#aliases","title":"Aliases","text":""},{"location":"hc_produced/#examples","title":"Examples","text":"Value Gas"},{"location":"hc_produced/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hc_produced/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"hc_produced/#schema-source","title":"Schema Source","text":""},{"location":"hc_produced/#linkml-source","title":"LinkML Source","text":"
name: hc_produced\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n  etc). If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: hydrocarbon type produced\nexamples:\n- value: Gas\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon type produced\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000989\nalias: hc_produced\ndomain_of:\n- Biosample\nrange: hc_produced_enum\nmultivalued: false\n\n
"},{"location":"hcr/","title":"Slot: hydrocarbon resource type (hcr)","text":"

Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000988

"},{"location":"hcr/#inheritance","title":"Inheritance","text":""},{"location":"hcr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr/#properties","title":"Properties","text":""},{"location":"hcr/#aliases","title":"Aliases","text":""},{"location":"hcr/#examples","title":"Examples","text":"Value Oil Sand"},{"location":"hcr/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"hcr/#schema-source","title":"Schema Source","text":""},{"location":"hcr/#linkml-source","title":"LinkML Source","text":"
name: hcr\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined\n  as a natural environmental feature containing large amounts of hydrocarbons at high\n  concentrations potentially suitable for commercial exploitation. This term should\n  not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich\n  environments with currently limited commercial interest such as seeps, outcrops,\n  gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\"\n  field\ntitle: hydrocarbon resource type\nexamples:\n- value: Oil Sand\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000988\nalias: hcr\ndomain_of:\n- Biosample\nrange: hcr_enum\nmultivalued: false\n\n
"},{"location":"hcr_fw_salinity/","title":"Slot: formation water salinity (hcr_fw_salinity)","text":"

Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS

URI: MIXS:0000406

"},{"location":"hcr_fw_salinity/#inheritance","title":"Inheritance","text":""},{"location":"hcr_fw_salinity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr_fw_salinity/#properties","title":"Properties","text":""},{"location":"hcr_fw_salinity/#aliases","title":"Aliases","text":""},{"location":"hcr_fw_salinity/#examples","title":"Examples","text":"Value"},{"location":"hcr_fw_salinity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr_fw_salinity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"hcr_fw_salinity/#schema-source","title":"Schema Source","text":""},{"location":"hcr_fw_salinity/#linkml-source","title":"LinkML Source","text":"
name: hcr_fw_salinity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original formation water salinity (prior to secondary recovery e.g. Waterflooding)\n  expressed as TDS\ntitle: formation water salinity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- formation water salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000406\nalias: hcr_fw_salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"hcr_geol_age/","title":"Slot: hydrocarbon resource geological age (hcr_geol_age)","text":"

Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000993

"},{"location":"hcr_geol_age/#inheritance","title":"Inheritance","text":""},{"location":"hcr_geol_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr_geol_age/#properties","title":"Properties","text":""},{"location":"hcr_geol_age/#aliases","title":"Aliases","text":""},{"location":"hcr_geol_age/#examples","title":"Examples","text":"Value Silurian"},{"location":"hcr_geol_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr_geol_age/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"hcr_geol_age/#schema-source","title":"Schema Source","text":""},{"location":"hcr_geol_age/#linkml-source","title":"LinkML Source","text":"
name: hcr_geol_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n  If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: hydrocarbon resource geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000993\nalias: hcr_geol_age\ndomain_of:\n- Biosample\nrange: hcr_geol_age_enum\nmultivalued: false\n\n
"},{"location":"hcr_pressure/","title":"Slot: hydrocarbon resource original pressure (hcr_pressure)","text":"

Original pressure of the hydrocarbon resource

URI: MIXS:0000395

"},{"location":"hcr_pressure/#inheritance","title":"Inheritance","text":""},{"location":"hcr_pressure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr_pressure/#properties","title":"Properties","text":""},{"location":"hcr_pressure/#aliases","title":"Aliases","text":""},{"location":"hcr_pressure/#examples","title":"Examples","text":"Value"},{"location":"hcr_pressure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr_pressure/#annotations","title":"Annotations","text":"property value expected_value measurement value range"},{"location":"hcr_pressure/#schema-source","title":"Schema Source","text":""},{"location":"hcr_pressure/#linkml-source","title":"LinkML Source","text":"
name: hcr_pressure\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: atmosphere, kilopascal\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original pressure of the hydrocarbon resource\ntitle: hydrocarbon resource original pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original pressure\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000395\nalias: hcr_pressure\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"hcr_temp/","title":"Slot: hydrocarbon resource original temperature (hcr_temp)","text":"

Original temperature of the hydrocarbon resource

URI: MIXS:0000393

"},{"location":"hcr_temp/#inheritance","title":"Inheritance","text":""},{"location":"hcr_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"hcr_temp/#properties","title":"Properties","text":""},{"location":"hcr_temp/#aliases","title":"Aliases","text":""},{"location":"hcr_temp/#examples","title":"Examples","text":"Value 150-295 degree Celsius"},{"location":"hcr_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"hcr_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value range"},{"location":"hcr_temp/#schema-source","title":"Schema Source","text":""},{"location":"hcr_temp/#linkml-source","title":"LinkML Source","text":"
name: hcr_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original temperature of the hydrocarbon resource\ntitle: hydrocarbon resource original temperature\nexamples:\n- value: 150-295 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original temperature\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000393\nalias: hcr_temp\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"heat_cool_type/","title":"Slot: heating and cooling system type (heat_cool_type)","text":"

Methods of conditioning or heating a room or building

URI: MIXS:0000766

"},{"location":"heat_cool_type/#inheritance","title":"Inheritance","text":""},{"location":"heat_cool_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"heat_cool_type/#properties","title":"Properties","text":""},{"location":"heat_cool_type/#aliases","title":"Aliases","text":""},{"location":"heat_cool_type/#examples","title":"Examples","text":"Value heat pump"},{"location":"heat_cool_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heat_cool_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"heat_cool_type/#schema-source","title":"Schema Source","text":""},{"location":"heat_cool_type/#linkml-source","title":"LinkML Source","text":"
name: heat_cool_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Methods of conditioning or heating a room or building\ntitle: heating and cooling system type\nexamples:\n- value: heat pump\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating and cooling system type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000766\nalias: heat_cool_type\ndomain_of:\n- Biosample\nrange: heat_cool_type_enum\nmultivalued: true\n\n
"},{"location":"heat_deliv_loc/","title":"Slot: heating delivery locations (heat_deliv_loc)","text":"

The location of heat delivery within the room

URI: MIXS:0000810

"},{"location":"heat_deliv_loc/#inheritance","title":"Inheritance","text":""},{"location":"heat_deliv_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"heat_deliv_loc/#properties","title":"Properties","text":""},{"location":"heat_deliv_loc/#aliases","title":"Aliases","text":""},{"location":"heat_deliv_loc/#examples","title":"Examples","text":"Value north"},{"location":"heat_deliv_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heat_deliv_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"heat_deliv_loc/#schema-source","title":"Schema Source","text":""},{"location":"heat_deliv_loc/#linkml-source","title":"LinkML Source","text":"
name: heat_deliv_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The location of heat delivery within the room\ntitle: heating delivery locations\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating delivery locations\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000810\nalias: heat_deliv_loc\ndomain_of:\n- Biosample\nrange: heat_deliv_loc_enum\nmultivalued: false\n\n
"},{"location":"heat_sys_deliv_meth/","title":"Slot: heating system delivery method (heat_sys_deliv_meth)","text":"

The method by which the heat is delivered through the system

URI: MIXS:0000812

"},{"location":"heat_sys_deliv_meth/#inheritance","title":"Inheritance","text":""},{"location":"heat_sys_deliv_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"heat_sys_deliv_meth/#properties","title":"Properties","text":""},{"location":"heat_sys_deliv_meth/#aliases","title":"Aliases","text":""},{"location":"heat_sys_deliv_meth/#examples","title":"Examples","text":"Value radiant"},{"location":"heat_sys_deliv_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heat_sys_deliv_meth/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"heat_sys_deliv_meth/#schema-source","title":"Schema Source","text":""},{"location":"heat_sys_deliv_meth/#linkml-source","title":"LinkML Source","text":"
name: heat_sys_deliv_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The method by which the heat is delivered through the system\ntitle: heating system delivery method\nexamples:\n- value: radiant\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system delivery method\nrank: 1000\nis_a: core field\nstring_serialization: '[conductive|radiant]'\nslot_uri: MIXS:0000812\nalias: heat_sys_deliv_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"heat_system_id/","title":"Slot: heating system identifier (heat_system_id)","text":"

The heating system identifier

URI: MIXS:0000833

"},{"location":"heat_system_id/#inheritance","title":"Inheritance","text":""},{"location":"heat_system_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"heat_system_id/#properties","title":"Properties","text":""},{"location":"heat_system_id/#aliases","title":"Aliases","text":""},{"location":"heat_system_id/#examples","title":"Examples","text":"Value"},{"location":"heat_system_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heat_system_id/#annotations","title":"Annotations","text":"property value expected_value unique identifier"},{"location":"heat_system_id/#schema-source","title":"Schema Source","text":""},{"location":"heat_system_id/#linkml-source","title":"LinkML Source","text":"
name: heat_system_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: unique identifier\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The heating system identifier\ntitle: heating system identifier\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000833\nalias: heat_system_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"heavy_metals/","title":"Slot: extreme_unusual_properties/heavy metals (heavy_metals)","text":"

Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.

URI: MIXS:0000652

"},{"location":"heavy_metals/#inheritance","title":"Inheritance","text":""},{"location":"heavy_metals/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"heavy_metals/#properties","title":"Properties","text":""},{"location":"heavy_metals/#aliases","title":"Aliases","text":""},{"location":"heavy_metals/#examples","title":"Examples","text":"Value mercury;0.09 micrograms per gram"},{"location":"heavy_metals/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heavy_metals/#annotations","title":"Annotations","text":"property value expected_value heavy metal name;measurement value unit"},{"location":"heavy_metals/#schema-source","title":"Schema Source","text":""},{"location":"heavy_metals/#linkml-source","title":"LinkML Source","text":"
name: heavy_metals\nannotations:\n  expected_value:\n    tag: expected_value\n    value: heavy metal name;measurement value unit\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per gram\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Heavy metals present in the sequenced sample and their concentrations.\n  For multiple heavy metals and concentrations, add multiple copies of this field.\ntitle: extreme_unusual_properties/heavy metals\nexamples:\n- value: mercury;0.09 micrograms per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000652\nalias: heavy_metals\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"heavy_metals_meth/","title":"Slot: extreme_unusual_properties/heavy metals method (heavy_metals_meth)","text":"

Reference or method used in determining heavy metals

URI: MIXS:0000343

"},{"location":"heavy_metals_meth/#inheritance","title":"Inheritance","text":""},{"location":"heavy_metals_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"heavy_metals_meth/#properties","title":"Properties","text":""},{"location":"heavy_metals_meth/#aliases","title":"Aliases","text":""},{"location":"heavy_metals_meth/#examples","title":"Examples","text":"Value"},{"location":"heavy_metals_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"heavy_metals_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"heavy_metals_meth/#schema-source","title":"Schema Source","text":""},{"location":"heavy_metals_meth/#linkml-source","title":"LinkML Source","text":"
name: heavy_metals_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining heavy metals\ntitle: extreme_unusual_properties/heavy metals method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000343\nalias: heavy_metals_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"height_carper_fiber/","title":"Slot: height carpet fiber mat (height_carper_fiber)","text":"

The average carpet fiber height in the indoor environment

URI: MIXS:0000167

"},{"location":"height_carper_fiber/#inheritance","title":"Inheritance","text":""},{"location":"height_carper_fiber/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"height_carper_fiber/#properties","title":"Properties","text":""},{"location":"height_carper_fiber/#aliases","title":"Aliases","text":""},{"location":"height_carper_fiber/#examples","title":"Examples","text":"Value"},{"location":"height_carper_fiber/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"height_carper_fiber/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"height_carper_fiber/#schema-source","title":"Schema Source","text":""},{"location":"height_carper_fiber/#linkml-source","title":"LinkML Source","text":"
name: height_carper_fiber\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average carpet fiber height in the indoor environment\ntitle: height carpet fiber mat\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- height carpet fiber mat\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000167\nalias: height_carper_fiber\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"herbicide_regm/","title":"Slot: herbicide regimen (herbicide_regm)","text":"

Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000561

"},{"location":"herbicide_regm/#inheritance","title":"Inheritance","text":""},{"location":"herbicide_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"herbicide_regm/#properties","title":"Properties","text":""},{"location":"herbicide_regm/#aliases","title":"Aliases","text":""},{"location":"herbicide_regm/#examples","title":"Examples","text":"Value atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"herbicide_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"herbicide_regm/#annotations","title":"Annotations","text":"property value expected_value herbicide name;herbicide amount;treatment interval and duration"},{"location":"herbicide_regm/#schema-source","title":"Schema Source","text":""},{"location":"herbicide_regm/#linkml-source","title":"LinkML Source","text":"
name: herbicide_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: herbicide name;herbicide amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of herbicides; information\n  about treatment involving use of growth hormones; should include the name of herbicide,\n  amount administered, treatment regimen including how many times the treatment was\n  repeated, how long each treatment lasted, and the start and end time of the entire\n  treatment; can include multiple regimens\ntitle: herbicide regimen\nexamples:\n- value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- herbicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000561\nalias: herbicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"highest_similarity_score/","title":"Slot: highest_similarity_score","text":"

URI: nmdc:highest_similarity_score

"},{"location":"highest_similarity_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"highest_similarity_score/#properties","title":"Properties","text":""},{"location":"highest_similarity_score/#todos","title":"TODOs","text":""},{"location":"highest_similarity_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"highest_similarity_score/#schema-source","title":"Schema Source","text":""},{"location":"highest_similarity_score/#linkml-source","title":"LinkML Source","text":"
name: highest_similarity_score\ntodos:\n- Yuri to fill in description\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: highest_similarity_score\ndomain_of:\n- MetaboliteIdentification\nrange: float\n\n
"},{"location":"homepage_website/","title":"Slot: homepage_website","text":"

The website address (URL) of an entity's homepage.

URI: nmdc:homepage_website

"},{"location":"homepage_website/#inheritance","title":"Inheritance","text":""},{"location":"homepage_website/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"homepage_website/#properties","title":"Properties","text":""},{"location":"homepage_website/#examples","title":"Examples","text":"Value https://www.neonscience.org/"},{"location":"homepage_website/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"homepage_website/#schema-source","title":"Schema Source","text":""},{"location":"homepage_website/#linkml-source","title":"LinkML Source","text":"
name: homepage_website\ndescription: The website address (URL) of an entity's homepage.\nexamples:\n- value: https://www.neonscience.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: websites\nalias: homepage_website\ndomain_of:\n- Study\nrange: string\nmultivalued: true\npattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\nmaximum_cardinality: 1\n\n
"},{"location":"horizon_meth/","title":"Slot: soil horizon method (horizon_meth)","text":"

Reference or method used in determining the horizon

URI: MIXS:0000321

"},{"location":"horizon_meth/#inheritance","title":"Inheritance","text":""},{"location":"horizon_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"horizon_meth/#properties","title":"Properties","text":""},{"location":"horizon_meth/#aliases","title":"Aliases","text":""},{"location":"horizon_meth/#examples","title":"Examples","text":"Value"},{"location":"horizon_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"horizon_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"horizon_meth/#schema-source","title":"Schema Source","text":""},{"location":"horizon_meth/#linkml-source","title":"LinkML Source","text":"
name: horizon_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining the horizon\ntitle: soil horizon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000321\nalias: horizon_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_age/","title":"Slot: host age (host_age)","text":"

Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees

URI: MIXS:0000255

"},{"location":"host_age/#inheritance","title":"Inheritance","text":""},{"location":"host_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_age/#properties","title":"Properties","text":""},{"location":"host_age/#aliases","title":"Aliases","text":""},{"location":"host_age/#examples","title":"Examples","text":"Value 10 days"},{"location":"host_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_age/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"host_age/#schema-source","title":"Schema Source","text":""},{"location":"host_age/#linkml-source","title":"LinkML Source","text":"
name: host_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: year, day, hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Age of host at the time of sampling; relevant scale depends on species\n  and study, e.g. Could be seconds for amoebae or centuries for trees\ntitle: host age\nexamples:\n- value: 10 days\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000255\nalias: host_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_body_habitat/","title":"Slot: host body habitat (host_body_habitat)","text":"

Original body habitat where the sample was obtained from

URI: MIXS:0000866

"},{"location":"host_body_habitat/#inheritance","title":"Inheritance","text":""},{"location":"host_body_habitat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_body_habitat/#properties","title":"Properties","text":""},{"location":"host_body_habitat/#aliases","title":"Aliases","text":""},{"location":"host_body_habitat/#examples","title":"Examples","text":"Value nasopharynx"},{"location":"host_body_habitat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_body_habitat/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"host_body_habitat/#schema-source","title":"Schema Source","text":""},{"location":"host_body_habitat/#linkml-source","title":"LinkML Source","text":"
name: host_body_habitat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original body habitat where the sample was obtained from\ntitle: host body habitat\nexamples:\n- value: nasopharynx\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body habitat\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000866\nalias: host_body_habitat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_body_product/","title":"Slot: host body product (host_body_product)","text":"

Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon

URI: MIXS:0000888

"},{"location":"host_body_product/#inheritance","title":"Inheritance","text":""},{"location":"host_body_product/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_body_product/#properties","title":"Properties","text":""},{"location":"host_body_product/#aliases","title":"Aliases","text":""},{"location":"host_body_product/#examples","title":"Examples","text":"Value Portion of mucus [fma66938]"},{"location":"host_body_product/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_body_product/#annotations","title":"Annotations","text":"property value expected_value FMA or UBERON"},{"location":"host_body_product/#schema-source","title":"Schema Source","text":""},{"location":"host_body_product/#linkml-source","title":"LinkML Source","text":"
name: host_body_product\nannotations:\n  expected_value:\n    tag: expected_value\n    value: FMA or UBERON\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Substance produced by the body, e.g. Stool, mucus, where the sample was\n  obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n  ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or\n  https://www.ebi.ac.uk/ols/ontologies/uberon\ntitle: host body product\nexamples:\n- value: Portion of mucus [fma66938]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body product\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000888\nalias: host_body_product\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"host_body_site/","title":"Slot: host body site (host_body_site)","text":"

Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON

URI: MIXS:0000867

"},{"location":"host_body_site/#inheritance","title":"Inheritance","text":""},{"location":"host_body_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_body_site/#properties","title":"Properties","text":""},{"location":"host_body_site/#aliases","title":"Aliases","text":""},{"location":"host_body_site/#examples","title":"Examples","text":"Value gill [UBERON:0002535]"},{"location":"host_body_site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_body_site/#annotations","title":"Annotations","text":"property value expected_value FMA or UBERON"},{"location":"host_body_site/#schema-source","title":"Schema Source","text":""},{"location":"host_body_site/#linkml-source","title":"LinkML Source","text":"
name: host_body_site\nannotations:\n  expected_value:\n    tag: expected_value\n    value: FMA or UBERON\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of body site where the sample was obtained from, such as a specific\n  organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n  (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n  please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\ntitle: host body site\nexamples:\n- value: gill [UBERON:0002535]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body site\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000867\nalias: host_body_site\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"host_body_temp/","title":"Slot: host body temperature (host_body_temp)","text":"

Core body temperature of the host when sample was collected

URI: MIXS:0000274

"},{"location":"host_body_temp/#inheritance","title":"Inheritance","text":""},{"location":"host_body_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_body_temp/#properties","title":"Properties","text":""},{"location":"host_body_temp/#aliases","title":"Aliases","text":""},{"location":"host_body_temp/#examples","title":"Examples","text":"Value 15 degree Celsius"},{"location":"host_body_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_body_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_body_temp/#schema-source","title":"Schema Source","text":""},{"location":"host_body_temp/#linkml-source","title":"LinkML Source","text":"
name: host_body_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Core body temperature of the host when sample was collected\ntitle: host body temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000274\nalias: host_body_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_color/","title":"Slot: host color (host_color)","text":"

The color of host

URI: MIXS:0000260

"},{"location":"host_color/#inheritance","title":"Inheritance","text":""},{"location":"host_color/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_color/#properties","title":"Properties","text":""},{"location":"host_color/#aliases","title":"Aliases","text":""},{"location":"host_color/#examples","title":"Examples","text":"Value"},{"location":"host_color/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_color/#annotations","title":"Annotations","text":"property value expected_value color"},{"location":"host_color/#schema-source","title":"Schema Source","text":""},{"location":"host_color/#linkml-source","title":"LinkML Source","text":"
name: host_color\nannotations:\n  expected_value:\n    tag: expected_value\n    value: color\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The color of host\ntitle: host color\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host color\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000260\nalias: host_color\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_common_name/","title":"Slot: host common name (host_common_name)","text":"

Common name of the host.

URI: MIXS:0000248

"},{"location":"host_common_name/#inheritance","title":"Inheritance","text":""},{"location":"host_common_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_common_name/#properties","title":"Properties","text":""},{"location":"host_common_name/#aliases","title":"Aliases","text":""},{"location":"host_common_name/#examples","title":"Examples","text":"Value human"},{"location":"host_common_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_common_name/#annotations","title":"Annotations","text":"property value expected_value common name"},{"location":"host_common_name/#schema-source","title":"Schema Source","text":""},{"location":"host_common_name/#linkml-source","title":"LinkML Source","text":"
name: host_common_name\nannotations:\n  expected_value:\n    tag: expected_value\n    value: common name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Common name of the host.\ntitle: host common name\nexamples:\n- value: human\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host common name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000248\nalias: host_common_name\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_diet/","title":"Slot: host diet (host_diet)","text":"

Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types

URI: MIXS:0000869

"},{"location":"host_diet/#inheritance","title":"Inheritance","text":""},{"location":"host_diet/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_diet/#properties","title":"Properties","text":""},{"location":"host_diet/#aliases","title":"Aliases","text":""},{"location":"host_diet/#examples","title":"Examples","text":"Value herbivore"},{"location":"host_diet/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_diet/#annotations","title":"Annotations","text":"property value expected_value diet type"},{"location":"host_diet/#schema-source","title":"Schema Source","text":""},{"location":"host_diet/#linkml-source","title":"LinkML Source","text":"
name: host_diet\nannotations:\n  expected_value:\n    tag: expected_value\n    value: diet type\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Type of diet depending on the host, for animals omnivore, herbivore etc.,\n  for humans high-fat, meditteranean etc.; can include multiple diet types\ntitle: host diet\nexamples:\n- value: herbivore\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host diet\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000869\nalias: host_diet\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"host_disease_stat/","title":"Slot: host disease status (host_disease_stat)","text":"

List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text

URI: MIXS:0000031

"},{"location":"host_disease_stat/#inheritance","title":"Inheritance","text":""},{"location":"host_disease_stat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_disease_stat/#properties","title":"Properties","text":""},{"location":"host_disease_stat/#aliases","title":"Aliases","text":""},{"location":"host_disease_stat/#examples","title":"Examples","text":"Value rabies [DOID:11260]"},{"location":"host_disease_stat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_disease_stat/#annotations","title":"Annotations","text":"property value expected_value disease name or Disease Ontology term"},{"location":"host_disease_stat/#schema-source","title":"Schema Source","text":""},{"location":"host_disease_stat/#linkml-source","title":"LinkML Source","text":"
name: host_disease_stat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: disease name or Disease Ontology term\ndescription: List of diseases with which the host has been diagnosed; can include\n  multiple diagnoses. The value of the field depends on host; for humans the terms\n  should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,\n  non-human host diseases are free text\ntitle: host disease status\nexamples:\n- value: rabies [DOID:11260]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host disease status\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000031\nalias: host_disease_stat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_dry_mass/","title":"Slot: host dry mass (host_dry_mass)","text":"

Measurement of dry mass

URI: MIXS:0000257

"},{"location":"host_dry_mass/#inheritance","title":"Inheritance","text":""},{"location":"host_dry_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_dry_mass/#properties","title":"Properties","text":""},{"location":"host_dry_mass/#aliases","title":"Aliases","text":""},{"location":"host_dry_mass/#examples","title":"Examples","text":"Value 500 gram"},{"location":"host_dry_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_dry_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_dry_mass/#schema-source","title":"Schema Source","text":""},{"location":"host_dry_mass/#linkml-source","title":"LinkML Source","text":"
name: host_dry_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilogram, gram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of dry mass\ntitle: host dry mass\nexamples:\n- value: 500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host dry mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000257\nalias: host_dry_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_family_relation/","title":"Slot: host family relationship (host_family_relation)","text":"

Familial relationships to other hosts in the same study; can include multiple relationships

URI: MIXS:0000872

"},{"location":"host_family_relation/#inheritance","title":"Inheritance","text":""},{"location":"host_family_relation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_family_relation/#properties","title":"Properties","text":""},{"location":"host_family_relation/#aliases","title":"Aliases","text":""},{"location":"host_family_relation/#examples","title":"Examples","text":"Value offspring;Mussel25"},{"location":"host_family_relation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_family_relation/#annotations","title":"Annotations","text":"property value expected_value relationship type;arbitrary identifier"},{"location":"host_family_relation/#schema-source","title":"Schema Source","text":""},{"location":"host_family_relation/#linkml-source","title":"LinkML Source","text":"
name: host_family_relation\nannotations:\n  expected_value:\n    tag: expected_value\n    value: relationship type;arbitrary identifier\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Familial relationships to other hosts in the same study; can include\n  multiple relationships\ntitle: host family relationship\nexamples:\n- value: offspring;Mussel25\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host family relationship\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0000872\nalias: host_family_relation\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\n
"},{"location":"host_genotype/","title":"Slot: host genotype (host_genotype)","text":"

Observed genotype

URI: MIXS:0000365

"},{"location":"host_genotype/#inheritance","title":"Inheritance","text":""},{"location":"host_genotype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_genotype/#properties","title":"Properties","text":""},{"location":"host_genotype/#aliases","title":"Aliases","text":""},{"location":"host_genotype/#examples","title":"Examples","text":"Value C57BL/6"},{"location":"host_genotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_genotype/#annotations","title":"Annotations","text":"property value expected_value genotype"},{"location":"host_genotype/#schema-source","title":"Schema Source","text":""},{"location":"host_genotype/#linkml-source","title":"LinkML Source","text":"
name: host_genotype\nannotations:\n  expected_value:\n    tag: expected_value\n    value: genotype\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Observed genotype\ntitle: host genotype\nexamples:\n- value: C57BL/6\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host genotype\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000365\nalias: host_genotype\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_growth_cond/","title":"Slot: host growth conditions (host_growth_cond)","text":"

Literature reference giving growth conditions of the host

URI: MIXS:0000871

"},{"location":"host_growth_cond/#inheritance","title":"Inheritance","text":""},{"location":"host_growth_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_growth_cond/#properties","title":"Properties","text":""},{"location":"host_growth_cond/#aliases","title":"Aliases","text":""},{"location":"host_growth_cond/#examples","title":"Examples","text":"Value https://academic.oup.com/icesjms/article/68/2/349/617247"},{"location":"host_growth_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_growth_cond/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url or free text"},{"location":"host_growth_cond/#schema-source","title":"Schema Source","text":""},{"location":"host_growth_cond/#linkml-source","title":"LinkML Source","text":"
name: host_growth_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url or free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Literature reference giving growth conditions of the host\ntitle: host growth conditions\nexamples:\n- value: https://academic.oup.com/icesjms/article/68/2/349/617247\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host growth conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000871\nalias: host_growth_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_height/","title":"Slot: host height (host_height)","text":"

The height of subject

URI: MIXS:0000264

"},{"location":"host_height/#inheritance","title":"Inheritance","text":""},{"location":"host_height/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_height/#properties","title":"Properties","text":""},{"location":"host_height/#aliases","title":"Aliases","text":""},{"location":"host_height/#examples","title":"Examples","text":"Value 0.1 meter"},{"location":"host_height/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_height/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_height/#schema-source","title":"Schema Source","text":""},{"location":"host_height/#linkml-source","title":"LinkML Source","text":"
name: host_height\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: centimeter, millimeter, meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The height of subject\ntitle: host height\nexamples:\n- value: 0.1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000264\nalias: host_height\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_last_meal/","title":"Slot: host last meal (host_last_meal)","text":"

Content of last meal and time since feeding; can include multiple values

URI: MIXS:0000870

"},{"location":"host_last_meal/#inheritance","title":"Inheritance","text":""},{"location":"host_last_meal/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_last_meal/#properties","title":"Properties","text":""},{"location":"host_last_meal/#aliases","title":"Aliases","text":""},{"location":"host_last_meal/#examples","title":"Examples","text":"Value corn feed;P2H"},{"location":"host_last_meal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_last_meal/#annotations","title":"Annotations","text":"property value expected_value content;duration"},{"location":"host_last_meal/#schema-source","title":"Schema Source","text":""},{"location":"host_last_meal/#linkml-source","title":"LinkML Source","text":"
name: host_last_meal\nannotations:\n  expected_value:\n    tag: expected_value\n    value: content;duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Content of last meal and time since feeding; can include multiple values\ntitle: host last meal\nexamples:\n- value: corn feed;P2H\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host last meal\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000870\nalias: host_last_meal\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"host_length/","title":"Slot: host length (host_length)","text":"

The length of subject

URI: MIXS:0000256

"},{"location":"host_length/#inheritance","title":"Inheritance","text":""},{"location":"host_length/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_length/#properties","title":"Properties","text":""},{"location":"host_length/#aliases","title":"Aliases","text":""},{"location":"host_length/#examples","title":"Examples","text":"Value 1 meter"},{"location":"host_length/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_length/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_length/#schema-source","title":"Schema Source","text":""},{"location":"host_length/#linkml-source","title":"LinkML Source","text":"
name: host_length\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: centimeter, millimeter, meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The length of subject\ntitle: host length\nexamples:\n- value: 1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host length\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000256\nalias: host_length\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_life_stage/","title":"Slot: host life stage (host_life_stage)","text":"

Description of life stage of host

URI: MIXS:0000251

"},{"location":"host_life_stage/#inheritance","title":"Inheritance","text":""},{"location":"host_life_stage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_life_stage/#properties","title":"Properties","text":""},{"location":"host_life_stage/#aliases","title":"Aliases","text":""},{"location":"host_life_stage/#examples","title":"Examples","text":"Value adult"},{"location":"host_life_stage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_life_stage/#annotations","title":"Annotations","text":"property value expected_value stage"},{"location":"host_life_stage/#schema-source","title":"Schema Source","text":""},{"location":"host_life_stage/#linkml-source","title":"LinkML Source","text":"
name: host_life_stage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: stage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Description of life stage of host\ntitle: host life stage\nexamples:\n- value: adult\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host life stage\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000251\nalias: host_life_stage\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_name/","title":"Slot: host_name","text":"

URI: nmdc:host_name

"},{"location":"host_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_name/#properties","title":"Properties","text":""},{"location":"host_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_name/#schema-source","title":"Schema Source","text":""},{"location":"host_name/#linkml-source","title":"LinkML Source","text":"
name: host_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: host_name\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"host_phenotype/","title":"Slot: host phenotype (host_phenotype)","text":"

Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP

URI: MIXS:0000874

"},{"location":"host_phenotype/#inheritance","title":"Inheritance","text":""},{"location":"host_phenotype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_phenotype/#properties","title":"Properties","text":""},{"location":"host_phenotype/#aliases","title":"Aliases","text":""},{"location":"host_phenotype/#examples","title":"Examples","text":"Value elongated [PATO:0001154]"},{"location":"host_phenotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_phenotype/#annotations","title":"Annotations","text":"property value expected_value PATO or HP"},{"location":"host_phenotype/#schema-source","title":"Schema Source","text":""},{"location":"host_phenotype/#linkml-source","title":"LinkML Source","text":"
name: host_phenotype\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PATO or HP\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Phenotype of human or other host. For phenotypic quality ontology (pato)\n  (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For\n  Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\ntitle: host phenotype\nexamples:\n- value: elongated [PATO:0001154]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host phenotype\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000874\nalias: host_phenotype\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"host_sex/","title":"Slot: host sex (host_sex)","text":"

Gender or physical sex of the host.

URI: MIXS:0000811

"},{"location":"host_sex/#inheritance","title":"Inheritance","text":""},{"location":"host_sex/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_sex/#properties","title":"Properties","text":""},{"location":"host_sex/#aliases","title":"Aliases","text":""},{"location":"host_sex/#examples","title":"Examples","text":"Value non-binary"},{"location":"host_sex/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_sex/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"host_sex/#schema-source","title":"Schema Source","text":""},{"location":"host_sex/#linkml-source","title":"LinkML Source","text":"
name: host_sex\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Gender or physical sex of the host.\ntitle: host sex\nexamples:\n- value: non-binary\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000811\nalias: host_sex\ndomain_of:\n- Biosample\nrange: host_sex_enum\nmultivalued: false\n\n
"},{"location":"host_shape/","title":"Slot: host shape (host_shape)","text":"

Morphological shape of host

URI: MIXS:0000261

"},{"location":"host_shape/#inheritance","title":"Inheritance","text":""},{"location":"host_shape/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_shape/#properties","title":"Properties","text":""},{"location":"host_shape/#aliases","title":"Aliases","text":""},{"location":"host_shape/#examples","title":"Examples","text":"Value round"},{"location":"host_shape/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_shape/#annotations","title":"Annotations","text":"property value expected_value shape"},{"location":"host_shape/#schema-source","title":"Schema Source","text":""},{"location":"host_shape/#linkml-source","title":"LinkML Source","text":"
name: host_shape\nannotations:\n  expected_value:\n    tag: expected_value\n    value: shape\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Morphological shape of host\ntitle: host shape\nexamples:\n- value: round\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host shape\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000261\nalias: host_shape\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_subject_id/","title":"Slot: host subject id (host_subject_id)","text":"

A unique identifier by which each subject can be referred to, de-identified.

URI: MIXS:0000861

"},{"location":"host_subject_id/#inheritance","title":"Inheritance","text":""},{"location":"host_subject_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_subject_id/#properties","title":"Properties","text":""},{"location":"host_subject_id/#aliases","title":"Aliases","text":""},{"location":"host_subject_id/#examples","title":"Examples","text":"Value MPI123"},{"location":"host_subject_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_subject_id/#annotations","title":"Annotations","text":"property value expected_value unique identifier"},{"location":"host_subject_id/#schema-source","title":"Schema Source","text":""},{"location":"host_subject_id/#linkml-source","title":"LinkML Source","text":"
name: host_subject_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: unique identifier\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A unique identifier by which each subject can be referred to, de-identified.\ntitle: host subject id\nexamples:\n- value: MPI123\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subject id\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000861\nalias: host_subject_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_subspecf_genlin/","title":"Slot: host subspecific genetic lineage (host_subspecf_genlin)","text":"

Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.

URI: MIXS:0001318

"},{"location":"host_subspecf_genlin/#inheritance","title":"Inheritance","text":""},{"location":"host_subspecf_genlin/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_subspecf_genlin/#properties","title":"Properties","text":""},{"location":"host_subspecf_genlin/#aliases","title":"Aliases","text":""},{"location":"host_subspecf_genlin/#examples","title":"Examples","text":"Value serovar:Newport, variety:glabrum, cultivar: Red Delicious"},{"location":"host_subspecf_genlin/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_subspecf_genlin/#annotations","title":"Annotations","text":"property value expected_value Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar."},{"location":"host_subspecf_genlin/#schema-source","title":"Schema Source","text":""},{"location":"host_subspecf_genlin/#linkml-source","title":"LinkML Source","text":"
name: host_subspecf_genlin\nannotations:\n  expected_value:\n    tag: expected_value\n    value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n      e.g. serovar, biotype, ecotype, variety, cultivar.\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about the genetic distinctness of the host organism below\n  the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n  or any relevant genetic typing schemes like Group I plasmid. Subspecies should not\n  be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name\n  and the lineage rank separated by a colon, e.g., biovar:abc123.\ntitle: host subspecific genetic lineage\nexamples:\n- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subspecific genetic lineage\nrank: 1000\nis_a: core field\nstring_serialization: '{rank name}:{text}'\nslot_uri: MIXS:0001318\nalias: host_subspecf_genlin\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\n
"},{"location":"host_substrate/","title":"Slot: host substrate (host_substrate)","text":"

The growth substrate of the host.

URI: MIXS:0000252

"},{"location":"host_substrate/#inheritance","title":"Inheritance","text":""},{"location":"host_substrate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_substrate/#properties","title":"Properties","text":""},{"location":"host_substrate/#aliases","title":"Aliases","text":""},{"location":"host_substrate/#examples","title":"Examples","text":"Value rock"},{"location":"host_substrate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_substrate/#annotations","title":"Annotations","text":"property value expected_value substrate name"},{"location":"host_substrate/#schema-source","title":"Schema Source","text":""},{"location":"host_substrate/#linkml-source","title":"LinkML Source","text":"
name: host_substrate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: substrate name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The growth substrate of the host.\ntitle: host substrate\nexamples:\n- value: rock\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host substrate\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000252\nalias: host_substrate\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"host_symbiont/","title":"Slot: observed host symbionts (host_symbiont)","text":"

The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.

URI: MIXS:0001298

"},{"location":"host_symbiont/#inheritance","title":"Inheritance","text":""},{"location":"host_symbiont/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_symbiont/#properties","title":"Properties","text":""},{"location":"host_symbiont/#aliases","title":"Aliases","text":""},{"location":"host_symbiont/#examples","title":"Examples","text":"Value flukeworms"},{"location":"host_symbiont/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_symbiont/#annotations","title":"Annotations","text":"property value expected_value species name or common name"},{"location":"host_symbiont/#schema-source","title":"Schema Source","text":""},{"location":"host_symbiont/#linkml-source","title":"LinkML Source","text":"
name: host_symbiont\nannotations:\n  expected_value:\n    tag: expected_value\n    value: species name or common name\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: The taxonomic name of the organism(s) found living in mutualistic, commensalistic,\n  or parasitic symbiosis with the specific host.\ntitle: observed host symbionts\nexamples:\n- value: flukeworms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed host symbionts\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001298\nalias: host_symbiont\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\n
"},{"location":"host_taxid/","title":"Slot: host taxid (host_taxid)","text":"

NCBI taxon id of the host, e.g. 9606

URI: MIXS:0000250

"},{"location":"host_taxid/#inheritance","title":"Inheritance","text":""},{"location":"host_taxid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_taxid/#properties","title":"Properties","text":""},{"location":"host_taxid/#aliases","title":"Aliases","text":""},{"location":"host_taxid/#comments","title":"Comments","text":""},{"location":"host_taxid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_taxid/#annotations","title":"Annotations","text":"property value expected_value NCBI taxon identifier"},{"location":"host_taxid/#schema-source","title":"Schema Source","text":""},{"location":"host_taxid/#linkml-source","title":"LinkML Source","text":"
name: host_taxid\nannotations:\n  expected_value:\n    tag: expected_value\n    value: NCBI taxon identifier\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: NCBI taxon id of the host, e.g. 9606\ntitle: host taxid\ncomments:\n- Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host taxid\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000250\nalias: host_taxid\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"host_tot_mass/","title":"Slot: host total mass (host_tot_mass)","text":"

Total mass of the host at collection, the unit depends on host

URI: MIXS:0000263

"},{"location":"host_tot_mass/#inheritance","title":"Inheritance","text":""},{"location":"host_tot_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_tot_mass/#properties","title":"Properties","text":""},{"location":"host_tot_mass/#aliases","title":"Aliases","text":""},{"location":"host_tot_mass/#examples","title":"Examples","text":"Value 2500 gram"},{"location":"host_tot_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_tot_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_tot_mass/#schema-source","title":"Schema Source","text":""},{"location":"host_tot_mass/#linkml-source","title":"LinkML Source","text":"
name: host_tot_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilogram, gram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total mass of the host at collection, the unit depends on host\ntitle: host total mass\nexamples:\n- value: 2500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host total mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000263\nalias: host_tot_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"host_wet_mass/","title":"Slot: host wet mass (host_wet_mass)","text":"

Measurement of wet mass

URI: MIXS:0000567

"},{"location":"host_wet_mass/#inheritance","title":"Inheritance","text":""},{"location":"host_wet_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_wet_mass/#properties","title":"Properties","text":""},{"location":"host_wet_mass/#aliases","title":"Aliases","text":""},{"location":"host_wet_mass/#examples","title":"Examples","text":"Value 1500 gram"},{"location":"host_wet_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"host_wet_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"host_wet_mass/#schema-source","title":"Schema Source","text":""},{"location":"host_wet_mass/#linkml-source","title":"LinkML Source","text":"
name: host_wet_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilogram, gram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of wet mass\ntitle: host wet mass\nexamples:\n- value: 1500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host wet mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000567\nalias: host_wet_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"humidity/","title":"Slot: humidity (humidity)","text":"

Amount of water vapour in the air, at the time of sampling

URI: MIXS:0000100

"},{"location":"humidity/#inheritance","title":"Inheritance","text":""},{"location":"humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"humidity/#properties","title":"Properties","text":""},{"location":"humidity/#aliases","title":"Aliases","text":""},{"location":"humidity/#examples","title":"Examples","text":"Value 25 gram per cubic meter"},{"location":"humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"humidity/#schema-source","title":"Schema Source","text":""},{"location":"humidity/#linkml-source","title":"LinkML Source","text":"
name: humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per cubic meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Amount of water vapour in the air, at the time of sampling\ntitle: humidity\nexamples:\n- value: 25 gram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000100\nalias: humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"humidity_regm/","title":"Slot: humidity regimen (humidity_regm)","text":"

Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000568

"},{"location":"humidity_regm/#inheritance","title":"Inheritance","text":""},{"location":"humidity_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"humidity_regm/#properties","title":"Properties","text":""},{"location":"humidity_regm/#aliases","title":"Aliases","text":""},{"location":"humidity_regm/#examples","title":"Examples","text":"Value 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"humidity_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"humidity_regm/#annotations","title":"Annotations","text":"property value expected_value humidity value;treatment interval and duration"},{"location":"humidity_regm/#schema-source","title":"Schema Source","text":""},{"location":"humidity_regm/#linkml-source","title":"LinkML Source","text":"
name: humidity_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: humidity value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per cubic meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to varying degree of\n  humidity; information about treatment involving use of growth hormones; should include\n  amount of humidity administered, treatment regimen including how many times the\n  treatment was repeated, how long each treatment lasted, and the start and end time\n  of the entire treatment; can include multiple regimens\ntitle: humidity regimen\nexamples:\n- value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000568\nalias: humidity_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"id/","title":"Slot: id","text":"

A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI

URI: nmdc:id

"},{"location":"id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes Site no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MaterialEntity no MetatranscriptomeAssembly yes Configuration A set of parameters that define the actions of a process and is shared among ... no StorageProcess A planned process with the objective to preserve and protect material entitie... yes ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... yes Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DataObject An object that primarily consists of symbols that represent information yes PlannedProcess no EnvironmentalMaterialTerm no NamedThing a databased entity or concept/class no MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes ProcessedSample yes ChemicalEntity An atom or molecule that can be represented with a chemical formula no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes CollectingBiosamplesFromSite yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... yes MetagenomeSequencing Initial sequencing activity that precedes any analysis yes NomAnalysis yes Instrument A material entity that is designed to perform a function in a scientific inve... yes InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no GeneProduct A molecule encoded by a gene that has an evolved function no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... yes Study A study summarizes the overall goal of a research initiative and outlines the... yes MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes CalibrationInformation A calibration object that is associated with a process yes Extraction A material separation in which a desired component of an input material is se... yes FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Pooling physical combination of several instances of like material yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component yes OntologyClass yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated yes MetaproteomicsAnalysis yes FiltrationProcess The process of segregation of phases; e yes MetabolomicsAnalysis yes ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes ProtocolExecution A PlannedProces that has PlannedProcess parts yes Manifest yes OrthologyGroup A set of genes or gene products in which all members are orthologous no Biosample Biological source material which can be characterized by an experiment yes LibraryPreparation yes"},{"location":"id/#properties","title":"Properties","text":""},{"location":"id/#examples","title":"Examples","text":"Value nmdc:mgmag-00-x012.1_7_c1"},{"location":"id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"id/#schema-source","title":"Schema Source","text":""},{"location":"id/#linkml-source","title":"LinkML Source","text":"
name: id\ndescription: A unique identifier for a thing. Must be either a CURIE shorthand for\n  a URI or a complete URI\nnotes:\n- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n  will be accepted\n- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n  via per-class id slot usage assertions\n- minting authority shoulders should probably be enumerated and checked in the pattern\nexamples:\n- value: nmdc:mgmag-00-x012.1_7_c1\n  description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- NamedThing\nrange: uriorcurie\nrequired: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"identifiers/","title":"Identifiers in NMDC","text":"

Identifiers are crucial for the NMDC, both for any data objects created (aka minted) and for any external objects referenced

Examples of entities that require identifiers:

Identifiers should be:

See McMurry et al, PMID:28662064 for more desiderata.

"},{"location":"identifiers/#curies-prefixed-ids","title":"CURIEs - prefixed IDs","text":"

Following McMurry et al we adopt the use of prefixed identifiers

The syntax is:

Prefix:LocalId\n

Examples:

These prefixed identifiers are also known as CURIEs (Compact URIs). There is a W3C specification for these

All prefixes should be registered with a standard identifier prefix system. These include:

"},{"location":"identifiers/#examples","title":"Examples","text":""},{"location":"identifiers/#insdc-biosamples","title":"INSDC BioSamples","text":"

Registry entry: https://registry.identifiers.org/registry/biosample

Example ID/CURIE: BIOSAMPLE:SAMEA2397676

Resolving via identifiers.org: https://identifiers.org/BIOSAMPLE:SAMEA2397676

Resolving via nt2.net: http://n2t.net/BIOSAMPLE:SAMEA2397676

"},{"location":"identifiers/#gold-identifiers","title":"GOLD identifiers","text":"

https://registry.identifiers.org/registry/gold

Example ID: GOLD:Gp0119849

Resolving via identifiers.org: https://identifiers.org/GOLD:Gp0119849

"},{"location":"identifiers/#identifiers-for-ontology-terms-and-function-descriptors","title":"identifiers for ontology terms and function descriptors","text":"

Most of the ontologies we use are in OBO. All OBO IDs are prefixed using the ontology ID space. The list of ID spaces can be found on http://obofoundry.org

For example the ID/CURIE ENVO:00002007 represents the class sediment and is expanded to a URI of http://purl.obolibrary.org/obo/ENVO_00002007

"},{"location":"identifiers/#kegg","title":"KEGG","text":"

KEGG is actually a set of databases, each with its own prefix, usually of form KEGG.$database, e.g.

"},{"location":"identifiers/#recommended-ids-for-use-within-nmdc","title":"Recommended IDs for use within NMDC","text":"

The NMDC schema is annotated with the set of IDs that are allowed to act as primary keys for instances of each class.

For example the class OrthologyGroup has a description of the IDs allowed on the class web page, the first listed is KEGG.ORTHOLOGY

The underlying yaml looks like this:

  orthology group:\n    is_a: functional annotation term\n    description: >-\n      A set of genes or gene products in which all members are orthologous\n    id_prefixes:\n      - KEGG.ORTHOLOGY  ## KO number\n      - EGGNOG\n      - PFAM\n      - TIGRFAM\n      - SUPFAM\n      - PANTHER.FAMILY\n    exact_mappings:\n      - biolink:GeneFamily\n

The full URLs for each is in the jsonld context file

"},{"location":"identifiers/#ids-minted-for-use-within-nmdc","title":"IDs minted for use within NMDC","text":"

The NMDC schema specifies legal identifiers for all of its classes. All data instances/records that are intended for upload into the NMDC metadata store must have an id field that follows this specification, which is discussed below.

NMDC offers a central identifier minting endpoint in order to save data contributors the trouble of hand-crafting ids.

The possibility of decentralized (or offline) minting of ids by trusted organizations has also been anticipated. id component 3 below (the shoulder) is used to indicate the organization that minted an id. LBL, which hosts the id minting endpoint will use one shoulder value. If another organization, like JGI or EMSL, needs to bulk-create ids outside of the central identifier minting endpoint, they would use different shoulders, to be determined by the NMDC schema and metadata team.

No matter where they are minted, all NMDC id values must match this abstract pattern:

nmdc:<type-code>-<shoulder>-<blade><.version><_locus>\n

The abstract pattern has six parts, delimited by hyphens (unless otherwise specified):

  1. nmdc: All NMDC identifiers will begin with this static prefix.

  2. <typecode>: An alphabetical code with a 1:1 correspondence to a class from the NMDC schema. Answers the question \"of what class is the data record that bears this id\"? Must consist of 1 to 6 lower case letters, although a minimum of 3 letters is suggested. The type code portion of an NMDC id must match the regular expression [a-z]{1,6}.

  3. <shoulder>: A code that indicates what organization minted the identifier. Shoulder values must be zero to six lower case letters, flanked by one digit on either side. Answers the question \"what organization minted this id\"? The central identifier endpoint, hosted at LBL, uses the shoulder 00. Should organizations like JGI or EMSL need to mint identifiers in bulk, they would be assigned other shoulders, so that id values aren't reused. The shoulder portion of an NMDC id must match the regular expression [0-9][a-z]{0,6}[0-9].

  4. <blade>: The fully unique part of the identifier under a given type code and shoulder namespace. The shoulder and blade together make up the key of the identifier. The blade is an alphanumeric string of open-ended length with at least one character, following the regular expression: [A-Za-z0-9]+.

  5. <.version>: Differentiates multiple iterations of a workflow. The delimiter used to separate the version from the blade and everything before it is a dot (.). The version is a potentially repeating alphanumeric pattern with a minimum length of 1 character. The version portion of an NMDC id must match the regular expression (\\.[A-Za-z0-9]+)*.

  6. <_locus>: Indicates the contig on which a genomic feature is found, along with its start and end coordinates. Delimited from the rest of the id by an underscore (_). The locus part, if present, must have at least one character from the set off uppercase letters, lower case letters, digits, underscores (_), dots (.) and hyphens (-). The regular expression that the locus will follow is: _[A-Za-z0-9_\\.-]+.

The per-part regular expression described above can be composed into one complete regular expression. Named capture groups have been used to tie in the part names.

^(?<prefix>nmdc):(?<typecode>[a-z]{1,6})-(?<shoulder>[0-9][a-z]{0,6}[0-9])-(?<blade>[A-Za-z0-9]+)(?<version>(\\.[A-Za-z0-9]+)*)(?<locus>_[A-Za-z0-9_\\.-]+)?$\n
"},{"location":"identifiers/#annotation-identifiers","title":"Annotation identifiers","text":"

Both metaG and metaT analyses produce GFF3 files. See issue 184 for more on how the GFF is modeled.

The main entity we care about in these is the [gene product] https://microbiomedata.github.io/nmdc-metadata/docs/GeneProduct) ID (usually a protein), this is what functional annotation hangs off.

This is typically a protein encoded by a CDS, e.g.

Ga0185794_41    GeneMark.hmm-2 v1.05    CDS     48      1037    56.13   +       0       ID=Ga0185794_41_48_1037;translation_table=11;start_type=ATG;product=5-methylthioadenosine/S-adenosylhomocysteine deaminase;product_source=KO:K12960;cath_funfam=3.20.20.140;cog=COG0402;ko=KO:K12960;ec_number=EC:3.5.4.28,EC:3.5.4.31;pfam=PF01979;superfamily=51338,51556\n

When converting col9 we ensure that each ID is correctly prefixed. So for example, we use KEGG.OTHOLOGY:K12960 not KO:K12960 as the former is the official prefix according to KEGG and identifiers.org

We will also later need a policy for IDs for the sequences in col1 (ie genome or transcript), please return later for more details...

"},{"location":"identifiers/#reuse-vs-minting-new-ids","title":"Reuse vs minting new IDs","text":"

In 2023 NMDC transitioned from reusing identifiers from other organizations to using NMDC minted identifiers as the primary identifier. In April 2024 NMDC will update legacy records to use NMDC minted identifers as the primary identifier. The table below provides information is how legacy identifiers can be found in updated records.

"},{"location":"identifiers/#identifier-mapping","title":"Identifier mapping","text":"Identifier Example NMDC Schema Class NMDC Schema Slot gold:Gs* gold:Gs0114675 Study gold_study_identifiers gold:Gb* gold:Gb0110739 Biosample gold_biosample_identifiers emsl:* emsl:63ca2f94-6647-11eb-ae93-0242ac130002 Biosample emsl_biosample_identifiers igsn:* igsn:IEWFS001H Biosample igsn_biosample_identifiers gold:Gp* gold:Gp0452734 OmicsProcessing gold_sequencing_project_identifiers emsl:* emsl:598506 OmicsProcessing alternative_identifiers

Some legacy data object identifiers were based on file md5sums, either with or without a prefix (nmdc, jgi, emsl). In some cases the legacy value can be found by removing the prefix and searching DataObject records on slot md5_checksum. If you are having trouble finding information based on legacy identifiers please contact support@microbiomedata.org.

"},{"location":"identifiers/#additional-details-on-legacy-identifiers","title":"Additional details on legacy identifiers","text":"

Legacy metagenomics omics objects look like this:

      id: \"gold:Gp0108335\"\n      name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n      has_input:\n        - \"gold:Gb0108335\"\n      part_of:\n        - \"gold:Gs0112340\"\n      has_output:\n        - \"jgi:551a20d30d878525404e90d5\"\n      omics_type: Metagenome\n      type: \"nmdc:OmicsProcessing\"\n      add_date: \"30-OCT-14 12.00.00.000000000 AM\"\n      mod_date: \"22-MAY-20 06.13.12.927000000 PM\"\n      ncbi_project_name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n      processing_institution: \"Joint Genome Institute\"\n      principal_investigator_name: \"Virginia Rich\"\n

the linked data object uses a jgi prefix and an md5 hash

      id: \"jgi:551a20d30d878525404e90d5\"\n      name: \"8871.1.114459.GCCAAT.fastq.gz\"\n      description: \"Raw sequencer read data\"\n      file_size_bytes: 17586370657\n      type: \"nmdc:DataObject\"\n

Legacy metaproteomics omics objects look like this:

      id: \"emsl:404590\"\n      name: \"FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n      description: \"High res MS with low res CID MSn\"\n      part_of:\n        - \"gold:Gs0110132\"\n      has_output:\n        - \"emsl:output_404590\"\n      omics_type: Proteomics\n      type: \"nmdc:OmicsProcessing\"\n      instrument_name: \"VOrbiETD03\"\n      processing_institution: \"Environmental Molecular Sciences Lab\"\n

the output data objects are formed from these:

      id: \"emsl:output_404590\"\n      name: \"output: FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n      description: \"High res MS with low res CID MSn\"\n      file_size_bytes: 503296678\n      type: \"nmdc:DataObject\"\n

the data objects use hashes (md5) prefixed with nmdc:

      name: \"404590_resultant.tsv\"\n      description: \"Aggregation of analysis tools{MSGFplus, MASIC} results\"\n      file_size_bytes: 10948480\n      type: \"nmdc:DataObject\"\n      id: \"nmdc:e0c70280a7a23c7c5cc1e589f72e896e\"\n
"},{"location":"identifiers/#mixs-term-identifiers","title":"MIxS term identifiers","text":"

We are working with the GSC to provide permanent IDs for MIxS terms. Note these terms are schema-level rather than data-level.

Please check this section later

For now we place these in the nmdc namespaces, e.g

nmdc:alt

"},{"location":"identifiers/#identifiers-and-semantic-web-uris","title":"Identifiers and semantic web URIs","text":"

We produce a JSON-LD context with the schema:

When this is combined with schema-conformant JSON, RDF can be automatically created using the intended URIs

"},{"location":"igsn_biosample_identifiers/","title":"Slot: IGSN Biosample Identifiers (igsn_biosample_identifiers)","text":"

A list of identifiers for the biosample from the IGSN database.

URI: nmdc:igsn_biosample_identifiers

"},{"location":"igsn_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"igsn_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"igsn_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"igsn_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"igsn_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"igsn_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: igsn_biosample_identifiers\ndescription: A list of identifiers for the biosample from the IGSN database.\ntitle: IGSN Biosample Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- igsn_identifiers\nalias: igsn_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"igsn_identifiers/","title":"Slot: igsn_identifiers","text":"

URI: nmdc:igsn_identifiers

"},{"location":"igsn_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database None Biosample"},{"location":"igsn_identifiers/#properties","title":"Properties","text":""},{"location":"igsn_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"igsn_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"igsn_identifiers/#linkml-source","title":"LinkML Source","text":"
name: igsn_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: igsn_identifiers\nrange: string\n\n
"},{"location":"img_identifiers/","title":"Slot: IMG Identifiers (img_identifiers)","text":"

A list of identifiers that relate the biosample to records in the IMG database.

URI: nmdc:img_identifiers

"},{"location":"img_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"img_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAnnotation yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes Biosample Biological source material which can be characterized by an experiment no"},{"location":"img_identifiers/#properties","title":"Properties","text":""},{"location":"img_identifiers/#todos","title":"TODOs","text":""},{"location":"img_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"img_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"img_identifiers/#linkml-source","title":"LinkML Source","text":"
name: img_identifiers\ndescription: A list of identifiers that relate the biosample to records in the IMG\n  database.\ntitle: IMG Identifiers\ntodos:\n- add is_a or mixin modeling, like other external_database_identifiers\n- what class would IMG records belong to?! Are they Studies, Biosamples, or something\n  else?\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nalias: img_identifiers\ndomain_of:\n- MetagenomeAnnotation\n- Biosample\n- MetatranscriptomeAnnotation\n- MetatranscriptomeExpressionAnalysis\n- MagsAnalysis\nrange: external_identifier\nmultivalued: true\npattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n\n
"},{"location":"in_manifest/","title":"Slot: in_manifest","text":"

URI: nmdc:in_manifest

"},{"location":"in_manifest/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"in_manifest/#properties","title":"Properties","text":""},{"location":"in_manifest/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"in_manifest/#schema-source","title":"Schema Source","text":""},{"location":"in_manifest/#linkml-source","title":"LinkML Source","text":"
name: in_manifest\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: in_manifest\ndomain_of:\n- DataObject\nrange: Manifest\nmultivalued: true\n\n
"},{"location":"inchi/","title":"Slot: inchi","text":"

URI: nmdc:inchi

"},{"location":"inchi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"inchi/#properties","title":"Properties","text":""},{"location":"inchi/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"inchi/#schema-source","title":"Schema Source","text":""},{"location":"inchi/#linkml-source","title":"LinkML Source","text":"
name: inchi\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi\ndomain_of:\n- ChemicalEntity\nrange: string\n\n
"},{"location":"inchi_key/","title":"Slot: inchi_key","text":"

URI: nmdc:inchi_key

"},{"location":"inchi_key/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"inchi_key/#properties","title":"Properties","text":""},{"location":"inchi_key/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"inchi_key/#schema-source","title":"Schema Source","text":""},{"location":"inchi_key/#linkml-source","title":"LinkML Source","text":"
name: inchi_key\nnotes:\n- 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n  K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n  testing. J Cheminform. 4:12'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi_key\ndomain_of:\n- ChemicalEntity\nrange: string\n\n
"},{"location":"indoor_space/","title":"Slot: indoor space (indoor_space)","text":"

A distinguishable space within a structure, the purpose for which discrete areas of a building is used

URI: MIXS:0000763

"},{"location":"indoor_space/#inheritance","title":"Inheritance","text":""},{"location":"indoor_space/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"indoor_space/#properties","title":"Properties","text":""},{"location":"indoor_space/#aliases","title":"Aliases","text":""},{"location":"indoor_space/#examples","title":"Examples","text":"Value foyer"},{"location":"indoor_space/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"indoor_space/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"indoor_space/#schema-source","title":"Schema Source","text":""},{"location":"indoor_space/#linkml-source","title":"LinkML Source","text":"
name: indoor_space\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A distinguishable space within a structure, the purpose for which discrete\n  areas of a building is used\ntitle: indoor space\nexamples:\n- value: foyer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor space\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000763\nalias: indoor_space\ndomain_of:\n- Biosample\nrange: indoor_space_enum\nmultivalued: false\n\n
"},{"location":"indoor_surf/","title":"Slot: indoor surface (indoor_surf)","text":"

Type of indoor surface

URI: MIXS:0000764

"},{"location":"indoor_surf/#inheritance","title":"Inheritance","text":""},{"location":"indoor_surf/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"indoor_surf/#properties","title":"Properties","text":""},{"location":"indoor_surf/#aliases","title":"Aliases","text":""},{"location":"indoor_surf/#examples","title":"Examples","text":"Value wall"},{"location":"indoor_surf/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"indoor_surf/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"indoor_surf/#schema-source","title":"Schema Source","text":""},{"location":"indoor_surf/#linkml-source","title":"LinkML Source","text":"
name: indoor_surf\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Type of indoor surface\ntitle: indoor surface\nexamples:\n- value: wall\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor surface\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000764\nalias: indoor_surf\ndomain_of:\n- Biosample\nrange: indoor_surf_enum\nmultivalued: false\n\n
"},{"location":"indust_eff_percent/","title":"Slot: industrial effluent percent (indust_eff_percent)","text":"

Percentage of industrial effluents received by wastewater treatment plant

URI: MIXS:0000662

"},{"location":"indust_eff_percent/#inheritance","title":"Inheritance","text":""},{"location":"indust_eff_percent/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"indust_eff_percent/#properties","title":"Properties","text":""},{"location":"indust_eff_percent/#aliases","title":"Aliases","text":""},{"location":"indust_eff_percent/#examples","title":"Examples","text":"Value"},{"location":"indust_eff_percent/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"indust_eff_percent/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"indust_eff_percent/#schema-source","title":"Schema Source","text":""},{"location":"indust_eff_percent/#linkml-source","title":"LinkML Source","text":"
name: indust_eff_percent\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Percentage of industrial effluents received by wastewater treatment plant\ntitle: industrial effluent percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- industrial effluent percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000662\nalias: indust_eff_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"infiltrations/","title":"Slot: infiltrations","text":"

The amount of time it takes to complete each infiltration activity

URI: nmdc:infiltrations

"},{"location":"infiltrations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"infiltrations/#properties","title":"Properties","text":""},{"location":"infiltrations/#aliases","title":"Aliases","text":""},{"location":"infiltrations/#examples","title":"Examples","text":"Value ['00:01:32', '00:00:53']"},{"location":"infiltrations/#see-also","title":"See Also","text":""},{"location":"infiltrations/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"infiltrations/#schema-source","title":"Schema Source","text":""},{"location":"infiltrations/#linkml-source","title":"LinkML Source","text":"
name: infiltrations\ndescription: The amount of time it takes to complete each infiltration activity\nexamples:\n- value: '[''00:01:32'', ''00:00:53'']'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1\naliases:\n- infiltration_1\n- infiltration_2\nrank: 1000\nlist_elements_ordered: true\nalias: infiltrations\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\npattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$\n\n
"},{"location":"inorg_particles/","title":"Slot: inorganic particles (inorg_particles)","text":"

Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles

URI: MIXS:0000664

"},{"location":"inorg_particles/#inheritance","title":"Inheritance","text":""},{"location":"inorg_particles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"inorg_particles/#properties","title":"Properties","text":""},{"location":"inorg_particles/#aliases","title":"Aliases","text":""},{"location":"inorg_particles/#examples","title":"Examples","text":"Value"},{"location":"inorg_particles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"inorg_particles/#annotations","title":"Annotations","text":"property value expected_value inorganic particle name;measurement value"},{"location":"inorg_particles/#schema-source","title":"Schema Source","text":""},{"location":"inorg_particles/#linkml-source","title":"LinkML Source","text":"
name: inorg_particles\nannotations:\n  expected_value:\n    tag: expected_value\n    value: inorganic particle name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of particles such as sand, grit, metal particles, ceramics,\n  etc.; can include multiple particles\ntitle: inorganic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inorganic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000664\nalias: inorg_particles\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"input_base_count/","title":"Slot: input_base_count","text":"

The nucleotide base count number of input reads for QC analysis.

URI: nmdc:input_base_count

"},{"location":"input_base_count/#inheritance","title":"Inheritance","text":""},{"location":"input_base_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_base_count/#properties","title":"Properties","text":""},{"location":"input_base_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_base_count/#schema-source","title":"Schema Source","text":""},{"location":"input_base_count/#linkml-source","title":"LinkML Source","text":"
name: input_base_count\ndescription: The nucleotide base count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_base_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"input_contig_num/","title":"Slot: input_contig_num","text":"

URI: nmdc:input_contig_num

"},{"location":"input_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"input_contig_num/#properties","title":"Properties","text":""},{"location":"input_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"input_contig_num/#linkml-source","title":"LinkML Source","text":"
name: input_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"input_mass/","title":"Slot: sample mass used (input_mass)","text":"

Total mass of sample used in activity.

URI: nmdc:input_mass

"},{"location":"input_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"input_mass/#properties","title":"Properties","text":""},{"location":"input_mass/#aliases","title":"Aliases","text":""},{"location":"input_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_mass/#schema-source","title":"Schema Source","text":""},{"location":"input_mass/#linkml-source","title":"LinkML Source","text":"
name: input_mass\ndescription: Total mass of sample used in activity.\ntitle: sample mass used\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample mass\n- sample weight\nexact_mappings:\n- MS:1000004\nnarrow_mappings:\n- MIXS:0000111\nrank: 1000\nalias: input_mass\ndomain_of:\n- Extraction\nrange: QuantityValue\n\n
"},{"location":"input_read_bases/","title":"Slot: input_read_bases","text":"

_TODO _

URI: nmdc:input_read_bases

"},{"location":"input_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_read_bases/#properties","title":"Properties","text":""},{"location":"input_read_bases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_read_bases/#schema-source","title":"Schema Source","text":""},{"location":"input_read_bases/#linkml-source","title":"LinkML Source","text":"
name: input_read_bases\ndescription: 'TODO      '\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_read_bases\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"input_read_count/","title":"Slot: input_read_count","text":"

The sequence count number of input reads for QC analysis.

URI: nmdc:input_read_count

"},{"location":"input_read_count/#inheritance","title":"Inheritance","text":""},{"location":"input_read_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_read_count/#properties","title":"Properties","text":""},{"location":"input_read_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_read_count/#schema-source","title":"Schema Source","text":""},{"location":"input_read_count/#linkml-source","title":"LinkML Source","text":"
name: input_read_count\ndescription: The sequence count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_read_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"input_volume/","title":"Slot: input_volume","text":"

The volume of the input sample.

URI: nmdc:input_volume

"},{"location":"input_volume/#properties","title":"Properties","text":""},{"location":"input_volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"input_volume/#schema-source","title":"Schema Source","text":""},{"location":"input_volume/#linkml-source","title":"LinkML Source","text":"
name: input_volume\ndescription: The volume of the input sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_volume\nrange: QuantityValue\n\n
"},{"location":"insdc_analysis_identifiers/","title":"Slot: insdc_analysis_identifiers","text":"

URI: nmdc:insdc_analysis_identifiers

"},{"location":"insdc_analysis_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_analysis_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_analysis_identifiers/#examples","title":"Examples","text":"Value https://www.ebi.ac.uk/metagenomics/runs/DRR218479 https://www.ebi.ac.uk/ena/browser/view/ERR436051"},{"location":"insdc_analysis_identifiers/#comments","title":"Comments","text":""},{"location":"insdc_analysis_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_analysis_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_analysis_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_analysis_identifiers\ncomments:\n- in INSDC this is a run but it corresponds to a GOLD analysis\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/runs/DRR218479\n  description: Illumina MiSeq paired end sequencing of SAMD00212331\n- value: https://www.ebi.ac.uk/ena/browser/view/ERR436051\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$\n\n
"},{"location":"insdc_assembly_identifiers/","title":"Slot: insdc_assembly_identifiers","text":"

URI: nmdc:insdc_assembly_identifiers

"},{"location":"insdc_assembly_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_assembly_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"insdc_assembly_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_assembly_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_assembly_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_assembly_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: assembly_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_assembly_identifiers\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: string\npattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n\n
"},{"location":"insdc_bioproject_identifiers/","title":"Slot: insdc_bioproject_identifiers","text":"

identifiers for corresponding project in INSDC Bioproject

URI: nmdc:insdc_bioproject_identifiers

"},{"location":"insdc_bioproject_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_bioproject_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"insdc_bioproject_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_bioproject_identifiers/#aliases","title":"Aliases","text":""},{"location":"insdc_bioproject_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/bioproject:PRJNA366857"},{"location":"insdc_bioproject_identifiers/#comments","title":"Comments","text":""},{"location":"insdc_bioproject_identifiers/#see-also","title":"See Also","text":""},{"location":"insdc_bioproject_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_bioproject_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_bioproject_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_bioproject_identifiers\ndescription: identifiers for corresponding project in INSDC Bioproject\ncomments:\n- these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n  one to one\nexamples:\n- value: https://bioregistry.io/bioproject:PRJNA366857\n  description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ncbi.nlm.nih.gov/bioproject/\n- https://www.ddbj.nig.ac.jp/bioproject/index-e.html\naliases:\n- NCBI bioproject identifiers\n- DDBJ bioproject identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_bioproject_identifiers\ndomain_of:\n- NucleotideSequencing\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n\n
"},{"location":"insdc_biosample_identifiers/","title":"Slot: insdc_biosample_identifiers","text":"

identifiers for corresponding sample in INSDC

URI: nmdc:insdc_biosample_identifiers

"},{"location":"insdc_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"insdc_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_biosample_identifiers/#aliases","title":"Aliases","text":""},{"location":"insdc_biosample_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/biosample:SAMEA5989477 https://bioregistry.io/biosample:SAMD00212331"},{"location":"insdc_biosample_identifiers/#see-also","title":"See Also","text":""},{"location":"insdc_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_biosample_identifiers\ndescription: identifiers for corresponding sample in INSDC\nexamples:\n- value: https://bioregistry.io/biosample:SAMEA5989477\n- value: https://bioregistry.io/biosample:SAMD00212331\n  description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/108\n- https://www.ebi.ac.uk/biosamples/\n- https://www.ncbi.nlm.nih.gov/biosample\n- https://www.ddbj.nig.ac.jp/biosample/index-e.html\naliases:\n- EBI biosample identifiers\n- NCBI biosample identifiers\n- DDBJ biosample identifiers\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n\n
"},{"location":"insdc_experiment_identifiers/","title":"Slot: insdc_experiment_identifiers","text":"

URI: nmdc:insdc_experiment_identifiers

"},{"location":"insdc_experiment_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_experiment_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"insdc_experiment_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_experiment_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_experiment_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_experiment_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_experiment_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_experiment_identifiers\ndomain_of:\n- NucleotideSequencing\n- DataObject\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n\n
"},{"location":"insdc_identifiers/","title":"Slot: insdc_identifiers","text":"

Any identifier covered by the International Nucleotide Sequence Database Collaboration

URI: nmdc:insdc_identifiers

"},{"location":"insdc_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA None insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject None Study, NucleotideSequencing insdc_biosample_identifiers identifiers for corresponding sample in INSDC None Biosample insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC None insdc_experiment_identifiers None DataObject, NucleotideSequencing insdc_analysis_identifiers None insdc_assembly_identifiers None MetatranscriptomeAssembly, MetagenomeAssembly"},{"location":"insdc_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_identifiers/#aliases","title":"Aliases","text":""},{"location":"insdc_identifiers/#comments","title":"Comments","text":""},{"location":"insdc_identifiers/#see-also","title":"See Also","text":""},{"location":"insdc_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_identifiers\ndescription: Any identifier covered by the International Nucleotide Sequence Database\n  Collaboration\ncomments:\n- note that we deliberately abstract over which of the partner databases accepted\n  the initial submission\n- 'the first letter of the accession indicates which partner accepted the initial\n  submission: E for ENA, D for DDBJ, or S or N for NCBI.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.insdc.org/\n- https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html\naliases:\n- EBI identifiers\n- NCBI identifiers\n- DDBJ identifiers\nrank: 1000\nmixin: true\nalias: insdc_identifiers\nrange: string\n\n
"},{"location":"insdc_secondary_sample_identifiers/","title":"Slot: insdc_secondary_sample_identifiers","text":"

secondary identifiers for corresponding sample in INSDC

URI: nmdc:insdc_secondary_sample_identifiers

"},{"location":"insdc_secondary_sample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_secondary_sample_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_secondary_sample_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/insdc.sra:DRS166340"},{"location":"insdc_secondary_sample_identifiers/#comments","title":"Comments","text":""},{"location":"insdc_secondary_sample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_secondary_sample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_secondary_sample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_secondary_sample_identifiers\ndescription: secondary identifiers for corresponding sample in INSDC\ncomments:\n- ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340\n  -> SAMD00212331\n- MGnify uses these as their primary sample IDs\nexamples:\n- value: https://bioregistry.io/insdc.sra:DRS166340\n  description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_secondary_sample_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^biosample:(E|D|S)RS[0-9]{6,}$\n\n
"},{"location":"insdc_sra_ena_study_identifiers/","title":"Slot: insdc_sra_ena_study_identifiers","text":"

identifiers for corresponding project in INSDC SRA / ENA

URI: nmdc:insdc_sra_ena_study_identifiers

"},{"location":"insdc_sra_ena_study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"insdc_sra_ena_study_identifiers/#properties","title":"Properties","text":""},{"location":"insdc_sra_ena_study_identifiers/#aliases","title":"Aliases","text":""},{"location":"insdc_sra_ena_study_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/insdc.sra:SRP121659"},{"location":"insdc_sra_ena_study_identifiers/#see-also","title":"See Also","text":""},{"location":"insdc_sra_ena_study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"insdc_sra_ena_study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"insdc_sra_ena_study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: insdc_sra_ena_study_identifiers\ndescription: identifiers for corresponding project in INSDC SRA / ENA\nexamples:\n- value: https://bioregistry.io/insdc.sra:SRP121659\n  description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/109\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\naliases:\n- EBI ENA study identifiers\n- NCBI SRA identifiers\n- DDBJ SRA identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_sra_ena_study_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$\n\n
"},{"location":"inside_lux/","title":"Slot: inside lux light (inside_lux)","text":"

The recorded value at sampling time (power density)

URI: MIXS:0000168

"},{"location":"inside_lux/#inheritance","title":"Inheritance","text":""},{"location":"inside_lux/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"inside_lux/#properties","title":"Properties","text":""},{"location":"inside_lux/#aliases","title":"Aliases","text":""},{"location":"inside_lux/#examples","title":"Examples","text":"Value"},{"location":"inside_lux/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"inside_lux/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"inside_lux/#schema-source","title":"Schema Source","text":""},{"location":"inside_lux/#linkml-source","title":"LinkML Source","text":"
name: inside_lux\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilowatt per square metre\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The recorded value at sampling time (power density)\ntitle: inside lux light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inside lux light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000168\nalias: inside_lux\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"instrument_set/","title":"Slot: instrument_set","text":"

This property links a database object to the set of instruments within it.

URI: nmdc:instrument_set

"},{"location":"instrument_set/#inheritance","title":"Inheritance","text":""},{"location":"instrument_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"instrument_set/#properties","title":"Properties","text":""},{"location":"instrument_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"instrument_set/#schema-source","title":"Schema Source","text":""},{"location":"instrument_set/#linkml-source","title":"LinkML Source","text":"
name: instrument_set\ndescription: This property links a database object to the set of instruments within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: instrument_set\ndomain_of:\n- Database\nrange: Instrument\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"instrument_used/","title":"Slot: instrument_used","text":"

What instrument was used during DataGeneration or MaterialProcessing.

URI: nmdc:instrument_used

"},{"location":"instrument_used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no FiltrationProcess The process of segregation of phases; e no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no Extraction A material separation in which a desired component of an input material is se... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no LibraryPreparation no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no"},{"location":"instrument_used/#properties","title":"Properties","text":""},{"location":"instrument_used/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"instrument_used/#schema-source","title":"Schema Source","text":""},{"location":"instrument_used/#linkml-source","title":"LinkML Source","text":"
name: instrument_used\ndescription: What instrument was used during DataGeneration or MaterialProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: instrument_used\ndomain_of:\n- MaterialProcessing\n- DataGeneration\nrange: Instrument\nmultivalued: true\n\n
"},{"location":"int_wall_cond/","title":"Slot: interior wall condition (int_wall_cond)","text":"

The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas

URI: MIXS:0000813

"},{"location":"int_wall_cond/#inheritance","title":"Inheritance","text":""},{"location":"int_wall_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"int_wall_cond/#properties","title":"Properties","text":""},{"location":"int_wall_cond/#aliases","title":"Aliases","text":""},{"location":"int_wall_cond/#examples","title":"Examples","text":"Value damaged"},{"location":"int_wall_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"int_wall_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"int_wall_cond/#schema-source","title":"Schema Source","text":""},{"location":"int_wall_cond/#linkml-source","title":"LinkML Source","text":"
name: int_wall_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the wall at the time of sampling; photos or\n  video preferred; use drawings to indicate location of damaged areas\ntitle: interior wall condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- interior wall condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000813\nalias: int_wall_cond\ndomain_of:\n- Biosample\nrange: int_wall_cond_enum\nmultivalued: false\n\n
"},{"location":"internal_calibration/","title":"Slot: internal_calibration","text":"

whether internal calibration was used, if false, external calibration was used

URI: nmdc:internal_calibration

"},{"location":"internal_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process yes"},{"location":"internal_calibration/#properties","title":"Properties","text":""},{"location":"internal_calibration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"internal_calibration/#schema-source","title":"Schema Source","text":""},{"location":"internal_calibration/#linkml-source","title":"LinkML Source","text":"
name: internal_calibration\ndescription: whether internal calibration was used, if false, external calibration\n  was used\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: internal_calibration\ndomain_of:\n- CalibrationInformation\nrange: boolean\n\n
"},{"location":"investigation_field/","title":"Slot: investigation_field","text":"

field describing aspect of the investigation/study to which the sample belongs

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:investigation_field

"},{"location":"investigation_field/#inheritance","title":"Inheritance","text":""},{"location":"investigation_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"investigation_field/#properties","title":"Properties","text":""},{"location":"investigation_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"investigation_field/#schema-source","title":"Schema Source","text":""},{"location":"investigation_field/#linkml-source","title":"LinkML Source","text":"
name: investigation field\ndescription: field describing aspect of the investigation/study to which the sample\n  belongs\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: investigation_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"ionization_source/","title":"Slot: ionization_source","text":"

The ionization source used to introduce processed samples into a mass spectrometer

URI: nmdc:ionization_source

"},{"location":"ionization_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"ionization_source/#properties","title":"Properties","text":""},{"location":"ionization_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ionization_source/#schema-source","title":"Schema Source","text":""},{"location":"ionization_source/#linkml-source","title":"LinkML Source","text":"
name: ionization_source\ndescription: The ionization source used to introduce processed samples into a mass\n  spectrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1000008\nrank: 1000\nalias: ionization_source\ndomain_of:\n- MassSpectrometryConfiguration\nrange: IonizationSourceEnum\n\n
"},{"location":"is_pressurized/","title":"Slot: is_pressurized","text":"

Whether or not pressure was applied to a thing or process.

URI: nmdc:is_pressurized

"},{"location":"is_pressurized/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"is_pressurized/#properties","title":"Properties","text":""},{"location":"is_pressurized/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"is_pressurized/#schema-source","title":"Schema Source","text":""},{"location":"is_pressurized/#linkml-source","title":"LinkML Source","text":"
name: is_pressurized\ndescription: Whether or not pressure was applied to a thing or process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_pressurized\ndomain_of:\n- FiltrationProcess\nrange: boolean\n\n
"},{"location":"is_stranded/","title":"Slot: is_stranded","text":"

Is the (RNA) library stranded or non-stranded (unstranded).

URI: nmdc:is_stranded

"},{"location":"is_stranded/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"is_stranded/#properties","title":"Properties","text":""},{"location":"is_stranded/#comments","title":"Comments","text":""},{"location":"is_stranded/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"is_stranded/#schema-source","title":"Schema Source","text":""},{"location":"is_stranded/#linkml-source","title":"LinkML Source","text":"
name: is_stranded\ndescription: Is the (RNA) library stranded or non-stranded (unstranded).\ncomments:\n- A value of true means the library is stranded, flase means non-stranded.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_stranded\ndomain_of:\n- LibraryPreparation\nrange: boolean\n\n
"},{"location":"isotope_exposure/","title":"Slot: isotope exposure/addition (isotope_exposure)","text":"

List isotope exposure or addition applied to your sample.

URI: nmdc:isotope_exposure

"},{"location":"isotope_exposure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"isotope_exposure/#properties","title":"Properties","text":""},{"location":"isotope_exposure/#examples","title":"Examples","text":"Value 13C glucose H218O"},{"location":"isotope_exposure/#comments","title":"Comments","text":""},{"location":"isotope_exposure/#todos","title":"TODOs","text":""},{"location":"isotope_exposure/#see-also","title":"See Also","text":""},{"location":"isotope_exposure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"isotope_exposure/#schema-source","title":"Schema Source","text":""},{"location":"isotope_exposure/#linkml-source","title":"LinkML Source","text":"
name: isotope_exposure\ndescription: List isotope exposure or addition applied to your sample.\ntitle: isotope exposure/addition\ntodos:\n- Can we make the H218O correctly super and subscripted?\ncomments:\n- This is required when your experimental design includes the use of isotopically\n  labeled compounds\nexamples:\n- value: 13C glucose\n- value: H218O\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000751\nrank: 16\nstring_serialization: '{termLabel} {[termID]}; {timestamp}'\nalias: isotope_exposure\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"iw_bt_date_well/","title":"Slot: injection water breakthrough date of specific well (iw_bt_date_well)","text":"

Injection water breakthrough date per well following a secondary and/or tertiary recovery

URI: MIXS:0001010

"},{"location":"iw_bt_date_well/#inheritance","title":"Inheritance","text":""},{"location":"iw_bt_date_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"iw_bt_date_well/#properties","title":"Properties","text":""},{"location":"iw_bt_date_well/#aliases","title":"Aliases","text":""},{"location":"iw_bt_date_well/#examples","title":"Examples","text":"Value 2018-05-11"},{"location":"iw_bt_date_well/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"iw_bt_date_well/#annotations","title":"Annotations","text":"property value expected_value timestamp"},{"location":"iw_bt_date_well/#schema-source","title":"Schema Source","text":""},{"location":"iw_bt_date_well/#linkml-source","title":"LinkML Source","text":"
name: iw_bt_date_well\nannotations:\n  expected_value:\n    tag: expected_value\n    value: timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Injection water breakthrough date per well following a secondary and/or\n  tertiary recovery\ntitle: injection water breakthrough date of specific well\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water breakthrough date of specific well\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001010\nalias: iw_bt_date_well\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"iwf/","title":"Slot: injection water fraction (iwf)","text":"

Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)

URI: MIXS:0000455

"},{"location":"iwf/#inheritance","title":"Inheritance","text":""},{"location":"iwf/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"iwf/#properties","title":"Properties","text":""},{"location":"iwf/#aliases","title":"Aliases","text":""},{"location":"iwf/#examples","title":"Examples","text":"Value"},{"location":"iwf/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"iwf/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"iwf/#schema-source","title":"Schema Source","text":""},{"location":"iwf/#linkml-source","title":"LinkML Source","text":"
name: iwf\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Proportion of the produced fluids derived from injected water at the\n  time of sampling. (e.g. 87%)\ntitle: injection water fraction\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water fraction\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000455\nalias: iwf\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"jgi_portal_analysis_project_identifiers/","title":"Slot: jgi_portal_analysis_project_identifiers","text":"

identifiers for corresponding analysis projects in JGI Portal

URI: nmdc:jgi_portal_analysis_project_identifiers

"},{"location":"jgi_portal_analysis_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"jgi_portal_analysis_project_identifiers/#properties","title":"Properties","text":""},{"location":"jgi_portal_analysis_project_identifiers/#examples","title":"Examples","text":"Value https://data.jgi.doe.gov/search?q=1414320"},{"location":"jgi_portal_analysis_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"jgi_portal_analysis_project_identifiers/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"jgi_portal_analysis_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"jgi_portal_analysis_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: jgi_portal_analysis_project_identifiers\nid_prefixes:\n- jgi.analysis\ndescription: identifiers for corresponding analysis projects in JGI Portal\nexamples:\n- value: https://data.jgi.doe.gov/search?q=1414320\n  description: Metagenome - Draft Assembly YELL_051-M-20210705-comp-DNA1\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- jgi_portal_identifiers\nalias: jgi_portal_analysis_project_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^jgi.analysis:[0-9]+$\n\n
"},{"location":"jgi_portal_identifiers/","title":"Slot: jgi_portal_identifiers","text":"

identifiers for entities according to JGI Portal

URI: nmdc:jgi_portal_identifiers

"},{"location":"jgi_portal_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... None Study jgi_portal_analysis_project_identifiers identifiers for corresponding analysis projects in JGI Portal None"},{"location":"jgi_portal_identifiers/#properties","title":"Properties","text":""},{"location":"jgi_portal_identifiers/#see-also","title":"See Also","text":""},{"location":"jgi_portal_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"jgi_portal_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"jgi_portal_identifiers/#linkml-source","title":"LinkML Source","text":"
name: jgi_portal_identifiers\ndescription: identifiers for entities according to JGI Portal\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://data.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: jgi_portal_identifiers\nrange: string\n\n
"},{"location":"jgi_portal_study_identifiers/","title":"Slot: JGI Portal Study identifiers (jgi_portal_study_identifiers)","text":"

Identifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier.

URI: nmdc:jgi_portal_study_identifiers

"},{"location":"jgi_portal_study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"jgi_portal_study_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"jgi_portal_study_identifiers/#properties","title":"Properties","text":""},{"location":"jgi_portal_study_identifiers/#examples","title":"Examples","text":"Value jgi.proposal:507130"},{"location":"jgi_portal_study_identifiers/#comments","title":"Comments","text":""},{"location":"jgi_portal_study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"jgi_portal_study_identifiers/#valid-id-prefixes","title":"Valid ID Prefixes","text":"

Instances of this class should have identifiers with one of the following prefixes:

"},{"location":"jgi_portal_study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"jgi_portal_study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: jgi_portal_study_identifiers\nid_prefixes:\n- jgi.proposal\ndescription: Identifiers that link a NMDC study to a website hosting raw and analyzed\n  data for a JGI proposal.  The suffix of the curie can used to query the GOLD API\n  and is interoperable with an award DOI from OSTI and a GOLD study identifier.\ntitle: JGI Portal Study identifiers\ncomments:\n- Could this could be considered a related identifier?\n- Curie suffix is the Site Award Number from an OSTI award page\n- Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD study\n  identifier gold:Gs0154044\n- bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\nexamples:\n- value: jgi.proposal:507130\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- jgi_portal_identifiers\nalias: jgi_portal_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^jgi.proposal:\\d+$\n\n
"},{"location":"known_as/","title":"Slot: known_as","text":"

URI: nmdc:known_as

"},{"location":"known_as/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"known_as/#properties","title":"Properties","text":""},{"location":"known_as/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"known_as/#schema-source","title":"Schema Source","text":""},{"location":"known_as/#linkml-source","title":"LinkML Source","text":"
name: known_as\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: known_as\ndomain_of:\n- PortionOfSubstance\nrange: ChemicalEntity\n\n
"},{"location":"language/","title":"Slot: language","text":"

Should use ISO 639-1 code e.g. \"en\", \"fr\"

URI: nmdc:language

"},{"location":"language/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextValue A basic string value no"},{"location":"language/#properties","title":"Properties","text":""},{"location":"language/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"language/#schema-source","title":"Schema Source","text":""},{"location":"language/#linkml-source","title":"LinkML Source","text":"
name: language\ndescription: Should use ISO 639-1 code e.g. \"en\", \"fr\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: language\ndomain_of:\n- TextValue\nrange: language code\n\n
"},{"location":"last_clean/","title":"Slot: last time swept/mopped/vacuumed (last_clean)","text":"

The last time the floor was cleaned (swept, mopped, vacuumed)

URI: MIXS:0000814

"},{"location":"last_clean/#inheritance","title":"Inheritance","text":""},{"location":"last_clean/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"last_clean/#properties","title":"Properties","text":""},{"location":"last_clean/#aliases","title":"Aliases","text":""},{"location":"last_clean/#examples","title":"Examples","text":"Value 2018-05-11:T14:30Z"},{"location":"last_clean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"last_clean/#annotations","title":"Annotations","text":"property value expected_value timestamp"},{"location":"last_clean/#schema-source","title":"Schema Source","text":""},{"location":"last_clean/#linkml-source","title":"LinkML Source","text":"
name: last_clean\nannotations:\n  expected_value:\n    tag: expected_value\n    value: timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The last time the floor was cleaned (swept, mopped, vacuumed)\ntitle: last time swept/mopped/vacuumed\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- last time swept/mopped/vacuumed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000814\nalias: last_clean\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"lat_lon/","title":"Slot: geographic location (latitude and longitude) (lat_lon)","text":"

The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system

URI: MIXS:0000009

"},{"location":"lat_lon/#inheritance","title":"Inheritance","text":""},{"location":"lat_lon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no"},{"location":"lat_lon/#properties","title":"Properties","text":""},{"location":"lat_lon/#aliases","title":"Aliases","text":""},{"location":"lat_lon/#examples","title":"Examples","text":"Value 50.586825 6.408977"},{"location":"lat_lon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"lat_lon/#annotations","title":"Annotations","text":"property value expected_value decimal degrees, limit to 8 decimal points"},{"location":"lat_lon/#schema-source","title":"Schema Source","text":""},{"location":"lat_lon/#linkml-source","title":"LinkML Source","text":"
name: lat_lon\nannotations:\n  expected_value:\n    tag: expected_value\n    value: decimal degrees,  limit to 8 decimal points\ndescription: The geographical origin of the sample as defined by latitude and longitude.\n  The values should be reported in decimal degrees and in WGS84 system\ntitle: geographic location (latitude and longitude)\nexamples:\n- value: 50.586825 6.408977\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (latitude and longitude)\nrank: 1000\nis_a: environment field\nstring_serialization: '{float} {float}'\nslot_uri: MIXS:0000009\nalias: lat_lon\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: GeolocationValue\nmultivalued: false\n\n
"},{"location":"latitude/","title":"Slot: latitude","text":"

latitude

URI: wgs84:lat

"},{"location":"latitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"latitude/#properties","title":"Properties","text":""},{"location":"latitude/#examples","title":"Examples","text":"Value -33.460524"},{"location":"latitude/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"latitude/#schema-source","title":"Schema Source","text":""},{"location":"latitude/#linkml-source","title":"LinkML Source","text":"
name: latitude\ndescription: latitude\nexamples:\n- value: '-33.460524'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:latitude\nrank: 1000\nslot_uri: wgs84:lat\nalias: latitude\ndomain_of:\n- GeolocationValue\nrange: decimal degree\n\n
"},{"location":"lbc_thirty/","title":"Slot: lime buffer capacity (at 30 minutes) (lbc_thirty)","text":"

lime buffer capacity, determined after 30 minute incubation

URI: nmdc:lbc_thirty

"},{"location":"lbc_thirty/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lbc_thirty/#properties","title":"Properties","text":""},{"location":"lbc_thirty/#aliases","title":"Aliases","text":""},{"location":"lbc_thirty/#examples","title":"Examples","text":"Value 543 mg/kg"},{"location":"lbc_thirty/#comments","title":"Comments","text":""},{"location":"lbc_thirty/#see-also","title":"See Also","text":""},{"location":"lbc_thirty/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"lbc_thirty/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"lbc_thirty/#schema-source","title":"Schema Source","text":""},{"location":"lbc_thirty/#linkml-source","title":"LinkML Source","text":"
name: lbc_thirty\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: ppm CaCO3/pH\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: lime buffer capacity, determined after 30 minute incubation\ntitle: lime buffer capacity (at 30 minutes)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n  pH unit\nexamples:\n- value: 543 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\n- https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\naliases:\n- lbc_thirty\n- lbc30\n- lime buffer capacity (at 30 minutes)\nrank: 1000\nalias: lbc_thirty\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"lbceq/","title":"Slot: lime buffer capacity (after 5 day incubation) (lbceq)","text":"

lime buffer capacity, determined at equilibrium after 5 day incubation

URI: nmdc:lbceq

"},{"location":"lbceq/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lbceq/#properties","title":"Properties","text":""},{"location":"lbceq/#aliases","title":"Aliases","text":""},{"location":"lbceq/#examples","title":"Examples","text":"Value 1575 mg/kg"},{"location":"lbceq/#comments","title":"Comments","text":""},{"location":"lbceq/#see-also","title":"See Also","text":""},{"location":"lbceq/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"lbceq/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"lbceq/#schema-source","title":"Schema Source","text":""},{"location":"lbceq/#linkml-source","title":"LinkML Source","text":"
name: lbceq\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: ppm CaCO3/pH\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: lime buffer capacity, determined at equilibrium after 5 day incubation\ntitle: lime buffer capacity (after 5 day incubation)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n  pH unit\nexamples:\n- value: 1575 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- lbceq\n- lime buffer capacity (at 5-day equilibrium)\nrank: 1000\nalias: lbceq\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"library_preparation_kit/","title":"Slot: library_preparation_kit","text":"

URI: nmdc:library_preparation_kit

"},{"location":"library_preparation_kit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_preparation_kit/#properties","title":"Properties","text":""},{"location":"library_preparation_kit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"library_preparation_kit/#schema-source","title":"Schema Source","text":""},{"location":"library_preparation_kit/#linkml-source","title":"LinkML Source","text":"
name: library_preparation_kit\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_preparation_kit\ndomain_of:\n- LibraryPreparation\nrange: string\n\n
"},{"location":"library_type/","title":"Slot: library type (library_type)","text":"

URI: nmdc:library_type

"},{"location":"library_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_type/#properties","title":"Properties","text":""},{"location":"library_type/#examples","title":"Examples","text":"Value DNA"},{"location":"library_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"library_type/#schema-source","title":"Schema Source","text":""},{"location":"library_type/#linkml-source","title":"LinkML Source","text":"
name: library_type\ntitle: library type\nexamples:\n- value: DNA\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_type\ndomain_of:\n- LibraryPreparation\nrange: LibraryTypeEnum\n\n
"},{"location":"light_intensity/","title":"Slot: light intensity (light_intensity)","text":"

Measurement of light intensity

URI: MIXS:0000706

"},{"location":"light_intensity/#inheritance","title":"Inheritance","text":""},{"location":"light_intensity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"light_intensity/#properties","title":"Properties","text":""},{"location":"light_intensity/#aliases","title":"Aliases","text":""},{"location":"light_intensity/#examples","title":"Examples","text":"Value 0.3 lux"},{"location":"light_intensity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"light_intensity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"light_intensity/#schema-source","title":"Schema Source","text":""},{"location":"light_intensity/#linkml-source","title":"LinkML Source","text":"
name: light_intensity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: lux\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of light intensity\ntitle: light intensity\nexamples:\n- value: 0.3 lux\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light intensity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000706\nalias: light_intensity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"light_regm/","title":"Slot: light regimen (light_regm)","text":"

Information about treatment(s) involving exposure to light, including both light intensity and quality.

URI: MIXS:0000569

"},{"location":"light_regm/#inheritance","title":"Inheritance","text":""},{"location":"light_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"light_regm/#properties","title":"Properties","text":""},{"location":"light_regm/#aliases","title":"Aliases","text":""},{"location":"light_regm/#examples","title":"Examples","text":"Value incandescant light;10 lux;450 nanometer"},{"location":"light_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"light_regm/#annotations","title":"Annotations","text":"property value expected_value exposure type;light intensity;light quality"},{"location":"light_regm/#schema-source","title":"Schema Source","text":""},{"location":"light_regm/#linkml-source","title":"LinkML Source","text":"
name: light_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: exposure type;light intensity;light quality\n  preferred_unit:\n    tag: preferred_unit\n    value: lux; micrometer, nanometer, angstrom\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information about treatment(s) involving exposure to light, including\n  both light intensity and quality.\ntitle: light regimen\nexamples:\n- value: incandescant light;10 lux;450 nanometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000569\nalias: light_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"light_type/","title":"Slot: light type (light_type)","text":"

Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light

URI: MIXS:0000769

"},{"location":"light_type/#inheritance","title":"Inheritance","text":""},{"location":"light_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"light_type/#properties","title":"Properties","text":""},{"location":"light_type/#aliases","title":"Aliases","text":""},{"location":"light_type/#examples","title":"Examples","text":"Value desk lamp"},{"location":"light_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"light_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"light_type/#schema-source","title":"Schema Source","text":""},{"location":"light_type/#linkml-source","title":"LinkML Source","text":"
name: light_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Application of light to achieve some practical or aesthetic effect. Lighting\n  includes the use of both artificial light sources such as lamps and light fixtures,\n  as well as natural illumination by capturing daylight. Can also include absence\n  of light\ntitle: light type\nexamples:\n- value: desk lamp\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000769\nalias: light_type\ndomain_of:\n- Biosample\nrange: light_type_enum\nmultivalued: true\n\n
"},{"location":"link_addit_analys/","title":"Slot: links to additional analysis (link_addit_analys)","text":"

Link to additional analysis results performed on the sample

URI: MIXS:0000340

"},{"location":"link_addit_analys/#inheritance","title":"Inheritance","text":""},{"location":"link_addit_analys/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"link_addit_analys/#properties","title":"Properties","text":""},{"location":"link_addit_analys/#aliases","title":"Aliases","text":""},{"location":"link_addit_analys/#examples","title":"Examples","text":"Value"},{"location":"link_addit_analys/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"link_addit_analys/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"link_addit_analys/#schema-source","title":"Schema Source","text":""},{"location":"link_addit_analys/#linkml-source","title":"LinkML Source","text":"
name: link_addit_analys\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Link to additional analysis results performed on the sample\ntitle: links to additional analysis\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- links to additional analysis\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000340\nalias: link_addit_analys\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"link_class_info/","title":"Slot: link to classification information (link_class_info)","text":"

Link to digitized soil maps or other soil classification information

URI: MIXS:0000329

"},{"location":"link_class_info/#inheritance","title":"Inheritance","text":""},{"location":"link_class_info/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"link_class_info/#properties","title":"Properties","text":""},{"location":"link_class_info/#aliases","title":"Aliases","text":""},{"location":"link_class_info/#examples","title":"Examples","text":"Value"},{"location":"link_class_info/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"link_class_info/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"link_class_info/#schema-source","title":"Schema Source","text":""},{"location":"link_class_info/#linkml-source","title":"LinkML Source","text":"
name: link_class_info\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Link to digitized soil maps or other soil classification information\ntitle: link to classification information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to classification information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000329\nalias: link_class_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"link_climate_info/","title":"Slot: link to climate information (link_climate_info)","text":"

Link to climate resource

URI: MIXS:0000328

"},{"location":"link_climate_info/#inheritance","title":"Inheritance","text":""},{"location":"link_climate_info/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"link_climate_info/#properties","title":"Properties","text":""},{"location":"link_climate_info/#aliases","title":"Aliases","text":""},{"location":"link_climate_info/#examples","title":"Examples","text":"Value"},{"location":"link_climate_info/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"link_climate_info/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"link_climate_info/#schema-source","title":"Schema Source","text":""},{"location":"link_climate_info/#linkml-source","title":"LinkML Source","text":"
name: link_climate_info\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Link to climate resource\ntitle: link to climate information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to climate information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000328\nalias: link_climate_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"lithology/","title":"Slot: lithology (lithology)","text":"

Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000990

"},{"location":"lithology/#inheritance","title":"Inheritance","text":""},{"location":"lithology/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lithology/#properties","title":"Properties","text":""},{"location":"lithology/#aliases","title":"Aliases","text":""},{"location":"lithology/#examples","title":"Examples","text":"Value Volcanic"},{"location":"lithology/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"lithology/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"lithology/#schema-source","title":"Schema Source","text":""},{"location":"lithology/#linkml-source","title":"LinkML Source","text":"
name: lithology\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n  If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: lithology\nexamples:\n- value: Volcanic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000990\nalias: lithology\ndomain_of:\n- Biosample\nrange: lithology_enum\nmultivalued: false\n\n
"},{"location":"local_class/","title":"Slot: soil_taxonomic/local classification (local_class)","text":"

Soil classification based on local soil classification system

URI: MIXS:0000330

"},{"location":"local_class/#inheritance","title":"Inheritance","text":""},{"location":"local_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no"},{"location":"local_class/#properties","title":"Properties","text":""},{"location":"local_class/#aliases","title":"Aliases","text":""},{"location":"local_class/#examples","title":"Examples","text":"Value"},{"location":"local_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"local_class/#annotations","title":"Annotations","text":"property value expected_value local classification name"},{"location":"local_class/#schema-source","title":"Schema Source","text":""},{"location":"local_class/#linkml-source","title":"LinkML Source","text":"
name: local_class\nannotations:\n  expected_value:\n    tag: expected_value\n    value: local classification name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Soil classification based on local soil classification system\ntitle: soil_taxonomic/local classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000330\nalias: local_class\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"local_class_meth/","title":"Slot: soil_taxonomic/local classification method (local_class_meth)","text":"

Reference or method used in determining the local soil classification

URI: MIXS:0000331

"},{"location":"local_class_meth/#inheritance","title":"Inheritance","text":""},{"location":"local_class_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"local_class_meth/#properties","title":"Properties","text":""},{"location":"local_class_meth/#aliases","title":"Aliases","text":""},{"location":"local_class_meth/#examples","title":"Examples","text":"Value"},{"location":"local_class_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"local_class_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"local_class_meth/#schema-source","title":"Schema Source","text":""},{"location":"local_class_meth/#linkml-source","title":"LinkML Source","text":"
name: local_class_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining the local soil classification\ntitle: soil_taxonomic/local classification method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000331\nalias: local_class_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"location/","title":"Slot: location","text":"

URI: nmdc:location

"},{"location":"location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"location/#properties","title":"Properties","text":""},{"location":"location/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"location/#schema-source","title":"Schema Source","text":""},{"location":"location/#linkml-source","title":"LinkML Source","text":"
name: location\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: location\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"longitude/","title":"Slot: longitude","text":"

longitude

URI: wgs84:long

"},{"location":"longitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"longitude/#properties","title":"Properties","text":""},{"location":"longitude/#examples","title":"Examples","text":"Value 150.168149"},{"location":"longitude/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"longitude/#schema-source","title":"Schema Source","text":""},{"location":"longitude/#linkml-source","title":"LinkML Source","text":"
name: longitude\ndescription: longitude\nexamples:\n- value: '150.168149'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:longitude\nrank: 1000\nslot_uri: wgs84:long\nalias: longitude\ndomain_of:\n- GeolocationValue\nrange: decimal degree\n\n
"},{"location":"low_depth_contig_num/","title":"Slot: low_depth_contig_num","text":"

URI: nmdc:low_depth_contig_num

"},{"location":"low_depth_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"low_depth_contig_num/#properties","title":"Properties","text":""},{"location":"low_depth_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"low_depth_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"low_depth_contig_num/#linkml-source","title":"LinkML Source","text":"
name: low_depth_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: low_depth_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"magnesium/","title":"Slot: magnesium (magnesium)","text":"

Concentration of magnesium in the sample

URI: MIXS:0000431

"},{"location":"magnesium/#inheritance","title":"Inheritance","text":""},{"location":"magnesium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"magnesium/#properties","title":"Properties","text":""},{"location":"magnesium/#aliases","title":"Aliases","text":""},{"location":"magnesium/#examples","title":"Examples","text":"Value 52.8 micromole per kilogram"},{"location":"magnesium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"magnesium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"magnesium/#schema-source","title":"Schema Source","text":""},{"location":"magnesium/#linkml-source","title":"LinkML Source","text":"
name: magnesium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per liter, milligram per liter, parts per million, micromole per kilogram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of magnesium in the sample\ntitle: magnesium\nexamples:\n- value: 52.8 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- magnesium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000431\nalias: magnesium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"mags_list/","title":"Slot: mags_list","text":"

URI: nmdc:mags_list

"},{"location":"mags_list/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"mags_list/#properties","title":"Properties","text":""},{"location":"mags_list/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mags_list/#schema-source","title":"Schema Source","text":""},{"location":"mags_list/#linkml-source","title":"LinkML Source","text":"
name: mags_list\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mags_list\ndomain_of:\n- MagsAnalysis\nrange: MagBin\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"manganese/","title":"Slot: manganese (manganese)","text":"

Concentration of manganese in the sample

URI: nmdc:manganese

"},{"location":"manganese/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"manganese/#properties","title":"Properties","text":""},{"location":"manganese/#aliases","title":"Aliases","text":""},{"location":"manganese/#examples","title":"Examples","text":"Value 24.7 mg/kg"},{"location":"manganese/#see-also","title":"See Also","text":""},{"location":"manganese/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"manganese/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"manganese/#schema-source","title":"Schema Source","text":""},{"location":"manganese/#linkml-source","title":"LinkML Source","text":"
name: manganese\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg (ppm)\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of manganese in the sample\ntitle: manganese\nexamples:\n- value: 24.7 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- manganese\nrank: 1000\nalias: manganese\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"manifest_category/","title":"Slot: manifest_category","text":"

The type of collection that describes the data in the collection.

URI: nmdc:manifest_category

"},{"location":"manifest_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Manifest no"},{"location":"manifest_category/#properties","title":"Properties","text":""},{"location":"manifest_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"manifest_category/#schema-source","title":"Schema Source","text":""},{"location":"manifest_category/#linkml-source","title":"LinkML Source","text":"
name: manifest_category\ndescription: The type of collection that describes the data in the collection.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: manifest_category\ndomain_of:\n- Manifest\nrange: ManifestCategoryEnum\nrequired: true\n\n
"},{"location":"manifest_set/","title":"Slot: manifest_set","text":"

This property links a database object to the set of manifests within it.

URI: nmdc:manifest_set

"},{"location":"manifest_set/#inheritance","title":"Inheritance","text":""},{"location":"manifest_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"manifest_set/#properties","title":"Properties","text":""},{"location":"manifest_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"manifest_set/#schema-source","title":"Schema Source","text":""},{"location":"manifest_set/#linkml-source","title":"LinkML Source","text":"
name: manifest_set\ndescription: This property links a database object to the set of manifests within\n  it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: manifest_set\ndomain_of:\n- Database\nrange: Manifest\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mass/","title":"Slot: mass (mass)","text":"

A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.

URI: nmdc:mass

"},{"location":"mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes"},{"location":"mass/#properties","title":"Properties","text":""},{"location":"mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mass/#schema-source","title":"Schema Source","text":""},{"location":"mass/#linkml-source","title":"LinkML Source","text":"
name: mass\ndescription: A physical quality that inheres in a bearer by virtue of the proportion\n  of the bearer's amount of matter.\ntitle: mass\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- PATO:0000125\nrank: 1000\nalias: mass\ndomain_of:\n- SubSamplingProcess\n- PortionOfSubstance\nrange: QuantityValue\n\n
"},{"location":"mass_analyzers/","title":"Slot: mass_analyzers","text":"

The kind of mass analyzer(s) used during the spectra collection.

URI: nmdc:mass_analyzers

"},{"location":"mass_analyzers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_analyzers/#properties","title":"Properties","text":""},{"location":"mass_analyzers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mass_analyzers/#schema-source","title":"Schema Source","text":""},{"location":"mass_analyzers/#linkml-source","title":"LinkML Source","text":"
name: mass_analyzers\ndescription: The kind of mass analyzer(s) used during the spectra collection.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1000443\nrank: 1000\nalias: mass_analyzers\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassAnalyzerEnum\nmultivalued: true\n\n
"},{"location":"mass_spectrometry_acquisition_strategy/","title":"Slot: mass_spectrometry_acquisition_strategy","text":"

Mode of running a mass spectrometer method by which m/z ranges are selected and ions possibly fragment.

URI: nmdc:mass_spectrometry_acquisition_strategy

"},{"location":"mass_spectrometry_acquisition_strategy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_spectrometry_acquisition_strategy/#properties","title":"Properties","text":""},{"location":"mass_spectrometry_acquisition_strategy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mass_spectrometry_acquisition_strategy/#schema-source","title":"Schema Source","text":""},{"location":"mass_spectrometry_acquisition_strategy/#linkml-source","title":"LinkML Source","text":"
name: mass_spectrometry_acquisition_strategy\ndescription: Mode of running a mass spectrometer method by which m/z ranges are selected\n  and ions possibly fragment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1003213\nrank: 1000\nalias: mass_spectrometry_acquisition_strategy\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassSpectrometryAcquisitionStrategyEnum\n\n
"},{"location":"mass_spectrum_collection_modes/","title":"Slot: mass_spectrum_collection_modes","text":"

Indicates whether mass spectra were collected in full profile, reduced profile, or centroid mode during acquisition.

URI: nmdc:mass_spectrum_collection_modes

"},{"location":"mass_spectrum_collection_modes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_spectrum_collection_modes/#properties","title":"Properties","text":""},{"location":"mass_spectrum_collection_modes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mass_spectrum_collection_modes/#schema-source","title":"Schema Source","text":""},{"location":"mass_spectrum_collection_modes/#linkml-source","title":"LinkML Source","text":"
name: mass_spectrum_collection_modes\ndescription: Indicates whether mass spectra were collected in full profile, reduced\n  profile, or centroid mode during acquisition.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mass_spectrum_collection_modes\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassSpectrumCollectionModeEnum\nmultivalued: true\n\n
"},{"location":"material_component_separation/","title":"Slot: material_component_separation","text":"

A material processing in which components of an input material become segregated in space

URI: nmdc:material_component_separation

"},{"location":"material_component_separation/#properties","title":"Properties","text":""},{"location":"material_component_separation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"material_component_separation/#schema-source","title":"Schema Source","text":""},{"location":"material_component_separation/#linkml-source","title":"LinkML Source","text":"
name: material_component_separation\ndescription: A material processing in which components of an input material become\n  segregated in space\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: material_component_separation\nrange: string\n\n
"},{"location":"material_processing_set/","title":"Slot: material_processing_set","text":"

This property links a database object to the set of material processing within it.

URI: nmdc:material_processing_set

"},{"location":"material_processing_set/#inheritance","title":"Inheritance","text":""},{"location":"material_processing_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"material_processing_set/#properties","title":"Properties","text":""},{"location":"material_processing_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"material_processing_set/#schema-source","title":"Schema Source","text":""},{"location":"material_processing_set/#linkml-source","title":"LinkML Source","text":"
name: material_processing_set\ndescription: This property links a database object to the set of material processing\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: material_processing_set\ndomain_of:\n- Database\nrange: MaterialProcessing\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"max_occup/","title":"Slot: maximum occupancy (max_occup)","text":"

The maximum amount of people allowed in the indoor environment

URI: MIXS:0000229

"},{"location":"max_occup/#inheritance","title":"Inheritance","text":""},{"location":"max_occup/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"max_occup/#properties","title":"Properties","text":""},{"location":"max_occup/#aliases","title":"Aliases","text":""},{"location":"max_occup/#examples","title":"Examples","text":"Value"},{"location":"max_occup/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"max_occup/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"max_occup/#schema-source","title":"Schema Source","text":""},{"location":"max_occup/#linkml-source","title":"LinkML Source","text":"
name: max_occup\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The maximum amount of people allowed in the indoor environment\ntitle: maximum occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- maximum occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000229\nalias: max_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"md5_checksum/","title":"Slot: md5_checksum","text":"

MD5 checksum of file (pre-compressed)

URI: nmdc:md5_checksum

"},{"location":"md5_checksum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"md5_checksum/#properties","title":"Properties","text":""},{"location":"md5_checksum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"md5_checksum/#schema-source","title":"Schema Source","text":""},{"location":"md5_checksum/#linkml-source","title":"LinkML Source","text":"
name: md5_checksum\ndescription: MD5 checksum of file (pre-compressed)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: md5_checksum\ndomain_of:\n- DataObject\nrange: string\n\n
"},{"location":"mean_frict_vel/","title":"Slot: mean friction velocity (mean_frict_vel)","text":"

Measurement of mean friction velocity

URI: MIXS:0000498

"},{"location":"mean_frict_vel/#inheritance","title":"Inheritance","text":""},{"location":"mean_frict_vel/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mean_frict_vel/#properties","title":"Properties","text":""},{"location":"mean_frict_vel/#aliases","title":"Aliases","text":""},{"location":"mean_frict_vel/#examples","title":"Examples","text":"Value 0.5 meter per second"},{"location":"mean_frict_vel/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mean_frict_vel/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"mean_frict_vel/#schema-source","title":"Schema Source","text":""},{"location":"mean_frict_vel/#linkml-source","title":"LinkML Source","text":"
name: mean_frict_vel\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of mean friction velocity\ntitle: mean friction velocity\nexamples:\n- value: 0.5 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000498\nalias: mean_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"mean_peak_frict_vel/","title":"Slot: mean peak friction velocity (mean_peak_frict_vel)","text":"

Measurement of mean peak friction velocity

URI: MIXS:0000502

"},{"location":"mean_peak_frict_vel/#inheritance","title":"Inheritance","text":""},{"location":"mean_peak_frict_vel/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mean_peak_frict_vel/#properties","title":"Properties","text":""},{"location":"mean_peak_frict_vel/#aliases","title":"Aliases","text":""},{"location":"mean_peak_frict_vel/#examples","title":"Examples","text":"Value 1 meter per second"},{"location":"mean_peak_frict_vel/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mean_peak_frict_vel/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"mean_peak_frict_vel/#schema-source","title":"Schema Source","text":""},{"location":"mean_peak_frict_vel/#linkml-source","title":"LinkML Source","text":"
name: mean_peak_frict_vel\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of mean peak friction velocity\ntitle: mean peak friction velocity\nexamples:\n- value: 1 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean peak friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000502\nalias: mean_peak_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"mech_struc/","title":"Slot: mechanical structure (mech_struc)","text":"

mechanical structure: a moving structure

URI: MIXS:0000815

"},{"location":"mech_struc/#inheritance","title":"Inheritance","text":""},{"location":"mech_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mech_struc/#properties","title":"Properties","text":""},{"location":"mech_struc/#aliases","title":"Aliases","text":""},{"location":"mech_struc/#examples","title":"Examples","text":"Value elevator"},{"location":"mech_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mech_struc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"mech_struc/#schema-source","title":"Schema Source","text":""},{"location":"mech_struc/#linkml-source","title":"LinkML Source","text":"
name: mech_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'mechanical structure: a moving structure'\ntitle: mechanical structure\nexamples:\n- value: elevator\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000815\nalias: mech_struc\ndomain_of:\n- Biosample\nrange: mech_struc_enum\nmultivalued: false\n\n
"},{"location":"mechanical_damage/","title":"Slot: mechanical damage (mechanical_damage)","text":"

Information about any mechanical damage exerted on the plant; can include multiple damages and sites

URI: MIXS:0001052

"},{"location":"mechanical_damage/#inheritance","title":"Inheritance","text":""},{"location":"mechanical_damage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mechanical_damage/#properties","title":"Properties","text":""},{"location":"mechanical_damage/#aliases","title":"Aliases","text":""},{"location":"mechanical_damage/#examples","title":"Examples","text":"Value pruning;bark"},{"location":"mechanical_damage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mechanical_damage/#annotations","title":"Annotations","text":"property value expected_value damage type;body site"},{"location":"mechanical_damage/#schema-source","title":"Schema Source","text":""},{"location":"mechanical_damage/#linkml-source","title":"LinkML Source","text":"
name: mechanical_damage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: damage type;body site\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about any mechanical damage exerted on the plant; can include\n  multiple damages and sites\ntitle: mechanical damage\nexamples:\n- value: pruning;bark\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical damage\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0001052\nalias: mechanical_damage\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"members_id/","title":"Slot: members_id","text":"

URI: nmdc:members_id

"},{"location":"members_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"members_id/#properties","title":"Properties","text":""},{"location":"members_id/#todos","title":"TODOs","text":""},{"location":"members_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"members_id/#schema-source","title":"Schema Source","text":""},{"location":"members_id/#linkml-source","title":"LinkML Source","text":"
name: members_id\ntodos:\n- this slot needs some basic textual annotations and constraints\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: members_id\ndomain_of:\n- MagBin\nrange: string\nmultivalued: true\n\n
"},{"location":"metabolite_identified/","title":"Slot: metabolite_identified","text":"

the specific metabolite identifier

URI: nmdc:metabolite_identified

"},{"location":"metabolite_identified/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"metabolite_identified/#properties","title":"Properties","text":""},{"location":"metabolite_identified/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metabolite_identified/#schema-source","title":"Schema Source","text":""},{"location":"metabolite_identified/#linkml-source","title":"LinkML Source","text":"
name: metabolite_identified\ndescription: the specific metabolite identifier\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metabolite_identified\ndomain_of:\n- MetaboliteIdentification\nrange: ChemicalEntity\n\n
"},{"location":"metagenome_annotation_id/","title":"Slot: metagenome_annotation_id","text":"

The identifier for the analysis activity that generated the functional annotation results, where the analysis activity is an instance of the/an appropriate subclass of WorkflowExecution

URI: nmdc:metagenome_annotation_id

"},{"location":"metagenome_annotation_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember yes"},{"location":"metagenome_annotation_id/#properties","title":"Properties","text":""},{"location":"metagenome_annotation_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_annotation_id/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_annotation_id/#linkml-source","title":"LinkML Source","text":"
name: metagenome_annotation_id\ndescription: The identifier for the analysis activity that generated the functional\n  annotation results, where the analysis activity is an instance of the/an appropriate\n  subclass of WorkflowExecution\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metagenome_annotation_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: WorkflowExecution\nrequired: true\nany_of:\n- range: MetagenomeAnnotation\n- range: MetatranscriptomeAnnotation\n\n
"},{"location":"metagenome_assembly_parameter/","title":"Slot: metagenome_assembly_parameter","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:metagenome_assembly_parameter

"},{"location":"metagenome_assembly_parameter/#inheritance","title":"Inheritance","text":""},{"location":"metagenome_assembly_parameter/#properties","title":"Properties","text":""},{"location":"metagenome_assembly_parameter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"metagenome_assembly_parameter/#schema-source","title":"Schema Source","text":""},{"location":"metagenome_assembly_parameter/#linkml-source","title":"LinkML Source","text":"
name: metagenome_assembly_parameter\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: metagenome_assembly_parameter\nrange: string\n\n
"},{"location":"methane/","title":"Slot: methane (methane)","text":"

Methane (gas) amount or concentration at the time of sampling

URI: MIXS:0000101

"},{"location":"methane/#inheritance","title":"Inheritance","text":""},{"location":"methane/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"methane/#properties","title":"Properties","text":""},{"location":"methane/#aliases","title":"Aliases","text":""},{"location":"methane/#examples","title":"Examples","text":"Value 1800 parts per billion"},{"location":"methane/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"methane/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"methane/#schema-source","title":"Schema Source","text":""},{"location":"methane/#linkml-source","title":"LinkML Source","text":"
name: methane\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, parts per billion, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Methane (gas) amount or concentration at the time of sampling\ntitle: methane\nexamples:\n- value: 1800 parts per billion\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- methane\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000101\nalias: methane\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"mgnify_analysis_identifiers/","title":"Slot: mgnify_analysis_identifiers","text":"

URI: nmdc:mgnify_analysis_identifiers

"},{"location":"mgnify_analysis_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"mgnify_analysis_identifiers/#properties","title":"Properties","text":""},{"location":"mgnify_analysis_identifiers/#examples","title":"Examples","text":"Value https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270"},{"location":"mgnify_analysis_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mgnify_analysis_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"mgnify_analysis_identifiers/#linkml-source","title":"LinkML Source","text":"
name: mgnify_analysis_identifiers\nnotes:\n- 'removed pattern: \"^mgnify:MGYA[0-9]+$\" ## TODO https://github.com/bioregistry/bioregistry/issues/109'\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270\n  description: combined analyses (taxonomic, functional) of sample ERS438107\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- mgnify_identifiers\nalias: mgnify_analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"mgnify_identifiers/","title":"Slot: mgnify_identifiers","text":"

URI: nmdc:mgnify_identifiers

"},{"location":"mgnify_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain mgnify_project_identifiers identifiers for corresponding project in MGnify None Study mgnify_analysis_identifiers None"},{"location":"mgnify_identifiers/#properties","title":"Properties","text":""},{"location":"mgnify_identifiers/#see-also","title":"See Also","text":""},{"location":"mgnify_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mgnify_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"mgnify_identifiers/#linkml-source","title":"LinkML Source","text":"
name: mgnify_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ebi.ac.uk/metagenomics/\nrank: 1000\nmixin: true\nalias: mgnify_identifiers\nrange: string\n\n
"},{"location":"mgnify_project_identifiers/","title":"Slot: mgnify_project_identifiers","text":"

identifiers for corresponding project in MGnify

URI: nmdc:mgnify_project_identifiers

"},{"location":"mgnify_project_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"mgnify_project_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"mgnify_project_identifiers/#properties","title":"Properties","text":""},{"location":"mgnify_project_identifiers/#examples","title":"Examples","text":"Value https://bioregistry.io/mgnify.proj:MGYS00005757"},{"location":"mgnify_project_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mgnify_project_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"mgnify_project_identifiers/#linkml-source","title":"LinkML Source","text":"
name: mgnify_project_identifiers\ndescription: identifiers for corresponding project in MGnify\nexamples:\n- value: https://bioregistry.io/mgnify.proj:MGYS00005757\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- mgnify_identifiers\nalias: mgnify_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^mgnify.proj:[A-Z]+[0-9]+$\n\n
"},{"location":"micro_biomass_c_meth/","title":"Slot: microbial biomass carbon method (micro_biomass_c_meth)","text":"

Reference or method used in determining microbial biomass carbon

URI: nmdc:micro_biomass_c_meth

"},{"location":"micro_biomass_c_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_c_meth/#properties","title":"Properties","text":""},{"location":"micro_biomass_c_meth/#examples","title":"Examples","text":"Value https://doi.org/10.1016/0038-0717(87)90052-6 https://doi.org/10.1016/0038-0717(87)90052-6"},{"location":"micro_biomass_c_meth/#comments","title":"Comments","text":""},{"location":"micro_biomass_c_meth/#todos","title":"TODOs","text":""},{"location":"micro_biomass_c_meth/#see-also","title":"See Also","text":""},{"location":"micro_biomass_c_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"micro_biomass_c_meth/#schema-source","title":"Schema Source","text":""},{"location":"micro_biomass_c_meth/#linkml-source","title":"LinkML Source","text":"
name: micro_biomass_c_meth\ndescription: Reference or method used in determining microbial biomass carbon\ntitle: microbial biomass carbon method\ntodos:\n- How should we separate values? | or ;? lets be consistent\ncomments:\n- required if \"microbial_biomass_c\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000339\nrank: 11\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_c_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"micro_biomass_meth/","title":"Slot: microbial biomass method (micro_biomass_meth)","text":"

Reference or method used in determining microbial biomass

URI: MIXS:0000339

"},{"location":"micro_biomass_meth/#inheritance","title":"Inheritance","text":""},{"location":"micro_biomass_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_meth/#properties","title":"Properties","text":""},{"location":"micro_biomass_meth/#aliases","title":"Aliases","text":""},{"location":"micro_biomass_meth/#examples","title":"Examples","text":"Value"},{"location":"micro_biomass_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"micro_biomass_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"micro_biomass_meth/#schema-source","title":"Schema Source","text":""},{"location":"micro_biomass_meth/#linkml-source","title":"LinkML Source","text":"
name: micro_biomass_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining microbial biomass\ntitle: microbial biomass method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000339\nalias: micro_biomass_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"micro_biomass_n_meth/","title":"Slot: microbial biomass nitrogen method (micro_biomass_n_meth)","text":"

Reference or method used in determining microbial biomass nitrogen

URI: nmdc:micro_biomass_n_meth

"},{"location":"micro_biomass_n_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_n_meth/#properties","title":"Properties","text":""},{"location":"micro_biomass_n_meth/#examples","title":"Examples","text":"Value https://doi.org/10.1016/0038-0717(87)90052-6 https://doi.org/10.1016/0038-0717(87)90052-6"},{"location":"micro_biomass_n_meth/#comments","title":"Comments","text":""},{"location":"micro_biomass_n_meth/#see-also","title":"See Also","text":""},{"location":"micro_biomass_n_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"micro_biomass_n_meth/#schema-source","title":"Schema Source","text":""},{"location":"micro_biomass_n_meth/#linkml-source","title":"LinkML Source","text":"
name: micro_biomass_n_meth\ndescription: Reference or method used in determining microbial biomass nitrogen\ntitle: microbial biomass nitrogen method\ncomments:\n- required if \"microbial_biomass_n\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000339\nrank: 13\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_n_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"microbial_biomass/","title":"Slot: microbial biomass (microbial_biomass)","text":"

The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units

URI: MIXS:0000650

"},{"location":"microbial_biomass/#inheritance","title":"Inheritance","text":""},{"location":"microbial_biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass/#properties","title":"Properties","text":""},{"location":"microbial_biomass/#aliases","title":"Aliases","text":""},{"location":"microbial_biomass/#examples","title":"Examples","text":"Value"},{"location":"microbial_biomass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"microbial_biomass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"microbial_biomass/#schema-source","title":"Schema Source","text":""},{"location":"microbial_biomass/#linkml-source","title":"LinkML Source","text":"
name: microbial_biomass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: ton, kilogram, gram per kilogram soil\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n  smaller than 5-10 micrometer. If you keep this, you would need to have correction\n  factors used for conversion to the final units\ntitle: microbial biomass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000650\nalias: microbial_biomass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"microbial_biomass_c/","title":"Slot: microbial biomass carbon (microbial_biomass_c)","text":"

The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.

URI: nmdc:microbial_biomass_c

"},{"location":"microbial_biomass_c/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_c/#properties","title":"Properties","text":""},{"location":"microbial_biomass_c/#examples","title":"Examples","text":"Value 0.05 ug C/g dry soil"},{"location":"microbial_biomass_c/#comments","title":"Comments","text":""},{"location":"microbial_biomass_c/#see-also","title":"See Also","text":""},{"location":"microbial_biomass_c/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"microbial_biomass_c/#schema-source","title":"Schema Source","text":""},{"location":"microbial_biomass_c/#linkml-source","title":"LinkML Source","text":"
name: microbial_biomass_c\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n  smaller than 5-10 micrometer.\ntitle: microbial biomass carbon\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n  method are required\nexamples:\n- value: 0.05 ug C/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 10\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_c\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"microbial_biomass_n/","title":"Slot: microbial biomass nitrogen (microbial_biomass_n)","text":"

The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.

URI: nmdc:microbial_biomass_n

"},{"location":"microbial_biomass_n/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_n/#properties","title":"Properties","text":""},{"location":"microbial_biomass_n/#examples","title":"Examples","text":"Value 0.05 ug N/g dry soil"},{"location":"microbial_biomass_n/#comments","title":"Comments","text":""},{"location":"microbial_biomass_n/#see-also","title":"See Also","text":""},{"location":"microbial_biomass_n/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"microbial_biomass_n/#schema-source","title":"Schema Source","text":""},{"location":"microbial_biomass_n/#linkml-source","title":"LinkML Source","text":"
name: microbial_biomass_n\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n  smaller than 5-10 micrometer.\ntitle: microbial biomass nitrogen\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n  method are required\nexamples:\n- value: 0.05 ug N/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 12\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_n\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"min_q_value/","title":"Slot: min_q_value","text":"

smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool

URI: nmdc:min_q_value

"},{"location":"min_q_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"min_q_value/#properties","title":"Properties","text":""},{"location":"min_q_value/#see-also","title":"See Also","text":""},{"location":"min_q_value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"min_q_value/#schema-source","title":"Schema Source","text":""},{"location":"min_q_value/#linkml-source","title":"LinkML Source","text":"
name: min_q_value\ndescription: smallest Q-Value associated with the peptide sequence as provided by\n  MSGFPlus tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- OBI:0001442\nrank: 1000\nalias: min_q_value\ndomain_of:\n- PeptideQuantification\nrange: float\n\n
"},{"location":"mineral_nutr_regm/","title":"Slot: mineral nutrient regimen (mineral_nutr_regm)","text":"

Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens

URI: MIXS:0000570

"},{"location":"mineral_nutr_regm/#inheritance","title":"Inheritance","text":""},{"location":"mineral_nutr_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"mineral_nutr_regm/#properties","title":"Properties","text":""},{"location":"mineral_nutr_regm/#aliases","title":"Aliases","text":""},{"location":"mineral_nutr_regm/#examples","title":"Examples","text":"Value potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"mineral_nutr_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mineral_nutr_regm/#annotations","title":"Annotations","text":"property value expected_value mineral nutrient name;mineral nutrient amount;treatment interval and duration"},{"location":"mineral_nutr_regm/#schema-source","title":"Schema Source","text":""},{"location":"mineral_nutr_regm/#linkml-source","title":"LinkML Source","text":"
name: mineral_nutr_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: mineral nutrient name;mineral nutrient amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving the use of mineral supplements;\n  should include the name of mineral nutrient, amount administered, treatment regimen\n  including how many times the treatment was repeated, how long each treatment lasted,\n  and the start and end time of the entire treatment; can include multiple mineral\n  nutrient regimens\ntitle: mineral nutrient regimen\nexamples:\n- value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000570\nalias: mineral_nutr_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"misc_param/","title":"Slot: miscellaneous parameter (misc_param)","text":"

Any other measurement performed or parameter collected, that is not listed here

URI: MIXS:0000752

"},{"location":"misc_param/#inheritance","title":"Inheritance","text":""},{"location":"misc_param/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"misc_param/#properties","title":"Properties","text":""},{"location":"misc_param/#aliases","title":"Aliases","text":""},{"location":"misc_param/#examples","title":"Examples","text":"Value Bicarbonate ion concentration;2075 micromole per kilogram"},{"location":"misc_param/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"misc_param/#annotations","title":"Annotations","text":"property value expected_value parameter name;measurement value"},{"location":"misc_param/#schema-source","title":"Schema Source","text":""},{"location":"misc_param/#linkml-source","title":"LinkML Source","text":"
name: misc_param\nannotations:\n  expected_value:\n    tag: expected_value\n    value: parameter name;measurement value\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Any other measurement performed or parameter collected, that is not listed\n  here\ntitle: miscellaneous parameter\nexamples:\n- value: Bicarbonate ion concentration;2075 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- miscellaneous parameter\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000752\nalias: misc_param\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"mod_date/","title":"Slot: mod_date","text":"

The last date on which the database information was modified.

URI: nmdc:mod_date

"},{"location":"mod_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no Biosample Biological source material which can be characterized by an experiment no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"mod_date/#properties","title":"Properties","text":""},{"location":"mod_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"mod_date/#schema-source","title":"Schema Source","text":""},{"location":"mod_date/#linkml-source","title":"LinkML Source","text":"
name: mod_date\ndescription: The last date on which the database information was modified.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mod_date\ndomain_of:\n- Biosample\n- DataGeneration\nrange: string\n\n
"},{"location":"model/","title":"Slot: model","text":"

URI: nmdc:model

"},{"location":"model/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Instrument A material entity that is designed to perform a function in a scientific inve... no"},{"location":"model/#properties","title":"Properties","text":""},{"location":"model/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"model/#schema-source","title":"Schema Source","text":""},{"location":"model/#linkml-source","title":"LinkML Source","text":"
name: model\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: model\ndomain_of:\n- Instrument\nrange: InstrumentModelEnum\n\n
"},{"location":"modifier_substance/","title":"Slot: modifier_substance","text":"

The type of modification being done

URI: nmdc:modifier_substance

"},{"location":"modifier_substance/#properties","title":"Properties","text":""},{"location":"modifier_substance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"modifier_substance/#schema-source","title":"Schema Source","text":""},{"location":"modifier_substance/#linkml-source","title":"LinkML Source","text":"
name: modifier_substance\ndescription: The type of modification being done\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: modifier_substance\nrange: string\n\n
"},{"location":"n_alkanes/","title":"Slot: n-alkanes (n_alkanes)","text":"

Concentration of n-alkanes; can include multiple n-alkanes

URI: MIXS:0000503

"},{"location":"n_alkanes/#inheritance","title":"Inheritance","text":""},{"location":"n_alkanes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"n_alkanes/#properties","title":"Properties","text":""},{"location":"n_alkanes/#aliases","title":"Aliases","text":""},{"location":"n_alkanes/#examples","title":"Examples","text":"Value n-hexadecane;100 milligram per liter"},{"location":"n_alkanes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"n_alkanes/#annotations","title":"Annotations","text":"property value expected_value n-alkane name;measurement value"},{"location":"n_alkanes/#schema-source","title":"Schema Source","text":""},{"location":"n_alkanes/#linkml-source","title":"LinkML Source","text":"
name: n_alkanes\nannotations:\n  expected_value:\n    tag: expected_value\n    value: n-alkane name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of n-alkanes; can include multiple n-alkanes\ntitle: n-alkanes\nexamples:\n- value: n-hexadecane;100 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- n-alkanes\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000503\nalias: n_alkanes\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"name/","title":"Slot: name","text":"

A human readable label for an entity

URI: nmdc:name

"},{"location":"name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no PersonValue An attribute value representing a person yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no Site no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MaterialEntity no MetatranscriptomeAssembly no Configuration A set of parameters that define the actions of a process and is shared among ... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DataObject An object that primarily consists of symbols that represent information yes PlannedProcess no EnvironmentalMaterialTerm no NamedThing a databased entity or concept/class no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no ProcessedSample no ChemicalEntity An atom or molecule that can be represented with a chemical formula no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no Instrument A material entity that is designed to perform a function in a scientific inve... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no GeneProduct A molecule encoded by a gene that has an evolved function no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Study A study summarizes the overall goal of a research initiative and outlines the... yes MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes CalibrationInformation A calibration object that is associated with a process no Extraction A material separation in which a desired component of an input material is se... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Protocol no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no OntologyClass no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes ProtocolExecution A PlannedProces that has PlannedProcess parts no Manifest no OrthologyGroup A set of genes or gene products in which all members are orthologous no Biosample Biological source material which can be characterized by an experiment no LibraryPreparation no"},{"location":"name/#properties","title":"Properties","text":""},{"location":"name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"name/#schema-source","title":"Schema Source","text":""},{"location":"name/#linkml-source","title":"LinkML Source","text":"
name: name\ndescription: A human readable label for an entity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: name\ndomain_of:\n- PersonValue\n- NamedThing\n- Protocol\nrange: string\n\n
"},{"location":"ncbi_lineage/","title":"Slot: ncbi_lineage","text":"

Comma delimited ordered list of NCBI taxonomy names.

URI: nmdc:ncbi_lineage

"},{"location":"ncbi_lineage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"ncbi_lineage/#properties","title":"Properties","text":""},{"location":"ncbi_lineage/#comments","title":"Comments","text":""},{"location":"ncbi_lineage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ncbi_lineage/#schema-source","title":"Schema Source","text":""},{"location":"ncbi_lineage/#linkml-source","title":"LinkML Source","text":"
name: ncbi_lineage\ndescription: Comma delimited ordered list of NCBI taxonomy names.\ncomments:\n- Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_lineage\ndomain_of:\n- EukEval\nrange: string\n\n
"},{"location":"ncbi_lineage_tax_ids/","title":"Slot: ncbi_lineage_tax_ids","text":"

Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)

URI: nmdc:ncbi_lineage_tax_ids

"},{"location":"ncbi_lineage_tax_ids/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"ncbi_lineage_tax_ids/#properties","title":"Properties","text":""},{"location":"ncbi_lineage_tax_ids/#comments","title":"Comments","text":""},{"location":"ncbi_lineage_tax_ids/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ncbi_lineage_tax_ids/#schema-source","title":"Schema Source","text":""},{"location":"ncbi_lineage_tax_ids/#linkml-source","title":"LinkML Source","text":"
name: ncbi_lineage_tax_ids\ndescription: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)\ncomments:\n- Example 1-131567-2759-2611352-33682-191814-2603949\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_lineage_tax_ids\ndomain_of:\n- EukEval\nrange: string\npattern: ^\\d+(-\\d+)*$\n\n
"},{"location":"ncbi_project_name/","title":"Slot: ncbi_project_name","text":"

URI: nmdc:ncbi_project_name

"},{"location":"ncbi_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"ncbi_project_name/#properties","title":"Properties","text":""},{"location":"ncbi_project_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ncbi_project_name/#schema-source","title":"Schema Source","text":""},{"location":"ncbi_project_name/#linkml-source","title":"LinkML Source","text":"
name: ncbi_project_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_project_name\ndomain_of:\n- NucleotideSequencing\nrange: string\n\n
"},{"location":"ncbi_taxonomy_name/","title":"Slot: ncbi_taxonomy_name","text":"

URI: nmdc:ncbi_taxonomy_name

"},{"location":"ncbi_taxonomy_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ncbi_taxonomy_name/#properties","title":"Properties","text":""},{"location":"ncbi_taxonomy_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ncbi_taxonomy_name/#schema-source","title":"Schema Source","text":""},{"location":"ncbi_taxonomy_name/#linkml-source","title":"LinkML Source","text":"
name: ncbi_taxonomy_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_taxonomy_name\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"neon_biosample_identifiers/","title":"Slot: neon_biosample_identifiers","text":"

URI: nmdc:neon_biosample_identifiers

"},{"location":"neon_biosample_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"neon_biosample_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"neon_biosample_identifiers/#properties","title":"Properties","text":""},{"location":"neon_biosample_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"neon_biosample_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"neon_biosample_identifiers/#linkml-source","title":"LinkML Source","text":"
name: neon_biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- neon_identifiers\nalias: neon_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"neon_identifiers/","title":"Slot: neon_identifiers","text":"

identifiers for entities according to NEON

URI: nmdc:neon_identifiers

"},{"location":"neon_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain neon_study_identifiers None Study neon_biosample_identifiers None Biosample"},{"location":"neon_identifiers/#properties","title":"Properties","text":""},{"location":"neon_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"neon_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"neon_identifiers/#linkml-source","title":"LinkML Source","text":"
name: neon_identifiers\ndescription: identifiers for entities according to NEON\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: neon_identifiers\nrange: string\n\n
"},{"location":"neon_study_identifiers/","title":"Slot: neon_study_identifiers","text":"

URI: nmdc:neon_study_identifiers

"},{"location":"neon_study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"neon_study_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"neon_study_identifiers/#properties","title":"Properties","text":""},{"location":"neon_study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"neon_study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"neon_study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: neon_study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- neon_identifiers\nalias: neon_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"nitrate/","title":"Slot: nitrate (nitrate)","text":"

Concentration of nitrate in the sample

URI: MIXS:0000425

"},{"location":"nitrate/#inheritance","title":"Inheritance","text":""},{"location":"nitrate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrate/#properties","title":"Properties","text":""},{"location":"nitrate/#aliases","title":"Aliases","text":""},{"location":"nitrate/#examples","title":"Examples","text":"Value 65 micromole per liter"},{"location":"nitrate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitrate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitrate/#schema-source","title":"Schema Source","text":""},{"location":"nitrate/#linkml-source","title":"LinkML Source","text":"
name: nitrate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrate in the sample\ntitle: nitrate\nexamples:\n- value: 65 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000425\nalias: nitrate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"nitrate_nitrogen/","title":"Slot: nitrate_nitrogen (nitrate_nitrogen)","text":"

Concentration of nitrate nitrogen in the sample

URI: nmdc:nitrate_nitrogen

"},{"location":"nitrate_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrate_nitrogen/#properties","title":"Properties","text":""},{"location":"nitrate_nitrogen/#aliases","title":"Aliases","text":""},{"location":"nitrate_nitrogen/#examples","title":"Examples","text":"Value 0.29 mg/kg"},{"location":"nitrate_nitrogen/#comments","title":"Comments","text":""},{"location":"nitrate_nitrogen/#see-also","title":"See Also","text":""},{"location":"nitrate_nitrogen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitrate_nitrogen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitrate_nitrogen/#schema-source","title":"Schema Source","text":""},{"location":"nitrate_nitrogen/#linkml-source","title":"LinkML Source","text":"
name: nitrate_nitrogen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrate nitrogen in the sample\ntitle: nitrate_nitrogen\ncomments:\n- often below some specified limit of detection\nexamples:\n- value: 0.29 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrate_nitrogen\n- NO3-N\nrank: 1000\nalias: nitrate_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"nitrite/","title":"Slot: nitrite (nitrite)","text":"

Concentration of nitrite in the sample

URI: MIXS:0000426

"},{"location":"nitrite/#inheritance","title":"Inheritance","text":""},{"location":"nitrite/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrite/#properties","title":"Properties","text":""},{"location":"nitrite/#aliases","title":"Aliases","text":""},{"location":"nitrite/#examples","title":"Examples","text":"Value 0.5 micromole per liter"},{"location":"nitrite/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitrite/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitrite/#schema-source","title":"Schema Source","text":""},{"location":"nitrite/#linkml-source","title":"LinkML Source","text":"
name: nitrite\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrite in the sample\ntitle: nitrite\nexamples:\n- value: 0.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000426\nalias: nitrite\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"nitrite_nitrogen/","title":"Slot: nitrite_nitrogen (nitrite_nitrogen)","text":"

Concentration of nitrite nitrogen in the sample

URI: nmdc:nitrite_nitrogen

"},{"location":"nitrite_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrite_nitrogen/#properties","title":"Properties","text":""},{"location":"nitrite_nitrogen/#aliases","title":"Aliases","text":""},{"location":"nitrite_nitrogen/#examples","title":"Examples","text":"Value 1.2 mg/kg"},{"location":"nitrite_nitrogen/#see-also","title":"See Also","text":""},{"location":"nitrite_nitrogen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitrite_nitrogen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitrite_nitrogen/#schema-source","title":"Schema Source","text":""},{"location":"nitrite_nitrogen/#linkml-source","title":"LinkML Source","text":"
name: nitrite_nitrogen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrite nitrogen in the sample\ntitle: nitrite_nitrogen\nexamples:\n- value: 1.2 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrite_nitrogen\n- NO2-N\nrank: 1000\nalias: nitrite_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"nitro/","title":"Slot: nitrogen (nitro)","text":"

Concentration of nitrogen (total)

URI: MIXS:0000504

"},{"location":"nitro/#inheritance","title":"Inheritance","text":""},{"location":"nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitro/#properties","title":"Properties","text":""},{"location":"nitro/#aliases","title":"Aliases","text":""},{"location":"nitro/#examples","title":"Examples","text":"Value 4.2 micromole per liter"},{"location":"nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"nitro/#schema-source","title":"Schema Source","text":""},{"location":"nitro/#linkml-source","title":"LinkML Source","text":"
name: nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of nitrogen (total)\ntitle: nitrogen\nexamples:\n- value: 4.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000504\nalias: nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"non_microb_biomass/","title":"Slot: non-microbial biomass (non_microb_biomass)","text":"

Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;

URI: nmdc:non_microb_biomass

"},{"location":"non_microb_biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass/#properties","title":"Properties","text":""},{"location":"non_microb_biomass/#examples","title":"Examples","text":"Value insect 0.23 ug; plant 1g"},{"location":"non_microb_biomass/#see-also","title":"See Also","text":""},{"location":"non_microb_biomass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"non_microb_biomass/#schema-source","title":"Schema Source","text":""},{"location":"non_microb_biomass/#linkml-source","title":"LinkML Source","text":"
name: non_microb_biomass\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n  e.g.insect, plant, total. Can include multiple measurements separated by ;\ntitle: non-microbial biomass\nexamples:\n- value: insect 0.23 ug; plant 1g\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000174\n- MIXS:0000650\nrank: 8\nstring_serialization: '{text};{float} {unit}'\nalias: non_microb_biomass\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"non_microb_biomass_method/","title":"Slot: non-microbial biomass method (non_microb_biomass_method)","text":"

Reference or method used in determining biomass

URI: nmdc:non_microb_biomass_method

"},{"location":"non_microb_biomass_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass_method/#properties","title":"Properties","text":""},{"location":"non_microb_biomass_method/#examples","title":"Examples","text":"Value https://doi.org/10.1038/s41467-021-26181-3"},{"location":"non_microb_biomass_method/#comments","title":"Comments","text":""},{"location":"non_microb_biomass_method/#see-also","title":"See Also","text":""},{"location":"non_microb_biomass_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"non_microb_biomass_method/#schema-source","title":"Schema Source","text":""},{"location":"non_microb_biomass_method/#linkml-source","title":"LinkML Source","text":"
name: non_microb_biomass_method\ndescription: Reference or method used in determining biomass\ntitle: non-microbial biomass method\ncomments:\n- required if \"non-microbial biomass\" is provided\nexamples:\n- value: https://doi.org/10.1038/s41467-021-26181-3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 9\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: non_microb_biomass_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"non_min_nutr_regm/","title":"Slot: non-mineral nutrient regimen (non_min_nutr_regm)","text":"

Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens

URI: MIXS:0000571

"},{"location":"non_min_nutr_regm/#inheritance","title":"Inheritance","text":""},{"location":"non_min_nutr_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_min_nutr_regm/#properties","title":"Properties","text":""},{"location":"non_min_nutr_regm/#aliases","title":"Aliases","text":""},{"location":"non_min_nutr_regm/#examples","title":"Examples","text":"Value carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"non_min_nutr_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"non_min_nutr_regm/#annotations","title":"Annotations","text":"property value expected_value non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration"},{"location":"non_min_nutr_regm/#schema-source","title":"Schema Source","text":""},{"location":"non_min_nutr_regm/#linkml-source","title":"LinkML Source","text":"
name: non_min_nutr_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n      and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving the exposure of plant to non-mineral\n  nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n  nutrient, amount administered, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include multiple non-mineral nutrient regimens\ntitle: non-mineral nutrient regimen\nexamples:\n- value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- non-mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000571\nalias: non_min_nutr_regm\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\n
"},{"location":"notes/","title":"Slot: notes","text":"

URI: nmdc:notes

"},{"location":"notes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"notes/#properties","title":"Properties","text":""},{"location":"notes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"notes/#schema-source","title":"Schema Source","text":""},{"location":"notes/#linkml-source","title":"LinkML Source","text":"
name: notes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: notes\ndomain_of:\n- Study\nrange: string\n\n
"},{"location":"nucl_acid_amp/","title":"Slot: nucleic acid amplification (nucl_acid_amp)","text":"

A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids

URI: MIXS:0000038

"},{"location":"nucl_acid_amp/#inheritance","title":"Inheritance","text":""},{"location":"nucl_acid_amp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"nucl_acid_amp/#properties","title":"Properties","text":""},{"location":"nucl_acid_amp/#aliases","title":"Aliases","text":""},{"location":"nucl_acid_amp/#examples","title":"Examples","text":"Value https://phylogenomics.me/protocols/16s-pcr-protocol/"},{"location":"nucl_acid_amp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nucl_acid_amp/#annotations","title":"Annotations","text":"property value expected_value PMID, DOI or URL"},{"location":"nucl_acid_amp/#schema-source","title":"Schema Source","text":""},{"location":"nucl_acid_amp/#linkml-source","title":"LinkML Source","text":"
name: nucl_acid_amp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n  procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of\n  specific nucleic acids\ntitle: nucleic acid amplification\nexamples:\n- value: https://phylogenomics.me/protocols/16s-pcr-protocol/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid amplification\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000038\nalias: nucl_acid_amp\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"nucl_acid_ext/","title":"Slot: nucleic acid extraction (nucl_acid_ext)","text":"

A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample

URI: MIXS:0000037

"},{"location":"nucl_acid_ext/#inheritance","title":"Inheritance","text":""},{"location":"nucl_acid_ext/#properties","title":"Properties","text":""},{"location":"nucl_acid_ext/#aliases","title":"Aliases","text":""},{"location":"nucl_acid_ext/#examples","title":"Examples","text":"Value https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf"},{"location":"nucl_acid_ext/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nucl_acid_ext/#annotations","title":"Annotations","text":"property value expected_value PMID, DOI or URL"},{"location":"nucl_acid_ext/#schema-source","title":"Schema Source","text":""},{"location":"nucl_acid_ext/#linkml-source","title":"LinkML Source","text":"
name: nucl_acid_ext\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n  procedure (SOP), that describes the material separation to recover the nucleic acid\n  fraction from a sample\ntitle: nucleic acid extraction\nexamples:\n- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid extraction\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000037\nalias: nucl_acid_ext\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"nucleic_acid_sequence_source_field/","title":"Slot: nucleic_acid_sequence_source_field","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:nucleic_acid_sequence_source_field

"},{"location":"nucleic_acid_sequence_source_field/#inheritance","title":"Inheritance","text":""},{"location":"nucleic_acid_sequence_source_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nucleic_acid_sequence_source_field/#properties","title":"Properties","text":""},{"location":"nucleic_acid_sequence_source_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"nucleic_acid_sequence_source_field/#schema-source","title":"Schema Source","text":""},{"location":"nucleic_acid_sequence_source_field/#linkml-source","title":"LinkML Source","text":"
name: nucleic acid sequence source field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: nucleic_acid_sequence_source_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"num_16s/","title":"Slot: num_16s","text":"

URI: nmdc:num_16s

"},{"location":"num_16s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_16s/#properties","title":"Properties","text":""},{"location":"num_16s/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_16s/#schema-source","title":"Schema Source","text":""},{"location":"num_16s/#linkml-source","title":"LinkML Source","text":"
name: num_16s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_16s\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"num_23s/","title":"Slot: num_23s","text":"

URI: nmdc:num_23s

"},{"location":"num_23s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_23s/#properties","title":"Properties","text":""},{"location":"num_23s/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_23s/#schema-source","title":"Schema Source","text":""},{"location":"num_23s/#linkml-source","title":"LinkML Source","text":"
name: num_23s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_23s\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"num_5s/","title":"Slot: num_5s","text":"

URI: nmdc:num_5s

"},{"location":"num_5s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_5s/#properties","title":"Properties","text":""},{"location":"num_5s/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_5s/#schema-source","title":"Schema Source","text":""},{"location":"num_5s/#linkml-source","title":"LinkML Source","text":"
name: num_5s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_5s\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"num_aligned_reads/","title":"Slot: num_aligned_reads","text":"

The sequence count number of input reads aligned to assembled contigs.

URI: nmdc:num_aligned_reads

"},{"location":"num_aligned_reads/#inheritance","title":"Inheritance","text":""},{"location":"num_aligned_reads/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"num_aligned_reads/#properties","title":"Properties","text":""},{"location":"num_aligned_reads/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_aligned_reads/#schema-source","title":"Schema Source","text":""},{"location":"num_aligned_reads/#linkml-source","title":"LinkML Source","text":"
name: num_aligned_reads\ndescription: The sequence count number of input reads aligned to assembled contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_aligned_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"num_input_reads/","title":"Slot: num_input_reads","text":"

The sequence count number of input reads for assembly.

URI: nmdc:num_input_reads

"},{"location":"num_input_reads/#inheritance","title":"Inheritance","text":""},{"location":"num_input_reads/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"num_input_reads/#properties","title":"Properties","text":""},{"location":"num_input_reads/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_input_reads/#schema-source","title":"Schema Source","text":""},{"location":"num_input_reads/#linkml-source","title":"LinkML Source","text":"
name: num_input_reads\ndescription: The sequence count number of input reads for assembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_input_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"num_t_rna/","title":"Slot: num_t_rna","text":"

URI: nmdc:num_t_rna

"},{"location":"num_t_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_t_rna/#properties","title":"Properties","text":""},{"location":"num_t_rna/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"num_t_rna/#schema-source","title":"Schema Source","text":""},{"location":"num_t_rna/#linkml-source","title":"LinkML Source","text":"
name: num_t_rna\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_t_rna\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"number_of_contig/","title":"Slot: number_of_contig","text":"

URI: nmdc:number_of_contig

"},{"location":"number_of_contig/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"number_of_contig/#properties","title":"Properties","text":""},{"location":"number_of_contig/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"number_of_contig/#schema-source","title":"Schema Source","text":""},{"location":"number_of_contig/#linkml-source","title":"LinkML Source","text":"
name: number_of_contig\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: number_of_contig\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"number_pets/","title":"Slot: number of pets (number_pets)","text":"

The number of pets residing in the sampled space

URI: MIXS:0000231

"},{"location":"number_pets/#inheritance","title":"Inheritance","text":""},{"location":"number_pets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"number_pets/#properties","title":"Properties","text":""},{"location":"number_pets/#aliases","title":"Aliases","text":""},{"location":"number_pets/#examples","title":"Examples","text":"Value"},{"location":"number_pets/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"number_pets/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"number_pets/#schema-source","title":"Schema Source","text":""},{"location":"number_pets/#linkml-source","title":"LinkML Source","text":"
name: number_pets\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of pets residing in the sampled space\ntitle: number of pets\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of pets\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000231\nalias: number_pets\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"number_plants/","title":"Slot: number of houseplants (number_plants)","text":"

The number of plant(s) in the sampling space

URI: MIXS:0000230

"},{"location":"number_plants/#inheritance","title":"Inheritance","text":""},{"location":"number_plants/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"number_plants/#properties","title":"Properties","text":""},{"location":"number_plants/#aliases","title":"Aliases","text":""},{"location":"number_plants/#examples","title":"Examples","text":"Value"},{"location":"number_plants/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"number_plants/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"number_plants/#schema-source","title":"Schema Source","text":""},{"location":"number_plants/#linkml-source","title":"LinkML Source","text":"
name: number_plants\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of plant(s) in the sampling space\ntitle: number of houseplants\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of houseplants\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000230\nalias: number_plants\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"number_resident/","title":"Slot: number of residents (number_resident)","text":"

The number of individuals currently occupying in the sampling location

URI: MIXS:0000232

"},{"location":"number_resident/#inheritance","title":"Inheritance","text":""},{"location":"number_resident/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"number_resident/#properties","title":"Properties","text":""},{"location":"number_resident/#aliases","title":"Aliases","text":""},{"location":"number_resident/#examples","title":"Examples","text":"Value"},{"location":"number_resident/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"number_resident/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"number_resident/#schema-source","title":"Schema Source","text":""},{"location":"number_resident/#linkml-source","title":"LinkML Source","text":"
name: number_resident\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of individuals currently occupying in the sampling location\ntitle: number of residents\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of residents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000232\nalias: number_resident\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"object_set/","title":"Slot: object_set","text":"

Applies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types

URI: nmdc:object_set

"},{"location":"object_set/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain chemical_entity_set This property links a database object to the set of chemical entities within ... ChemicalEntity Database biosample_set This property links a database object to the set of samples within it Biosample Database study_set This property links a database object to the set of studies within it Study Database field_research_site_set FieldResearchSite Database collecting_biosamples_from_site_set CollectingBiosamplesFromSite Database data_object_set This property links a database object to the set of data objects within it DataObject Database genome_feature_set This property links a database object to the set of all features GenomeFeature Database functional_annotation_set This property links a database object to the set of all functional annotation... FunctionalAnnotation Database workflow_execution_set This property links a database object to the set of workflow executions WorkflowExecution Database data_generation_set This property links a database object to the set of data generations within i... DataGeneration Database processed_sample_set This property links a database object to the set of processed samples within ... ProcessedSample Database instrument_set This property links a database object to the set of instruments within it Instrument Database calibration_set This property links a database object to the set of calibrations within it CalibrationInformation Database configuration_set This property links a database object to the set of configurations within it Configuration Database manifest_set This property links a database object to the set of manifests within it Manifest Database protocol_execution_set This property links a database object to the set of protocol executions withi... ProtocolExecution Database storage_process_set This property links a database object to the set of storage processes within ... StorageProcess Database material_processing_set This property links a database object to the set of material processing withi... MaterialProcessing Database"},{"location":"object_set/#properties","title":"Properties","text":""},{"location":"object_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"object_set/#schema-source","title":"Schema Source","text":""},{"location":"object_set/#linkml-source","title":"LinkML Source","text":"
name: object_set\ndescription: Applies to a property that links a database object to a set of objects.\n  This is necessary in a json document to provide context for a list, and to allow\n  for a single json object that combines multiple object types\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: object_set\nrange: string\nmultivalued: true\ninlined_as_list: true\n\n
"},{"location":"objective/","title":"Slot: objective","text":"

The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.

URI: nmdc:objective

"},{"location":"objective/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"objective/#properties","title":"Properties","text":""},{"location":"objective/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"objective/#schema-source","title":"Schema Source","text":""},{"location":"objective/#linkml-source","title":"LinkML Source","text":"
name: objective\ndescription: The scientific objectives associated with the entity. It SHOULD correspond\n  to scientific norms for objectives field in a structured abstract.\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- SIO:000337\nrank: 1000\nalias: objective\ndomain_of:\n- Study\nrange: string\n\n
"},{"location":"occup_density_samp/","title":"Slot: occupant density at sampling (occup_density_samp)","text":"

Average number of occupants at time of sampling per square footage

URI: MIXS:0000217

"},{"location":"occup_density_samp/#inheritance","title":"Inheritance","text":""},{"location":"occup_density_samp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"occup_density_samp/#properties","title":"Properties","text":""},{"location":"occup_density_samp/#aliases","title":"Aliases","text":""},{"location":"occup_density_samp/#examples","title":"Examples","text":"Value"},{"location":"occup_density_samp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"occup_density_samp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"occup_density_samp/#schema-source","title":"Schema Source","text":""},{"location":"occup_density_samp/#linkml-source","title":"LinkML Source","text":"
name: occup_density_samp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Average number of occupants at time of sampling per square footage\ntitle: occupant density at sampling\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupant density at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000217\nalias: occup_density_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"occup_document/","title":"Slot: occupancy documentation (occup_document)","text":"

The type of documentation of occupancy

URI: MIXS:0000816

"},{"location":"occup_document/#inheritance","title":"Inheritance","text":""},{"location":"occup_document/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"occup_document/#properties","title":"Properties","text":""},{"location":"occup_document/#aliases","title":"Aliases","text":""},{"location":"occup_document/#examples","title":"Examples","text":"Value estimate"},{"location":"occup_document/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"occup_document/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"occup_document/#schema-source","title":"Schema Source","text":""},{"location":"occup_document/#linkml-source","title":"LinkML Source","text":"
name: occup_document\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of documentation of occupancy\ntitle: occupancy documentation\nexamples:\n- value: estimate\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy documentation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000816\nalias: occup_document\ndomain_of:\n- Biosample\nrange: occup_document_enum\nmultivalued: false\n\n
"},{"location":"occup_samp/","title":"Slot: occupancy at sampling (occup_samp)","text":"

Number of occupants present at time of sample within the given space

URI: MIXS:0000772

"},{"location":"occup_samp/#inheritance","title":"Inheritance","text":""},{"location":"occup_samp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"occup_samp/#properties","title":"Properties","text":""},{"location":"occup_samp/#aliases","title":"Aliases","text":""},{"location":"occup_samp/#examples","title":"Examples","text":"Value 10"},{"location":"occup_samp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"occup_samp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"occup_samp/#schema-source","title":"Schema Source","text":""},{"location":"occup_samp/#linkml-source","title":"LinkML Source","text":"
name: occup_samp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Number of occupants present at time of sample within the given space\ntitle: occupancy at sampling\nexamples:\n- value: '10'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000772\nalias: occup_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"omics_processing_identifiers/","title":"Slot: omics_processing_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:omics_processing_identifiers

"},{"location":"omics_processing_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"omics_processing_identifiers/#properties","title":"Properties","text":""},{"location":"omics_processing_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"omics_processing_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"omics_processing_identifiers/#linkml-source","title":"LinkML Source","text":"
name: omics_processing_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: omics_processing_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"omics_type/","title":"Slot: omics_type (DEPRECATED)

The type of omics data

URI: nmdc:omics_type

","text":""},{"location":"omics_type/#properties","title":"Properties","text":""},{"location":"omics_type/#examples","title":"Examples","text":"Value metatranscriptome metagenome"},{"location":"omics_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"omics_type/#schema-source","title":"Schema Source","text":""},{"location":"omics_type/#linkml-source","title":"LinkML Source","text":"
name: omics_type\ndescription: The type of omics data\ndeprecated: 'True'\nexamples:\n- value: metatranscriptome\n- value: metagenome\nfrom_schema: https://w3id.org/nmdc/nmdc\ndeprecated_element_has_exact_replacement: analyte_category\nrank: 1000\nalias: omics_type\nrange: string\n\n
"},{"location":"orcid/","title":"Slot: orcid","text":"

The ORCID of a person.

URI: nmdc:orcid

"},{"location":"orcid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"orcid/#properties","title":"Properties","text":""},{"location":"orcid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"orcid/#schema-source","title":"Schema Source","text":""},{"location":"orcid/#linkml-source","title":"LinkML Source","text":"
name: orcid\ndescription: The ORCID of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: orcid\ndomain_of:\n- PersonValue\nrange: string\n\n
"},{"location":"ordered_mobile_phases/","title":"Slot: ordered_mobile_phases","text":"

The solution(s) that moves through a chromatography column.

URI: nmdc:ordered_mobile_phases

"},{"location":"ordered_mobile_phases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no"},{"location":"ordered_mobile_phases/#properties","title":"Properties","text":""},{"location":"ordered_mobile_phases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ordered_mobile_phases/#schema-source","title":"Schema Source","text":""},{"location":"ordered_mobile_phases/#linkml-source","title":"LinkML Source","text":"
name: ordered_mobile_phases\ndescription: The solution(s) that moves through a chromatography column.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: ordered_mobile_phases\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: MobilePhaseSegment\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"org_carb/","title":"Slot: organic carbon (org_carb)","text":"

Concentration of organic carbon

URI: MIXS:0000508

"},{"location":"org_carb/#inheritance","title":"Inheritance","text":""},{"location":"org_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_carb/#properties","title":"Properties","text":""},{"location":"org_carb/#aliases","title":"Aliases","text":""},{"location":"org_carb/#examples","title":"Examples","text":"Value 1.5 microgram per liter"},{"location":"org_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"org_carb/#schema-source","title":"Schema Source","text":""},{"location":"org_carb/#linkml-source","title":"LinkML Source","text":"
name: org_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of organic carbon\ntitle: organic carbon\nexamples:\n- value: 1.5 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000508\nalias: org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"org_count_qpcr_info/","title":"Slot: organism count qPCR information (org_count_qpcr_info)","text":"

If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)

URI: MIXS:0000099

"},{"location":"org_count_qpcr_info/#inheritance","title":"Inheritance","text":""},{"location":"org_count_qpcr_info/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_count_qpcr_info/#properties","title":"Properties","text":""},{"location":"org_count_qpcr_info/#aliases","title":"Aliases","text":""},{"location":"org_count_qpcr_info/#examples","title":"Examples","text":"Value"},{"location":"org_count_qpcr_info/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_count_qpcr_info/#annotations","title":"Annotations","text":"property value expected_value gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles"},{"location":"org_count_qpcr_info/#schema-source","title":"Schema Source","text":""},{"location":"org_count_qpcr_info/#linkml-source","title":"LinkML Source","text":"
name: org_count_qpcr_info\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n      denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n      elongation:degrees_minutes; total cycles\n  preferred_unit:\n    tag: preferred_unit\n    value: number of cells per gram (or ml or cm^2)\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'If qpcr was used for the cell count, the target gene name, the primer\n  sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n  FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n  annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n  30 cycles)'\ntitle: organism count qPCR information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count qPCR information\nrank: 1000\nis_a: core field\nstring_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n  elongation:degrees_minutes; total cycles'\nslot_uri: MIXS:0000099\nalias: org_count_qpcr_info\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"org_matter/","title":"Slot: organic matter (org_matter)","text":"

Concentration of organic matter

URI: MIXS:0000204

"},{"location":"org_matter/#inheritance","title":"Inheritance","text":""},{"location":"org_matter/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_matter/#properties","title":"Properties","text":""},{"location":"org_matter/#aliases","title":"Aliases","text":""},{"location":"org_matter/#examples","title":"Examples","text":"Value 1.75 milligram per cubic meter"},{"location":"org_matter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_matter/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"org_matter/#schema-source","title":"Schema Source","text":""},{"location":"org_matter/#linkml-source","title":"LinkML Source","text":"
name: org_matter\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of organic matter\ntitle: organic matter\nexamples:\n- value: 1.75 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000204\nalias: org_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"org_nitro/","title":"Slot: organic nitrogen (org_nitro)","text":"

Concentration of organic nitrogen

URI: MIXS:0000205

"},{"location":"org_nitro/#inheritance","title":"Inheritance","text":""},{"location":"org_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_nitro/#properties","title":"Properties","text":""},{"location":"org_nitro/#aliases","title":"Aliases","text":""},{"location":"org_nitro/#examples","title":"Examples","text":"Value 4 micromole per liter"},{"location":"org_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"org_nitro/#schema-source","title":"Schema Source","text":""},{"location":"org_nitro/#linkml-source","title":"LinkML Source","text":"
name: org_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of organic nitrogen\ntitle: organic nitrogen\nexamples:\n- value: 4 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000205\nalias: org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"org_nitro_method/","title":"Slot: organic nitrogen method (org_nitro_method)","text":"

Method used for obtaining organic nitrogen

URI: nmdc:org_nitro_method

"},{"location":"org_nitro_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_nitro_method/#properties","title":"Properties","text":""},{"location":"org_nitro_method/#examples","title":"Examples","text":"Value https://doi.org/10.1016/0038-0717(85)90144-0"},{"location":"org_nitro_method/#comments","title":"Comments","text":""},{"location":"org_nitro_method/#see-also","title":"See Also","text":""},{"location":"org_nitro_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_nitro_method/#schema-source","title":"Schema Source","text":""},{"location":"org_nitro_method/#linkml-source","title":"LinkML Source","text":"
name: org_nitro_method\ndescription: Method used for obtaining organic nitrogen\ntitle: organic nitrogen method\ncomments:\n- required if \"org_nitro\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(85)90144-0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000338\n- MIXS:0000205\nrank: 14\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: org_nitro_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\n
"},{"location":"org_particles/","title":"Slot: organic particles (org_particles)","text":"

Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.

URI: MIXS:0000665

"},{"location":"org_particles/#inheritance","title":"Inheritance","text":""},{"location":"org_particles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_particles/#properties","title":"Properties","text":""},{"location":"org_particles/#aliases","title":"Aliases","text":""},{"location":"org_particles/#examples","title":"Examples","text":"Value"},{"location":"org_particles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"org_particles/#annotations","title":"Annotations","text":"property value expected_value particle name;measurement value"},{"location":"org_particles/#schema-source","title":"Schema Source","text":""},{"location":"org_particles/#linkml-source","title":"LinkML Source","text":"
name: org_particles\nannotations:\n  expected_value:\n    tag: expected_value\n    value: particle name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of particles such as faeces, hairs, food, vomit, paper\n  fibers, plant material, humus, etc.\ntitle: organic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000665\nalias: org_particles\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"organism_count/","title":"Slot: organism count (organism_count)","text":"

Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)

URI: MIXS:0000103

"},{"location":"organism_count/#inheritance","title":"Inheritance","text":""},{"location":"organism_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"organism_count/#properties","title":"Properties","text":""},{"location":"organism_count/#aliases","title":"Aliases","text":""},{"location":"organism_count/#examples","title":"Examples","text":"Value total prokaryotes;3.5e7 cells per milliliter;qPCR"},{"location":"organism_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"organism_count/#annotations","title":"Annotations","text":"property value expected_value organism name;measurement value;enumeration"},{"location":"organism_count/#schema-source","title":"Schema Source","text":""},{"location":"organism_count/#linkml-source","title":"LinkML Source","text":"
name: organism_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: organism name;measurement value;enumeration\n  preferred_unit:\n    tag: preferred_unit\n    value: number of cells per cubic meter, number of cells per milliliter, number\n      of cells per cubic centimeter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: 'Total cell count of any organism (or group of organisms) per gram, volume\n  or area of sample, should include name of organism followed by count. The method\n  that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided.\n  (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\ntitle: organism count\nexamples:\n- value: total prokaryotes;3.5e7 cells per milliliter;qPCR\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000103\nalias: organism_count\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"other_treatment/","title":"Slot: other treatments (other_treatment)","text":"

Other treatments applied to your samples that are not applicable to the provided fields

URI: nmdc:other_treatment

"},{"location":"other_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"other_treatment/#properties","title":"Properties","text":""},{"location":"other_treatment/#comments","title":"Comments","text":""},{"location":"other_treatment/#see-also","title":"See Also","text":""},{"location":"other_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"other_treatment/#schema-source","title":"Schema Source","text":""},{"location":"other_treatment/#linkml-source","title":"LinkML Source","text":"
name: other_treatment\ndescription: Other treatments applied to your samples that are not applicable to the\n  provided fields\ntitle: other treatments\nnotes:\n- Values entered here will be used to determine potential new slots.\ncomments:\n- This is an open text field to provide any treatments that cannot be captured in\n  the provided slots.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000300\nrank: 15\nstring_serialization: '{text}'\nalias: other_treatment\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"output_base_count/","title":"Slot: output_base_count","text":"

After QC analysis nucleotide base count number.

URI: nmdc:output_base_count

"},{"location":"output_base_count/#inheritance","title":"Inheritance","text":""},{"location":"output_base_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_base_count/#properties","title":"Properties","text":""},{"location":"output_base_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"output_base_count/#schema-source","title":"Schema Source","text":""},{"location":"output_base_count/#linkml-source","title":"LinkML Source","text":"
name: output_base_count\ndescription: After QC analysis nucleotide base count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_base_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"output_read_bases/","title":"Slot: output_read_bases","text":"

TODO

URI: nmdc:output_read_bases

"},{"location":"output_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_read_bases/#properties","title":"Properties","text":""},{"location":"output_read_bases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"output_read_bases/#schema-source","title":"Schema Source","text":""},{"location":"output_read_bases/#linkml-source","title":"LinkML Source","text":"
name: output_read_bases\ndescription: TODO\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: output_read_bases\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"output_read_count/","title":"Slot: output_read_count","text":"

After QC analysis sequence count number.

URI: nmdc:output_read_count

"},{"location":"output_read_count/#inheritance","title":"Inheritance","text":""},{"location":"output_read_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_read_count/#properties","title":"Properties","text":""},{"location":"output_read_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"output_read_count/#schema-source","title":"Schema Source","text":""},{"location":"output_read_count/#linkml-source","title":"LinkML Source","text":"
name: output_read_count\ndescription: After QC analysis sequence count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_read_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\n
"},{"location":"owc_tvdss/","title":"Slot: oil water contact depth (owc_tvdss)","text":"

Depth of the original oil water contact (OWC) zone (average) (m TVDSS)

URI: MIXS:0000405

"},{"location":"owc_tvdss/#inheritance","title":"Inheritance","text":""},{"location":"owc_tvdss/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"owc_tvdss/#properties","title":"Properties","text":""},{"location":"owc_tvdss/#aliases","title":"Aliases","text":""},{"location":"owc_tvdss/#examples","title":"Examples","text":"Value"},{"location":"owc_tvdss/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"owc_tvdss/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"owc_tvdss/#schema-source","title":"Schema Source","text":""},{"location":"owc_tvdss/#linkml-source","title":"LinkML Source","text":"
name: owc_tvdss\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\ntitle: oil water contact depth\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oil water contact depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000405\nalias: owc_tvdss\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"oxy_stat_samp/","title":"Slot: oxygenation status of sample (oxy_stat_samp)","text":"

Oxygenation status of sample

URI: MIXS:0000753

"},{"location":"oxy_stat_samp/#inheritance","title":"Inheritance","text":""},{"location":"oxy_stat_samp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"oxy_stat_samp/#properties","title":"Properties","text":""},{"location":"oxy_stat_samp/#aliases","title":"Aliases","text":""},{"location":"oxy_stat_samp/#examples","title":"Examples","text":"Value aerobic"},{"location":"oxy_stat_samp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"oxy_stat_samp/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"oxy_stat_samp/#schema-source","title":"Schema Source","text":""},{"location":"oxy_stat_samp/#linkml-source","title":"LinkML Source","text":"
name: oxy_stat_samp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Oxygenation status of sample\ntitle: oxygenation status of sample\nexamples:\n- value: aerobic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygenation status of sample\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000753\nalias: oxy_stat_samp\ndomain_of:\n- Biosample\nrange: oxy_stat_samp_enum\nmultivalued: false\n\n
"},{"location":"oxygen/","title":"Slot: oxygen (oxygen)","text":"

Oxygen (gas) amount or concentration at the time of sampling

URI: MIXS:0000104

"},{"location":"oxygen/#inheritance","title":"Inheritance","text":""},{"location":"oxygen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"oxygen/#properties","title":"Properties","text":""},{"location":"oxygen/#aliases","title":"Aliases","text":""},{"location":"oxygen/#examples","title":"Examples","text":"Value 600 parts per million"},{"location":"oxygen/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"oxygen/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"oxygen/#schema-source","title":"Schema Source","text":""},{"location":"oxygen/#linkml-source","title":"LinkML Source","text":"
name: oxygen\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Oxygen (gas) amount or concentration at the time of sampling\ntitle: oxygen\nexamples:\n- value: 600 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000104\nalias: oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"part_of/","title":"Slot: part_of","text":"

Links a resource to another resource that either logically or physically includes it.

URI: dcterms:isPartOf

"},{"location":"part_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes"},{"location":"part_of/#properties","title":"Properties","text":""},{"location":"part_of/#aliases","title":"Aliases","text":""},{"location":"part_of/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"part_of/#schema-source","title":"Schema Source","text":""},{"location":"part_of/#linkml-source","title":"LinkML Source","text":"
name: part_of\ndescription: Links a resource to another resource that either logically or physically\n  includes it.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- is part of\nrank: 1000\nslot_uri: dcterms:isPartOf\nalias: part_of\ndomain_of:\n- FieldResearchSite\n- Study\nrange: NamedThing\nmultivalued: true\n\n
"},{"location":"part_org_carb/","title":"Slot: particulate organic carbon (part_org_carb)","text":"

Concentration of particulate organic carbon

URI: MIXS:0000515

"},{"location":"part_org_carb/#inheritance","title":"Inheritance","text":""},{"location":"part_org_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"part_org_carb/#properties","title":"Properties","text":""},{"location":"part_org_carb/#aliases","title":"Aliases","text":""},{"location":"part_org_carb/#examples","title":"Examples","text":"Value 1.92 micromole per liter"},{"location":"part_org_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"part_org_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"part_org_carb/#schema-source","title":"Schema Source","text":""},{"location":"part_org_carb/#linkml-source","title":"LinkML Source","text":"
name: part_org_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of particulate organic carbon\ntitle: particulate organic carbon\nexamples:\n- value: 1.92 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000515\nalias: part_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"part_org_nitro/","title":"Slot: particulate organic nitrogen (part_org_nitro)","text":"

Concentration of particulate organic nitrogen

URI: MIXS:0000719

"},{"location":"part_org_nitro/#inheritance","title":"Inheritance","text":""},{"location":"part_org_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"part_org_nitro/#properties","title":"Properties","text":""},{"location":"part_org_nitro/#aliases","title":"Aliases","text":""},{"location":"part_org_nitro/#examples","title":"Examples","text":"Value 0.3 micromole per liter"},{"location":"part_org_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"part_org_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"part_org_nitro/#schema-source","title":"Schema Source","text":""},{"location":"part_org_nitro/#linkml-source","title":"LinkML Source","text":"
name: part_org_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of particulate organic nitrogen\ntitle: particulate organic nitrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000719\nalias: part_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"particle_class/","title":"Slot: particle classification (particle_class)","text":"

Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values

URI: MIXS:0000206

"},{"location":"particle_class/#inheritance","title":"Inheritance","text":""},{"location":"particle_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"particle_class/#properties","title":"Properties","text":""},{"location":"particle_class/#aliases","title":"Aliases","text":""},{"location":"particle_class/#examples","title":"Examples","text":"Value"},{"location":"particle_class/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"particle_class/#annotations","title":"Annotations","text":"property value expected_value particle name;measurement value"},{"location":"particle_class/#schema-source","title":"Schema Source","text":""},{"location":"particle_class/#linkml-source","title":"LinkML Source","text":"
name: particle_class\nannotations:\n  expected_value:\n    tag: expected_value\n    value: particle name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micrometer\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Particles are classified, based on their size, into six general categories:clay,\n  silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded\n  by the name of the particle type; can include multiple values\ntitle: particle classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particle classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000206\nalias: particle_class\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"pcr_cond/","title":"Slot: pcr conditions (pcr_cond)","text":"

Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'

URI: MIXS:0000049

"},{"location":"pcr_cond/#inheritance","title":"Inheritance","text":""},{"location":"pcr_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation yes"},{"location":"pcr_cond/#properties","title":"Properties","text":""},{"location":"pcr_cond/#aliases","title":"Aliases","text":""},{"location":"pcr_cond/#examples","title":"Examples","text":"Value initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35"},{"location":"pcr_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pcr_cond/#annotations","title":"Annotations","text":"property value expected_value initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles"},{"location":"pcr_cond/#schema-source","title":"Schema Source","text":""},{"location":"pcr_cond/#linkml-source","title":"LinkML Source","text":"
name: pcr_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n      elongation:degrees_minutes;total cycles\ndescription: Description of reaction conditions and components of PCR in the form\n  of 'initial denaturation:94degC_1.5min; annealing=...'\ntitle: pcr conditions\nexamples:\n- value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr conditions\nrank: 1000\nis_a: sequencing field\nstring_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n  elongation:degrees_minutes;total cycles\nslot_uri: MIXS:0000049\nalias: pcr_cond\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"pcr_cycles/","title":"Slot: pcr_cycles","text":"

URI: nmdc:pcr_cycles

"},{"location":"pcr_cycles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"pcr_cycles/#properties","title":"Properties","text":""},{"location":"pcr_cycles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pcr_cycles/#schema-source","title":"Schema Source","text":""},{"location":"pcr_cycles/#linkml-source","title":"LinkML Source","text":"
name: pcr_cycles\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0002475\nrank: 1000\nalias: pcr_cycles\ndomain_of:\n- LibraryPreparation\nrange: integer\n\n
"},{"location":"pcr_primers/","title":"Slot: pcr primers (pcr_primers)","text":"

PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters

URI: MIXS:0000046

"},{"location":"pcr_primers/#inheritance","title":"Inheritance","text":""},{"location":"pcr_primers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"pcr_primers/#properties","title":"Properties","text":""},{"location":"pcr_primers/#aliases","title":"Aliases","text":""},{"location":"pcr_primers/#examples","title":"Examples","text":"Value FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT"},{"location":"pcr_primers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pcr_primers/#annotations","title":"Annotations","text":"property value expected_value FWD: forward primer sequence;REV:reverse primer sequence"},{"location":"pcr_primers/#schema-source","title":"Schema Source","text":""},{"location":"pcr_primers/#linkml-source","title":"LinkML Source","text":"
name: pcr_primers\nannotations:\n  expected_value:\n    tag: expected_value\n    value: 'FWD: forward primer sequence;REV:reverse primer sequence'\ndescription: PCR primers that were used to amplify the sequence of the targeted gene,\n  locus or subfragment. This field should contain all the primers used for a single\n  PCR reaction if multiple forward or reverse primers are present in a single PCR\n  reaction. The primer sequence should be reported in uppercase letters\ntitle: pcr primers\nexamples:\n- value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr primers\nrank: 1000\nis_a: sequencing field\nstring_serialization: FWD:{dna};REV:{dna}\nslot_uri: MIXS:0000046\nalias: pcr_primers\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"peptide_sequence/","title":"Slot: peptide_sequence","text":"

URI: nmdc:peptide_sequence

"},{"location":"peptide_sequence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sequence/#properties","title":"Properties","text":""},{"location":"peptide_sequence/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"peptide_sequence/#schema-source","title":"Schema Source","text":""},{"location":"peptide_sequence/#linkml-source","title":"LinkML Source","text":"
name: peptide_sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence\ndomain_of:\n- PeptideQuantification\nrange: string\n\n
"},{"location":"peptide_sequence_count/","title":"Slot: peptide_sequence_count","text":"

count of peptide sequences grouped to the best_protein

URI: nmdc:peptide_sequence_count

"},{"location":"peptide_sequence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"peptide_sequence_count/#properties","title":"Properties","text":""},{"location":"peptide_sequence_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"peptide_sequence_count/#schema-source","title":"Schema Source","text":""},{"location":"peptide_sequence_count/#linkml-source","title":"LinkML Source","text":"
name: peptide_sequence_count\ndescription: count of peptide sequences grouped to the best_protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\n
"},{"location":"peptide_spectral_count/","title":"Slot: peptide_spectral_count","text":"

sum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file

URI: nmdc:peptide_spectral_count

"},{"location":"peptide_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_spectral_count/#properties","title":"Properties","text":""},{"location":"peptide_spectral_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"peptide_spectral_count/#schema-source","title":"Schema Source","text":""},{"location":"peptide_spectral_count/#linkml-source","title":"LinkML Source","text":"
name: peptide_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the peptide sequence\n  within a given LC-MS/MS data file\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_spectral_count\ndomain_of:\n- PeptideQuantification\nrange: integer\n\n
"},{"location":"peptide_sum_masic_abundance/","title":"Slot: peptide_sum_masic_abundance","text":"

combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool

URI: nmdc:peptide_sum_masic_abundance

"},{"location":"peptide_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sum_masic_abundance/#properties","title":"Properties","text":""},{"location":"peptide_sum_masic_abundance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"peptide_sum_masic_abundance/#schema-source","title":"Schema Source","text":""},{"location":"peptide_sum_masic_abundance/#linkml-source","title":"LinkML Source","text":"
name: peptide_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n  with the peptide sequence from a given LC-MS/MS data file using the MASIC tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sum_masic_abundance\ndomain_of:\n- PeptideQuantification\nrange: integer\n\n
"},{"location":"permeability/","title":"Slot: permeability (permeability)","text":"

Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))

URI: MIXS:0000404

"},{"location":"permeability/#inheritance","title":"Inheritance","text":""},{"location":"permeability/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"permeability/#properties","title":"Properties","text":""},{"location":"permeability/#aliases","title":"Aliases","text":""},{"location":"permeability/#examples","title":"Examples","text":"Value"},{"location":"permeability/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"permeability/#annotations","title":"Annotations","text":"property value expected_value measurement value range"},{"location":"permeability/#schema-source","title":"Schema Source","text":""},{"location":"permeability/#linkml-source","title":"LinkML Source","text":"
name: permeability\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: mD\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Measure of the ability of a hydrocarbon resource to allow fluids to\n  pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\ntitle: permeability\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- permeability\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} - {integer} {unit}'\nslot_uri: MIXS:0000404\nalias: permeability\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"perturbation/","title":"Slot: perturbation (perturbation)","text":"

Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types

URI: MIXS:0000754

"},{"location":"perturbation/#inheritance","title":"Inheritance","text":""},{"location":"perturbation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"perturbation/#properties","title":"Properties","text":""},{"location":"perturbation/#aliases","title":"Aliases","text":""},{"location":"perturbation/#examples","title":"Examples","text":"Value antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M"},{"location":"perturbation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"perturbation/#annotations","title":"Annotations","text":"property value expected_value perturbation type name;perturbation interval and duration"},{"location":"perturbation/#schema-source","title":"Schema Source","text":""},{"location":"perturbation/#linkml-source","title":"LinkML Source","text":"
name: perturbation\nannotations:\n  expected_value:\n    tag: expected_value\n    value: perturbation type name;perturbation interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Type of perturbation, e.g. chemical administration, physical disturbance,\n  etc., coupled with perturbation regimen including how many times the perturbation\n  was repeated, how long each perturbation lasted, and the start and end time of the\n  entire perturbation period; can include multiple perturbation types\ntitle: perturbation\nexamples:\n- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- perturbation\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000754\nalias: perturbation\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"pesticide_regm/","title":"Slot: pesticide regimen (pesticide_regm)","text":"

Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens

URI: MIXS:0000573

"},{"location":"pesticide_regm/#inheritance","title":"Inheritance","text":""},{"location":"pesticide_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pesticide_regm/#properties","title":"Properties","text":""},{"location":"pesticide_regm/#aliases","title":"Aliases","text":""},{"location":"pesticide_regm/#examples","title":"Examples","text":"Value pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"pesticide_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pesticide_regm/#annotations","title":"Annotations","text":"property value expected_value pesticide name;pesticide amount;treatment interval and duration"},{"location":"pesticide_regm/#schema-source","title":"Schema Source","text":""},{"location":"pesticide_regm/#linkml-source","title":"LinkML Source","text":"
name: pesticide_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: pesticide name;pesticide amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of insecticides; should include\n  the name of pesticide, amount administered, treatment regimen including how many\n  times the treatment was repeated, how long each treatment lasted, and the start\n  and end time of the entire treatment; can include multiple pesticide regimens\ntitle: pesticide regimen\nexamples:\n- value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pesticide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000573\nalias: pesticide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"petroleum_hydrocarb/","title":"Slot: petroleum hydrocarbon (petroleum_hydrocarb)","text":"

Concentration of petroleum hydrocarbon

URI: MIXS:0000516

"},{"location":"petroleum_hydrocarb/#inheritance","title":"Inheritance","text":""},{"location":"petroleum_hydrocarb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"petroleum_hydrocarb/#properties","title":"Properties","text":""},{"location":"petroleum_hydrocarb/#aliases","title":"Aliases","text":""},{"location":"petroleum_hydrocarb/#examples","title":"Examples","text":"Value 0.05 micromole per liter"},{"location":"petroleum_hydrocarb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"petroleum_hydrocarb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"petroleum_hydrocarb/#schema-source","title":"Schema Source","text":""},{"location":"petroleum_hydrocarb/#linkml-source","title":"LinkML Source","text":"
name: petroleum_hydrocarb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of petroleum hydrocarbon\ntitle: petroleum hydrocarbon\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- petroleum hydrocarbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000516\nalias: petroleum_hydrocarb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ph/","title":"Slot: pH (ph)","text":"

Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid

URI: MIXS:0001001

"},{"location":"ph/#inheritance","title":"Inheritance","text":""},{"location":"ph/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ph/#properties","title":"Properties","text":""},{"location":"ph/#aliases","title":"Aliases","text":""},{"location":"ph/#examples","title":"Examples","text":"Value 7.2"},{"location":"ph/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ph/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ph/#schema-source","title":"Schema Source","text":""},{"location":"ph/#linkml-source","title":"LinkML Source","text":"
name: ph\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Ph measurement of the sample, or liquid portion of sample, or aqueous\n  phase of the fluid\ntitle: pH\nexamples:\n- value: '7.2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001001\nalias: ph\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\n
"},{"location":"ph_meth/","title":"Slot: pH method (ph_meth)","text":"

Reference or method used in determining ph

URI: MIXS:0001106

"},{"location":"ph_meth/#inheritance","title":"Inheritance","text":""},{"location":"ph_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"ph_meth/#properties","title":"Properties","text":""},{"location":"ph_meth/#aliases","title":"Aliases","text":""},{"location":"ph_meth/#examples","title":"Examples","text":"Value"},{"location":"ph_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ph_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"ph_meth/#schema-source","title":"Schema Source","text":""},{"location":"ph_meth/#linkml-source","title":"LinkML Source","text":"
name: ph_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining ph\ntitle: pH method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001106\nalias: ph_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"ph_regm/","title":"Slot: pH regimen (ph_regm)","text":"

Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen

URI: MIXS:0001056

"},{"location":"ph_regm/#inheritance","title":"Inheritance","text":""},{"location":"ph_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ph_regm/#properties","title":"Properties","text":""},{"location":"ph_regm/#aliases","title":"Aliases","text":""},{"location":"ph_regm/#examples","title":"Examples","text":"Value 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M"},{"location":"ph_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ph_regm/#annotations","title":"Annotations","text":"property value expected_value measurement value;treatment interval and duration"},{"location":"ph_regm/#schema-source","title":"Schema Source","text":""},{"location":"ph_regm/#linkml-source","title":"LinkML Source","text":"
name: ph_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;treatment interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving exposure of plants to varying levels\n  of ph of the growth media, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include multiple regimen\ntitle: pH regimen\nexamples:\n- value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001056\nalias: ph_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"phaeopigments/","title":"Slot: phaeopigments (phaeopigments)","text":"

Concentration of phaeopigments; can include multiple phaeopigments

URI: MIXS:0000180

"},{"location":"phaeopigments/#inheritance","title":"Inheritance","text":""},{"location":"phaeopigments/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"phaeopigments/#properties","title":"Properties","text":""},{"location":"phaeopigments/#aliases","title":"Aliases","text":""},{"location":"phaeopigments/#examples","title":"Examples","text":"Value 2.5 milligram per cubic meter"},{"location":"phaeopigments/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phaeopigments/#annotations","title":"Annotations","text":"property value expected_value phaeopigment name;measurement value"},{"location":"phaeopigments/#schema-source","title":"Schema Source","text":""},{"location":"phaeopigments/#linkml-source","title":"LinkML Source","text":"
name: phaeopigments\nannotations:\n  expected_value:\n    tag: expected_value\n    value: phaeopigment name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of phaeopigments; can include multiple phaeopigments\ntitle: phaeopigments\nexamples:\n- value: 2.5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phaeopigments\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000180\nalias: phaeopigments\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"phase/","title":"Slot: phase","text":"

The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.

URI: nmdc:phase

"},{"location":"phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"phase/#properties","title":"Properties","text":""},{"location":"phase/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phase/#schema-source","title":"Schema Source","text":""},{"location":"phase/#linkml-source","title":"LinkML Source","text":"
name: phase\ndescription: The phase for a coding sequence entity. For example, phase of a CDS as\n  represented in a GFF3 with a value of 0, 1 or 2.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:phase\nrank: 1000\nalias: phase\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 0\nmaximum_value: 2\n\n
"},{"location":"phosphate/","title":"Slot: phosphate (phosphate)","text":"

Concentration of phosphate

URI: MIXS:0000505

"},{"location":"phosphate/#inheritance","title":"Inheritance","text":""},{"location":"phosphate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"phosphate/#properties","title":"Properties","text":""},{"location":"phosphate/#aliases","title":"Aliases","text":""},{"location":"phosphate/#examples","title":"Examples","text":"Value 0.7 micromole per liter"},{"location":"phosphate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phosphate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"phosphate/#schema-source","title":"Schema Source","text":""},{"location":"phosphate/#linkml-source","title":"LinkML Source","text":"
name: phosphate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of phosphate\ntitle: phosphate\nexamples:\n- value: 0.7 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000505\nalias: phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"phosplipid_fatt_acid/","title":"Slot: phospholipid fatty acid (phosplipid_fatt_acid)","text":"

Concentration of phospholipid fatty acids; can include multiple values

URI: MIXS:0000181

"},{"location":"phosplipid_fatt_acid/#inheritance","title":"Inheritance","text":""},{"location":"phosplipid_fatt_acid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"phosplipid_fatt_acid/#properties","title":"Properties","text":""},{"location":"phosplipid_fatt_acid/#aliases","title":"Aliases","text":""},{"location":"phosplipid_fatt_acid/#examples","title":"Examples","text":"Value 2.98 milligram per liter"},{"location":"phosplipid_fatt_acid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"phosplipid_fatt_acid/#annotations","title":"Annotations","text":"property value expected_value phospholipid fatty acid name;measurement value"},{"location":"phosplipid_fatt_acid/#schema-source","title":"Schema Source","text":""},{"location":"phosplipid_fatt_acid/#linkml-source","title":"LinkML Source","text":"
name: phosplipid_fatt_acid\nannotations:\n  expected_value:\n    tag: expected_value\n    value: phospholipid fatty acid name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mole per gram, mole per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of phospholipid fatty acids; can include multiple values\ntitle: phospholipid fatty acid\nexamples:\n- value: 2.98 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phospholipid fatty acid\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000181\nalias: phosplipid_fatt_acid\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"photon_flux/","title":"Slot: photon flux (photon_flux)","text":"

Measurement of photon flux

URI: MIXS:0000725

"},{"location":"photon_flux/#inheritance","title":"Inheritance","text":""},{"location":"photon_flux/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"photon_flux/#properties","title":"Properties","text":""},{"location":"photon_flux/#aliases","title":"Aliases","text":""},{"location":"photon_flux/#examples","title":"Examples","text":"Value 3.926 micromole photons per second per square meter"},{"location":"photon_flux/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"photon_flux/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"photon_flux/#schema-source","title":"Schema Source","text":""},{"location":"photon_flux/#linkml-source","title":"LinkML Source","text":"
name: photon_flux\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: number of photons per second per unit area\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of photon flux\ntitle: photon flux\nexamples:\n- value: 3.926 micromole photons per second per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- photon flux\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000725\nalias: photon_flux\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"plant_growth_med/","title":"Slot: plant growth medium (plant_growth_med)","text":"

Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary

URI: MIXS:0001057

"},{"location":"plant_growth_med/#inheritance","title":"Inheritance","text":""},{"location":"plant_growth_med/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"plant_growth_med/#properties","title":"Properties","text":""},{"location":"plant_growth_med/#aliases","title":"Aliases","text":""},{"location":"plant_growth_med/#examples","title":"Examples","text":"Value hydroponic plant culture media [EO:0007067]"},{"location":"plant_growth_med/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"plant_growth_med/#annotations","title":"Annotations","text":"property value expected_value EO or enumeration"},{"location":"plant_growth_med/#schema-source","title":"Schema Source","text":""},{"location":"plant_growth_med/#linkml-source","title":"LinkML Source","text":"
name: plant_growth_med\nannotations:\n  expected_value:\n    tag: expected_value\n    value: EO or enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Specification of the media for growing the plants or tissue cultured\n  samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro\n  liquid culture medium. Recommended value is a specific value from EO:plant growth\n  medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or\n  other controlled vocabulary\ntitle: plant growth medium\nexamples:\n- value: hydroponic plant culture media [EO:0007067]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant growth medium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001057\nalias: plant_growth_med\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"plant_product/","title":"Slot: plant product (plant_product)","text":"

Substance produced by the plant, where the sample was obtained from

URI: MIXS:0001058

"},{"location":"plant_product/#inheritance","title":"Inheritance","text":""},{"location":"plant_product/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"plant_product/#properties","title":"Properties","text":""},{"location":"plant_product/#aliases","title":"Aliases","text":""},{"location":"plant_product/#examples","title":"Examples","text":"Value xylem sap [PO:0025539]"},{"location":"plant_product/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"plant_product/#annotations","title":"Annotations","text":"property value expected_value product name"},{"location":"plant_product/#schema-source","title":"Schema Source","text":""},{"location":"plant_product/#linkml-source","title":"LinkML Source","text":"
name: plant_product\nannotations:\n  expected_value:\n    tag: expected_value\n    value: product name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Substance produced by the plant, where the sample was obtained from\ntitle: plant product\nexamples:\n- value: xylem sap [PO:0025539]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant product\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001058\nalias: plant_product\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"plant_sex/","title":"Slot: plant sex (plant_sex)","text":"

Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.

URI: MIXS:0001059

"},{"location":"plant_sex/#inheritance","title":"Inheritance","text":""},{"location":"plant_sex/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"plant_sex/#properties","title":"Properties","text":""},{"location":"plant_sex/#aliases","title":"Aliases","text":""},{"location":"plant_sex/#examples","title":"Examples","text":"Value Hermaphroditic"},{"location":"plant_sex/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"plant_sex/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"plant_sex/#schema-source","title":"Schema Source","text":""},{"location":"plant_sex/#linkml-source","title":"LinkML Source","text":"
name: plant_sex\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate,\n  monoecieous, hermaphrodite.\ntitle: plant sex\nexamples:\n- value: Hermaphroditic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001059\nalias: plant_sex\ndomain_of:\n- Biosample\nrange: plant_sex_enum\nmultivalued: false\n\n
"},{"location":"plant_struc/","title":"Slot: plant structure (plant_struc)","text":"

Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.

URI: MIXS:0001060

"},{"location":"plant_struc/#inheritance","title":"Inheritance","text":""},{"location":"plant_struc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"plant_struc/#properties","title":"Properties","text":""},{"location":"plant_struc/#aliases","title":"Aliases","text":""},{"location":"plant_struc/#examples","title":"Examples","text":"Value epidermis [PO:0005679]"},{"location":"plant_struc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"plant_struc/#annotations","title":"Annotations","text":"property value expected_value PO"},{"location":"plant_struc/#schema-source","title":"Schema Source","text":""},{"location":"plant_struc/#linkml-source","title":"LinkML Source","text":"
name: plant_struc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PO\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of plant structure the sample was obtained from; for Plant Ontology\n  (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n  e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex\n  of it can be recorded here.\ntitle: plant structure\nexamples:\n- value: epidermis [PO:0005679]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant structure\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0001060\nalias: plant_struc\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"polarity_mode/","title":"Slot: polarity_mode","text":"

the polarity of which ions are generated and detected

URI: nmdc:polarity_mode

"},{"location":"polarity_mode/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"polarity_mode/#properties","title":"Properties","text":""},{"location":"polarity_mode/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"polarity_mode/#schema-source","title":"Schema Source","text":""},{"location":"polarity_mode/#linkml-source","title":"LinkML Source","text":"
name: polarity_mode\ndescription: the polarity of which ions are generated and detected\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: polarity_mode\ndomain_of:\n- MassSpectrometryConfiguration\nrange: PolarityModeEnum\n\n
"},{"location":"pollutants/","title":"Slot: pollutants (pollutants)","text":"

Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant

URI: MIXS:0000107

"},{"location":"pollutants/#inheritance","title":"Inheritance","text":""},{"location":"pollutants/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pollutants/#properties","title":"Properties","text":""},{"location":"pollutants/#aliases","title":"Aliases","text":""},{"location":"pollutants/#examples","title":"Examples","text":"Value lead;0.15 microgram per cubic meter"},{"location":"pollutants/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pollutants/#annotations","title":"Annotations","text":"property value expected_value pollutant name;measurement value"},{"location":"pollutants/#schema-source","title":"Schema Source","text":""},{"location":"pollutants/#linkml-source","title":"LinkML Source","text":"
name: pollutants\nannotations:\n  expected_value:\n    tag: expected_value\n    value: pollutant name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, mole per liter, milligram per liter, microgram per cubic meter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Pollutant types and, amount or concentrations measured at the time of\n  sampling; can report multiple pollutants by entering numeric values preceded by\n  name of pollutant\ntitle: pollutants\nexamples:\n- value: lead;0.15 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pollutants\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000107\nalias: pollutants\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"pool_dna_extracts/","title":"Slot: pooling of DNA extracts (if done) (pool_dna_extracts)","text":"

Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given

URI: MIXS:0000325

"},{"location":"pool_dna_extracts/#inheritance","title":"Inheritance","text":""},{"location":"pool_dna_extracts/#properties","title":"Properties","text":""},{"location":"pool_dna_extracts/#aliases","title":"Aliases","text":""},{"location":"pool_dna_extracts/#examples","title":"Examples","text":"Value yes;5"},{"location":"pool_dna_extracts/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pool_dna_extracts/#annotations","title":"Annotations","text":"property value expected_value pooling status;number of pooled extracts"},{"location":"pool_dna_extracts/#schema-source","title":"Schema Source","text":""},{"location":"pool_dna_extracts/#linkml-source","title":"LinkML Source","text":"
name: pool_dna_extracts\nannotations:\n  expected_value:\n    tag: expected_value\n    value: pooling status;number of pooled extracts\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Indicate whether multiple DNA extractions were mixed. If the answer yes,\n  the number of extracts that were pooled should be given\ntitle: pooling of DNA extracts (if done)\nexamples:\n- value: yes;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pooling of DNA extracts (if done)\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{integer}'\nslot_uri: MIXS:0000325\nalias: pool_dna_extracts\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"porosity/","title":"Slot: porosity (porosity)","text":"

Porosity of deposited sediment is volume of voids divided by the total volume of sample

URI: MIXS:0000211

"},{"location":"porosity/#inheritance","title":"Inheritance","text":""},{"location":"porosity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"porosity/#properties","title":"Properties","text":""},{"location":"porosity/#aliases","title":"Aliases","text":""},{"location":"porosity/#examples","title":"Examples","text":"Value"},{"location":"porosity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"porosity/#annotations","title":"Annotations","text":"property value expected_value measurement value or range"},{"location":"porosity/#schema-source","title":"Schema Source","text":""},{"location":"porosity/#linkml-source","title":"LinkML Source","text":"
name: porosity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value or range\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Porosity of deposited sediment is volume of voids divided by the total\n  volume of sample\ntitle: porosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- porosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000211\nalias: porosity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"potassium/","title":"Slot: potassium (potassium)","text":"

Concentration of potassium in the sample

URI: MIXS:0000430

"},{"location":"potassium/#inheritance","title":"Inheritance","text":""},{"location":"potassium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"potassium/#properties","title":"Properties","text":""},{"location":"potassium/#aliases","title":"Aliases","text":""},{"location":"potassium/#examples","title":"Examples","text":"Value 463 milligram per liter"},{"location":"potassium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"potassium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"potassium/#schema-source","title":"Schema Source","text":""},{"location":"potassium/#linkml-source","title":"LinkML Source","text":"
name: potassium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of potassium in the sample\ntitle: potassium\nexamples:\n- value: 463 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- potassium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000430\nalias: potassium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"pour_point/","title":"Slot: pour point (pour_point)","text":"

Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)

URI: MIXS:0000127

"},{"location":"pour_point/#inheritance","title":"Inheritance","text":""},{"location":"pour_point/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pour_point/#properties","title":"Properties","text":""},{"location":"pour_point/#aliases","title":"Aliases","text":""},{"location":"pour_point/#examples","title":"Examples","text":"Value"},{"location":"pour_point/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pour_point/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"pour_point/#schema-source","title":"Schema Source","text":""},{"location":"pour_point/#linkml-source","title":"LinkML Source","text":"
name: pour_point\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Temperature at which a liquid becomes semi solid and loses its flow\n  characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a\n  high paraffin content, typically found in crude deriving from a larger proportion\n  of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\ntitle: pour point\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pour point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000127\nalias: pour_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"pre_treatment/","title":"Slot: pre-treatment (pre_treatment)","text":"

The process of pre-treatment removes materials that can be easily collected from the raw wastewater

URI: MIXS:0000348

"},{"location":"pre_treatment/#inheritance","title":"Inheritance","text":""},{"location":"pre_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pre_treatment/#properties","title":"Properties","text":""},{"location":"pre_treatment/#aliases","title":"Aliases","text":""},{"location":"pre_treatment/#examples","title":"Examples","text":"Value"},{"location":"pre_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pre_treatment/#annotations","title":"Annotations","text":"property value expected_value pre-treatment type"},{"location":"pre_treatment/#schema-source","title":"Schema Source","text":""},{"location":"pre_treatment/#linkml-source","title":"LinkML Source","text":"
name: pre_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: pre-treatment type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The process of pre-treatment removes materials that can be easily collected\n  from the raw wastewater\ntitle: pre-treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pre-treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000348\nalias: pre_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"prefixes_curies_ids_mappings_etc/","title":"Notes about prefixes, CURIEs, identifiers and mappings:","text":""},{"location":"prefixes_curies_ids_mappings_etc/#an-nmdc-and-linkml-perspective","title":"An NMDC and LinkML perspective","text":""},{"location":"prefixes_curies_ids_mappings_etc/#first-draft-2023-09-18","title":"First Draft: 2023-09-18","text":""},{"location":"prefixes_curies_ids_mappings_etc/#the-nmdc-schema-is-a-framework-for-describing-multi-omics-microbiome-experiments","title":"The nmdc-schema is a framework for describing multi-omics microbiome experiments.","text":"

All metadata gathered and stored by the NMDC community must validate against the nmdc-schema.

"},{"location":"prefixes_curies_ids_mappings_etc/#the-nmdc-schema-is-expressed-in-the-linkml-schema-language","title":"The nmdc-schema is expressed in the LinkML schema language.","text":"

LinkML uses structures like classes, slots (for relationships and properties), types and enumerations. People with object-oriented programming experience might find this familiar.

"},{"location":"prefixes_curies_ids_mappings_etc/#the-name-linkml-indicates-that-its-a-modeling-language-for-linked-data","title":"The name \"LinkML\" indicates that it's a modeling language for linked data.","text":"

LinkML schemas generally make good use of terminology from external resources, especially ontologies, especially those from the OBO Foundry. In return, LinkML schema elements and the corresponding data should be interoperable with other ontologies and semantic databases.

"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-element-identifiers-in-the-schema-with-uris-and-curies","title":"Asserting element identifiers in the schema with URIs and CURIEs","text":"

One consequence of this semantic/linked data orientation is that all schema elements are identified by a URI, most often in the compact CURIe form: a prefix and a local identifier. Even if a class isn't decorated with a class_uri annotation, it will always have a key (in a JSON, YAML or Python Obj sense), which is sometimes reiterated as the name. In that case, the class' URI will be <prefix>:<key>. LinkML schemas should have default prefix assertions, but any element can use a different prefix, as long as an expansion is provided.

"},{"location":"prefixes_curies_ids_mappings_etc/#prefixes-in-linkml-schemas","title":"Prefixes in LinkML schemas","text":"

Prefixes used in a LinkML must be associated with an expansion in the schema (which may include imported modules). Ideally, the expanded URI should be web resolvable, but that is not required. The prefixes can be expanded to base URIs owned by a particular resource, or they can be expanded to base URIs owned by some resolving service, like the bioregistry.

"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-mappings-in-the-nmdc-schema","title":"Asserting mappings in the nmdc-schema","text":"

As mentioned above, URIs are assigned to most elements of a LinkML schema, either explicitly by the schema authors, or implicitly through the default prefix and the element's key. If an external prefix is used, that means the semantics of the element are identical to the external term, unless otherwise refined. Sometimes it is desirable to associate a LinkML schema element with a term from an external resource, without asserting that the semantics are identical. In this case, a variety of mapping terms can be used.

Adding mappings to a schema element is one of the best and most compact ways to clarify the meaning of that element.

Schema contributors are strongly encouraged to use mappings whose prefixes are already defined in the schema. Schema contributors are always responsible for having a holistic understanding of an external term to be mapped into the schema. This means gaining familiarity with the parent and child terms, as well as any other axioms applied to the term. The EBI Ontology Lookup Service is a good place to look for these details.

When it appears necessary to use a mapping whose prefix isn't already defined in the schema, the contributor is responsible for having a holistic understanding of the external namespace (not just the term to be mapped). There are several ways to start assessing an ontology that is being considered as a source of mappings. If the ontology is in the OBO Foundry, one can look at the OBO Foundry Dashboard.

"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-identifiers-in-linkml-data","title":"Asserting identifiers in LinkML data","text":"

Generally speaking, the smallest atom of LinkML data is an instance of one class. LinkML slots take values, but always in the context of some class (on the right hand side). LinkML data files are frequently collections of instances of one or more classes. The is no requirement that these classes provide a slot whose value uniquely identifies the instances, but LinkML provides a mechanism that is broadly followed: one slot available in each class is annotated with identifier: true. (Or at least, that's what it would look like in a YAML serialization.) That means that the slot is required in all instances of the class, and that any collection of instances from that class must have unique values in that slot. It is also typical to say that the range of the is type uriorcurie.

"},{"location":"prefixes_curies_ids_mappings_etc/#mentioning-identifiers-in-linkml-data","title":"Mentioning identifiers in LinkML data","text":"

A common pattern in the nmdc-schema is asserting that some identifiable process has inputs and outputs. 

pooling_set:\n  - id: pooling:1\n    inputs:\n      - biosample:1\n      - biosample:2\n      - biosample:3\n  - id: pooling:2\n    inputs:\n      - biosample:4\n      - biosample:5\n      - biosample:6\n

Here we have declared the existence of two pooling processes. A CURIe identifier is asserted for both of them, and three inputs are mentioned for each. The example CURIes above don't necessarily follow any nmdc-schema identifier pattern rules. If these were real CURIes, then the pooling and biosample prefixes would have to be defined in the schema files.

In this case, let's assume definitions for the biosample inputs should be defined elsewhere in an NMDC data set. Cases in which biosamples are mentioned without being defined would be considered violations of the referential integrity. The development of referential integrity validators for LinkML has begun in Autumn, 2023.

Another pattern is saying that something defined within a NMDC data set is equivalent to something defined elsewhere.

biosample_set:\n    - id: biosample:1\n      gold_biosample_identifiers:\n        - gold:1\n        - gold:2\n

In this case, the gold prefix must be defined in the schema. When expanded to URIs via the prefix definitions, these gold_biosample_identifiers would all be web-resolvable.

"},{"location":"prefixes_curies_ids_mappings_etc/#constraining-mentioned-identifiers","title":"Constraining mentioned identifiers","text":"

We can limit the values that go into any slot by using a pattern constraint. We can also use the id_prefixes constraint to limit the prefixes that are used in whatever slot has been declared to be the identifier of a class. (Attributes of a class are supposed to be cascaded to subclasses, via the is_a attribute. This may not always be the case though. In the nmdc-schema we have been using a belt-and-suspenders approach of re-declaring the uriorcurie range )

All prefixes used in the id_prefixes constraint must be defined in the schema. We should have a standing practice of reflecting on the declared id_prefixes, and removing prefixes that haven't been used yet and are not likely to eer be used.

Maintenance of the prefix portions of a pattern will generally require more manual checking. We shouldn't be constraining the values of slots to use a prefix that isn't declared, but no checks are automatically applied.

"},{"location":"prefixes_curies_ids_mappings_etc/#using-uris-supports-scoping-and-self-documentation","title":"Using URIs supports scoping and self-documentation","text":"

Any class could use any slot with any range to \"link to\" something external. A Person could have a place_of_birth slot, and that could take unconstrained string or enumerated values like \"Switzerland\". But that doesn't provide much support for people looking up more information about the place_of_birth. You could create wikidata_place_of_birth and dbpedia_place_of_birth slots and add annotations to the slot to aid in external lookups, but that isn't a good practice if supporting several external targets. A better practice is to have one place_of_birth slot, with the uriorcuire range. Then users can provide values like <http://www.wikidata.org/entity/Q39> or <http://dbpedia.org/resource/Switzerland>. Then there is no ambiguity about the target of the link.

"},{"location":"prefixes_curies_ids_mappings_etc/#using-curies-makes-things-more-compact-and-readable","title":"Using CURIes makes things more compact and readable","text":"

If the schema contains prefix definitions like wd: <http://www.wikidata.org/entity/> and dbpedia: <http://dbpedia.org/resource/>, then the values can be written as wd:Q39 and dbpedia:Switzerland. This is more compact and readable, but it requires that the prefixes be defined in the schema. Then, more constraint can be imposed with a pattern on the place_of_birth slot like '^(wd|dbpedia):.+$'

"},{"location":"prefixes_curies_ids_mappings_etc/#where-to-find-a-report-of-nmdc-prefixes","title":"Where to find a report of NMDC prefixes","text":""},{"location":"prefixes_curies_ids_mappings_etc/#prefix-id-and-curie-notes","title":"PREFIX, id and CURIe notes","text":""},{"location":"prefixes_curies_ids_mappings_etc/#see-locallintlog","title":"see local/lint.log","text":""},{"location":"prefixes_curies_ids_mappings_etc/#use-bioregistry-not-identifiersorg-but","title":"use bioregistry, not identifiers.org, BUT","text":"

warning Schema maps prefix 'CHEMBL.COMPOUND' to namespace 'https://bioregistry.io/chembl.compound:' instead of namespace 'http://identifiers.org/chembl.compound/' (canonical_prefixes)

warning Schema maps prefix 'rdf' to namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' instead of using prefix ' RDF' (canonical_prefixes) warning Schema maps prefix 'rdfs' to namespace 'http://www.w3.org/2000/01/rdf-schema#' instead of using prefix 'RDFS' ( canonical_prefixes)

"},{"location":"prefixes_curies_ids_mappings_etc/#typecodes","title":"Typecodes","text":"

Not only does NMDC require the use of the nmdc prefix in the primary identifier for data instances, but we also define a pattern that the local portion of the ids must follow. For example, an example id from the NamedThing class is 'nmdc:mgmag-00-x012.1_7_c1'. The text that comes immediately after the nmdc prefix and colon, and before the first hyphen is the typecode, mgmag in this case. Typecodes must correspond 1:1 to a class in the NMDC schema. The typecodes currently in use are available from the nmdc-runtime API: https://api.microbiomedata.org/nmdcschema/typecodes

The typecodes for each class are auto-discovered each time the nmdc-runtime API is restarted, and the API is restarted each time it is bound to a new version of the nmdc-schem.

We do not currently have any criteria for good typecodes, other than they are ideally between 3 and 6 characters in length.

"},{"location":"prefixes_curies_ids_mappings_etc/#unresolved","title":"unresolved","text":""},{"location":"pres_animal_insect/","title":"Slot: presence of pets, animals, or insects (pres_animal_insect)","text":"

The type and number of animals or insects present in the sampling space.

URI: MIXS:0000819

"},{"location":"pres_animal_insect/#inheritance","title":"Inheritance","text":""},{"location":"pres_animal_insect/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pres_animal_insect/#properties","title":"Properties","text":""},{"location":"pres_animal_insect/#aliases","title":"Aliases","text":""},{"location":"pres_animal_insect/#examples","title":"Examples","text":"Value cat;5"},{"location":"pres_animal_insect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pres_animal_insect/#annotations","title":"Annotations","text":"property value expected_value enumeration;count"},{"location":"pres_animal_insect/#schema-source","title":"Schema Source","text":""},{"location":"pres_animal_insect/#linkml-source","title":"LinkML Source","text":"
name: pres_animal_insect\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration;count\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type and number of animals or insects present in the sampling space.\ntitle: presence of pets, animals, or insects\nexamples:\n- value: cat;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- presence of pets, animals, or insects\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000819\nalias: pres_animal_insect\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\npattern: ^(cat|dog|rodent|snake|other);\\d+$\n\n
"},{"location":"pressure/","title":"Slot: pressure (pressure)","text":"

Pressure to which the sample is subject to, in atmospheres

URI: MIXS:0000412

"},{"location":"pressure/#inheritance","title":"Inheritance","text":""},{"location":"pressure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"pressure/#properties","title":"Properties","text":""},{"location":"pressure/#aliases","title":"Aliases","text":""},{"location":"pressure/#examples","title":"Examples","text":"Value 50 atmosphere"},{"location":"pressure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"pressure/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"pressure/#schema-source","title":"Schema Source","text":""},{"location":"pressure/#linkml-source","title":"LinkML Source","text":"
name: pressure\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: atmosphere\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Pressure to which the sample is subject to, in atmospheres\ntitle: pressure\nexamples:\n- value: 50 atmosphere\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000412\nalias: pressure\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"prev_land_use_meth/","title":"Slot: history/previous land use method (prev_land_use_meth)","text":"

Reference or method used in determining previous land use and dates

URI: MIXS:0000316

"},{"location":"prev_land_use_meth/#inheritance","title":"Inheritance","text":""},{"location":"prev_land_use_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"prev_land_use_meth/#properties","title":"Properties","text":""},{"location":"prev_land_use_meth/#aliases","title":"Aliases","text":""},{"location":"prev_land_use_meth/#examples","title":"Examples","text":"Value"},{"location":"prev_land_use_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"prev_land_use_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"prev_land_use_meth/#schema-source","title":"Schema Source","text":""},{"location":"prev_land_use_meth/#linkml-source","title":"LinkML Source","text":"
name: prev_land_use_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining previous land use and dates\ntitle: history/previous land use method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000316\nalias: prev_land_use_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"previous_land_use/","title":"Slot: history/previous land use (previous_land_use)","text":"

Previous land use and dates

URI: MIXS:0000315

"},{"location":"previous_land_use/#inheritance","title":"Inheritance","text":""},{"location":"previous_land_use/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"previous_land_use/#properties","title":"Properties","text":""},{"location":"previous_land_use/#aliases","title":"Aliases","text":""},{"location":"previous_land_use/#examples","title":"Examples","text":"Value"},{"location":"previous_land_use/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"previous_land_use/#annotations","title":"Annotations","text":"property value expected_value land use name;date"},{"location":"previous_land_use/#schema-source","title":"Schema Source","text":""},{"location":"previous_land_use/#linkml-source","title":"LinkML Source","text":"
name: previous_land_use\nannotations:\n  expected_value:\n    tag: expected_value\n    value: land use name;date\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Previous land use and dates\ntitle: history/previous land use\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{timestamp}'\nslot_uri: MIXS:0000315\nalias: previous_land_use\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"primary_prod/","title":"Slot: primary production (primary_prod)","text":"

Measurement of primary production, generally measured as isotope uptake

URI: MIXS:0000728

"},{"location":"primary_prod/#inheritance","title":"Inheritance","text":""},{"location":"primary_prod/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"primary_prod/#properties","title":"Properties","text":""},{"location":"primary_prod/#aliases","title":"Aliases","text":""},{"location":"primary_prod/#examples","title":"Examples","text":"Value 100 milligram per cubic meter per day"},{"location":"primary_prod/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"primary_prod/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"primary_prod/#schema-source","title":"Schema Source","text":""},{"location":"primary_prod/#linkml-source","title":"LinkML Source","text":"
name: primary_prod\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per cubic meter per day, gram per square meter per day\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of primary production, generally measured as isotope uptake\ntitle: primary production\nexamples:\n- value: 100 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000728\nalias: primary_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"primary_treatment/","title":"Slot: primary treatment (primary_treatment)","text":"

The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed

URI: MIXS:0000349

"},{"location":"primary_treatment/#inheritance","title":"Inheritance","text":""},{"location":"primary_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"primary_treatment/#properties","title":"Properties","text":""},{"location":"primary_treatment/#aliases","title":"Aliases","text":""},{"location":"primary_treatment/#examples","title":"Examples","text":"Value"},{"location":"primary_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"primary_treatment/#annotations","title":"Annotations","text":"property value expected_value primary treatment type"},{"location":"primary_treatment/#schema-source","title":"Schema Source","text":""},{"location":"primary_treatment/#linkml-source","title":"LinkML Source","text":"
name: primary_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: primary treatment type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The process to produce both a generally homogeneous liquid capable of\n  being treated biologically and a sludge that can be separately treated or processed\ntitle: primary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000349\nalias: primary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"principal_investigator/","title":"Slot: principal_investigator","text":"

Principal Investigator who led the study and/or generated the dataset.

URI: nmdc:principal_investigator

"},{"location":"principal_investigator/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no Study A study summarizes the overall goal of a research initiative and outlines the... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"principal_investigator/#properties","title":"Properties","text":""},{"location":"principal_investigator/#aliases","title":"Aliases","text":""},{"location":"principal_investigator/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"principal_investigator/#schema-source","title":"Schema Source","text":""},{"location":"principal_investigator/#linkml-source","title":"LinkML Source","text":"
name: principal_investigator\ndescription: Principal Investigator who led the study and/or generated the dataset.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- PI\nrank: 1000\nalias: principal_investigator\ndomain_of:\n- Study\n- DataGeneration\nrange: PersonValue\n\n
"},{"location":"processed_sample_set/","title":"Slot: processed_sample_set","text":"

This property links a database object to the set of processed samples within it.

URI: nmdc:processed_sample_set

"},{"location":"processed_sample_set/#inheritance","title":"Inheritance","text":""},{"location":"processed_sample_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"processed_sample_set/#properties","title":"Properties","text":""},{"location":"processed_sample_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"processed_sample_set/#schema-source","title":"Schema Source","text":""},{"location":"processed_sample_set/#linkml-source","title":"LinkML Source","text":"
name: processed_sample_set\ndescription: This property links a database object to the set of processed samples\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: processed_sample_set\ndomain_of:\n- Database\nrange: ProcessedSample\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"processing_institution/","title":"Slot: processing_institution","text":"

The organization that processed the sample.

URI: nmdc:processing_institution

"},{"location":"processing_institution/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeAssembly no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no PlannedProcess no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ProtocolExecution A PlannedProces that has PlannedProcess parts no LibraryPreparation no"},{"location":"processing_institution/#properties","title":"Properties","text":""},{"location":"processing_institution/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"processing_institution/#schema-source","title":"Schema Source","text":""},{"location":"processing_institution/#linkml-source","title":"LinkML Source","text":"
name: processing_institution\ndescription: The organization that processed the sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: processing_institution\ndomain_of:\n- PlannedProcess\nrange: ProcessingInstitutionEnum\n\n
"},{"location":"prod_rate/","title":"Slot: production rate (prod_rate)","text":"

Oil and/or gas production rates per well (e.g. 524 m3 / day)

URI: MIXS:0000452

"},{"location":"prod_rate/#inheritance","title":"Inheritance","text":""},{"location":"prod_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"prod_rate/#properties","title":"Properties","text":""},{"location":"prod_rate/#aliases","title":"Aliases","text":""},{"location":"prod_rate/#examples","title":"Examples","text":"Value"},{"location":"prod_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"prod_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"prod_rate/#schema-source","title":"Schema Source","text":""},{"location":"prod_rate/#linkml-source","title":"LinkML Source","text":"
name: prod_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic meter per day\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Oil and/or gas production rates per well (e.g. 524 m3 / day)\ntitle: production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000452\nalias: prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"prod_start_date/","title":"Slot: production start date (prod_start_date)","text":"

Date of field's first production

URI: MIXS:0001008

"},{"location":"prod_start_date/#inheritance","title":"Inheritance","text":""},{"location":"prod_start_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"prod_start_date/#properties","title":"Properties","text":""},{"location":"prod_start_date/#aliases","title":"Aliases","text":""},{"location":"prod_start_date/#examples","title":"Examples","text":"Value 2018-05-11"},{"location":"prod_start_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"prod_start_date/#annotations","title":"Annotations","text":"property value expected_value timestamp"},{"location":"prod_start_date/#schema-source","title":"Schema Source","text":""},{"location":"prod_start_date/#linkml-source","title":"LinkML Source","text":"
name: prod_start_date\nannotations:\n  expected_value:\n    tag: expected_value\n    value: timestamp\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Date of field's first production\ntitle: production start date\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001008\nalias: prod_start_date\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\n
"},{"location":"profile_image_url/","title":"Slot: profile_image_url","text":"

A url that points to an image of a person.

URI: nmdc:profile_image_url

"},{"location":"profile_image_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person no"},{"location":"profile_image_url/#properties","title":"Properties","text":""},{"location":"profile_image_url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"profile_image_url/#schema-source","title":"Schema Source","text":""},{"location":"profile_image_url/#linkml-source","title":"LinkML Source","text":"
name: profile_image_url\ndescription: A url that points to an image of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: profile_image_url\ndomain_of:\n- PersonValue\nrange: string\n\n
"},{"location":"profile_position/","title":"Slot: profile position (profile_position)","text":"

Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas

URI: MIXS:0001084

"},{"location":"profile_position/#inheritance","title":"Inheritance","text":""},{"location":"profile_position/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"profile_position/#properties","title":"Properties","text":""},{"location":"profile_position/#aliases","title":"Aliases","text":""},{"location":"profile_position/#examples","title":"Examples","text":"Value summit"},{"location":"profile_position/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"profile_position/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"profile_position/#schema-source","title":"Schema Source","text":""},{"location":"profile_position/#linkml-source","title":"LinkML Source","text":"
name: profile_position\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Cross-sectional position in the hillslope where sample was collected.sample\n  area position in relation to surrounding areas\ntitle: profile position\nexamples:\n- value: summit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- profile position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001084\nalias: profile_position\ndomain_of:\n- Biosample\nrange: profile_position_enum\nmultivalued: false\n\n
"},{"location":"project_id/","title":"Slot: project ID (project_id)","text":"

Proposal IDs or names associated with dataset

URI: nmdc:project_id

"},{"location":"project_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"project_id/#properties","title":"Properties","text":""},{"location":"project_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"project_id/#schema-source","title":"Schema Source","text":""},{"location":"project_id/#linkml-source","title":"LinkML Source","text":"
name: project_id\ndescription: Proposal IDs or names associated with dataset\ntitle: project ID\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: project_id\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"proport_woa_temperature/","title":"Slot: proport_woa_temperature","text":"

URI: nmdc:proport_woa_temperature

"},{"location":"proport_woa_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proport_woa_temperature/#properties","title":"Properties","text":""},{"location":"proport_woa_temperature/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"proport_woa_temperature/#schema-source","title":"Schema Source","text":""},{"location":"proport_woa_temperature/#linkml-source","title":"LinkML Source","text":"
name: proport_woa_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: proport_woa_temperature\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"proposal_dna/","title":"Slot: DNA proposal ID (proposal_dna)","text":"

URI: nmdc:proposal_dna

"},{"location":"proposal_dna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_dna/#properties","title":"Properties","text":""},{"location":"proposal_dna/#examples","title":"Examples","text":"Value 504000"},{"location":"proposal_dna/#comments","title":"Comments","text":""},{"location":"proposal_dna/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"proposal_dna/#schema-source","title":"Schema Source","text":""},{"location":"proposal_dna/#linkml-source","title":"LinkML Source","text":"
name: proposal_dna\ntitle: DNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_dna\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\n
"},{"location":"proposal_rna/","title":"Slot: RNA proposal ID (proposal_rna)","text":"

URI: nmdc:proposal_rna

"},{"location":"proposal_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_rna/#properties","title":"Properties","text":""},{"location":"proposal_rna/#examples","title":"Examples","text":"Value 504000"},{"location":"proposal_rna/#comments","title":"Comments","text":""},{"location":"proposal_rna/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"proposal_rna/#schema-source","title":"Schema Source","text":""},{"location":"proposal_rna/#linkml-source","title":"LinkML Source","text":"
name: proposal_rna\ntitle: RNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"protein_spectral_count/","title":"Slot: protein_spectral_count","text":"

sum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file

URI: nmdc:protein_spectral_count

"},{"location":"protein_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_spectral_count/#properties","title":"Properties","text":""},{"location":"protein_spectral_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protein_spectral_count/#schema-source","title":"Schema Source","text":""},{"location":"protein_spectral_count/#linkml-source","title":"LinkML Source","text":"
name: protein_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the best protein within\n  a given LC-MS/MS data file\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_spectral_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\n
"},{"location":"protein_sum_masic_abundance/","title":"Slot: protein_sum_masic_abundance","text":"

combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool

URI: nmdc:protein_sum_masic_abundance

"},{"location":"protein_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_sum_masic_abundance/#properties","title":"Properties","text":""},{"location":"protein_sum_masic_abundance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protein_sum_masic_abundance/#schema-source","title":"Schema Source","text":""},{"location":"protein_sum_masic_abundance/#linkml-source","title":"LinkML Source","text":"
name: protein_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n  with the best protein from a given LC-MS/MS data file using the MASIC tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_sum_masic_abundance\ndomain_of:\n- ProteinQuantification\nrange: integer\n\n
"},{"location":"protocol_execution_category/","title":"Slot: protocol_execution_category","text":"

URI: nmdc:protocol_execution_category

"},{"location":"protocol_execution_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProtocolExecution A PlannedProces that has PlannedProcess parts no"},{"location":"protocol_execution_category/#properties","title":"Properties","text":""},{"location":"protocol_execution_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protocol_execution_category/#schema-source","title":"Schema Source","text":""},{"location":"protocol_execution_category/#linkml-source","title":"LinkML Source","text":"
name: protocol_execution_category\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_execution_category\ndomain_of:\n- ProtocolExecution\nrange: ProtocolCategoryEnum\nrequired: true\n\n
"},{"location":"protocol_execution_set/","title":"Slot: protocol_execution_set","text":"

This property links a database object to the set of protocol executions within it.

URI: nmdc:protocol_execution_set

"},{"location":"protocol_execution_set/#inheritance","title":"Inheritance","text":""},{"location":"protocol_execution_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"protocol_execution_set/#properties","title":"Properties","text":""},{"location":"protocol_execution_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protocol_execution_set/#schema-source","title":"Schema Source","text":""},{"location":"protocol_execution_set/#linkml-source","title":"LinkML Source","text":"
name: protocol_execution_set\ndescription: This property links a database object to the set of protocol executions\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: protocol_execution_set\ndomain_of:\n- Database\nrange: ProtocolExecution\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"protocol_link/","title":"Slot: protocol_link","text":"

URI: nmdc:protocol_link

"},{"location":"protocol_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeAssembly no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no PlannedProcess no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Study A study summarizes the overall goal of a research initiative and outlines the... yes Extraction A material separation in which a desired component of an input material is se... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ProtocolExecution A PlannedProces that has PlannedProcess parts no LibraryPreparation no"},{"location":"protocol_link/#properties","title":"Properties","text":""},{"location":"protocol_link/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"protocol_link/#schema-source","title":"Schema Source","text":""},{"location":"protocol_link/#linkml-source","title":"LinkML Source","text":"
name: protocol_link\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_link\ndomain_of:\n- PlannedProcess\n- Study\nrange: Protocol\n\n
"},{"location":"qc_comment/","title":"Slot: qc_comment","text":"

Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).

URI: nmdc:qc_comment

"},{"location":"qc_comment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeAssembly no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no PlannedProcess no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ProtocolExecution A PlannedProces that has PlannedProcess parts no LibraryPreparation no"},{"location":"qc_comment/#properties","title":"Properties","text":""},{"location":"qc_comment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"qc_comment/#schema-source","title":"Schema Source","text":""},{"location":"qc_comment/#linkml-source","title":"LinkML Source","text":"
name: qc_comment\ndescription: Slot to store additional comments about laboratory or workflow output.\n  For workflow output it may describe the particular workflow stage that failed. (ie\n  Failed at call-stage due to a malformed fastq file).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_comment\ndomain_of:\n- PlannedProcess\nrange: string\n\n
"},{"location":"qc_failure_what/","title":"Slot: qc_failure_what","text":"

Provides a summary about what caused a lab or workflow process to fail

URI: nmdc:qc_failure_what

"},{"location":"qc_failure_what/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FailureCategorization no"},{"location":"qc_failure_what/#properties","title":"Properties","text":""},{"location":"qc_failure_what/#comments","title":"Comments","text":""},{"location":"qc_failure_what/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"qc_failure_what/#schema-source","title":"Schema Source","text":""},{"location":"qc_failure_what/#linkml-source","title":"LinkML Source","text":"
name: qc_failure_what\ndescription: Provides a summary about what caused a lab or workflow process to fail\ncomments:\n- For example, low read count from a sequencer, malformed fastq files, etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_failure_what\ndomain_of:\n- FailureCategorization\nrange: FailureWhatEnum\n\n
"},{"location":"qc_failure_where/","title":"Slot: qc_failure_where","text":"

Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results.

URI: nmdc:qc_failure_where

"},{"location":"qc_failure_where/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FailureCategorization no"},{"location":"qc_failure_where/#properties","title":"Properties","text":""},{"location":"qc_failure_where/#comments","title":"Comments","text":""},{"location":"qc_failure_where/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"qc_failure_where/#schema-source","title":"Schema Source","text":""},{"location":"qc_failure_where/#linkml-source","title":"LinkML Source","text":"
name: qc_failure_where\ndescription: Describes the nmdc schema class that corresonds to where the failure\n  occurred. Most commonly this would be the same as Class that generated the results.\ncomments:\n- If the assembly size was too small to proceed to annotation failure_where would\n  be MetagenomeAssembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_failure_where\ndomain_of:\n- FailureCategorization\nrange: FailureWhereEnum\n\n
"},{"location":"qc_status/","title":"Slot: qc_status","text":"

Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)

URI: nmdc:qc_status

"},{"location":"qc_status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeAssembly no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no PlannedProcess no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ProtocolExecution A PlannedProces that has PlannedProcess parts no LibraryPreparation no"},{"location":"qc_status/#properties","title":"Properties","text":""},{"location":"qc_status/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"qc_status/#schema-source","title":"Schema Source","text":""},{"location":"qc_status/#linkml-source","title":"LinkML Source","text":"
name: qc_status\ndescription: Stores information about the result of a process (ie the process of sequencing\n  a library may have for qc_status of 'fail' if not enough data was generated)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_status\ndomain_of:\n- PlannedProcess\nrange: StatusEnum\n\n
"},{"location":"quad_pos/","title":"Slot: quadrant position (quad_pos)","text":"

The quadrant position of the sampling room within the building

URI: MIXS:0000820

"},{"location":"quad_pos/#inheritance","title":"Inheritance","text":""},{"location":"quad_pos/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"quad_pos/#properties","title":"Properties","text":""},{"location":"quad_pos/#aliases","title":"Aliases","text":""},{"location":"quad_pos/#examples","title":"Examples","text":"Value West side"},{"location":"quad_pos/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"quad_pos/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"quad_pos/#schema-source","title":"Schema Source","text":""},{"location":"quad_pos/#linkml-source","title":"LinkML Source","text":"
name: quad_pos\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The quadrant position of the sampling room within the building\ntitle: quadrant position\nexamples:\n- value: West side\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- quadrant position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000820\nalias: quad_pos\ndomain_of:\n- Biosample\nrange: quad_pos_enum\nmultivalued: false\n\n
"},{"location":"radiation_regm/","title":"Slot: radiation regimen (radiation_regm)","text":"

Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens

URI: MIXS:0000575

"},{"location":"radiation_regm/#inheritance","title":"Inheritance","text":""},{"location":"radiation_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"radiation_regm/#properties","title":"Properties","text":""},{"location":"radiation_regm/#aliases","title":"Aliases","text":""},{"location":"radiation_regm/#examples","title":"Examples","text":"Value gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"radiation_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"radiation_regm/#annotations","title":"Annotations","text":"property value expected_value radiation type name;radiation amount;treatment interval and duration"},{"location":"radiation_regm/#schema-source","title":"Schema Source","text":""},{"location":"radiation_regm/#linkml-source","title":"LinkML Source","text":"
name: radiation_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: radiation type name;radiation amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: rad, gray\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving exposure of plant or a plant part\n  to a particular radiation regimen; should include the radiation type, amount or\n  intensity administered, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include multiple radiation regimens\ntitle: radiation regimen\nexamples:\n- value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- radiation regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000575\nalias: radiation_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"rainfall_regm/","title":"Slot: rainfall regimen (rainfall_regm)","text":"

Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000576

"},{"location":"rainfall_regm/#inheritance","title":"Inheritance","text":""},{"location":"rainfall_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rainfall_regm/#properties","title":"Properties","text":""},{"location":"rainfall_regm/#aliases","title":"Aliases","text":""},{"location":"rainfall_regm/#examples","title":"Examples","text":"Value 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"rainfall_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rainfall_regm/#annotations","title":"Annotations","text":"property value expected_value measurement value;treatment interval and duration"},{"location":"rainfall_regm/#schema-source","title":"Schema Source","text":""},{"location":"rainfall_regm/#linkml-source","title":"LinkML Source","text":"
name: rainfall_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to a given amount of\n  rainfall, treatment regimen including how many times the treatment was repeated,\n  how long each treatment lasted, and the start and end time of the entire treatment;\n  can include multiple regimens\ntitle: rainfall regimen\nexamples:\n- value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rainfall regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000576\nalias: rainfall_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"reactor_type/","title":"Slot: reactor type (reactor_type)","text":"

Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage

URI: MIXS:0000350

"},{"location":"reactor_type/#inheritance","title":"Inheritance","text":""},{"location":"reactor_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"reactor_type/#properties","title":"Properties","text":""},{"location":"reactor_type/#aliases","title":"Aliases","text":""},{"location":"reactor_type/#examples","title":"Examples","text":"Value"},{"location":"reactor_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reactor_type/#annotations","title":"Annotations","text":"property value expected_value reactor type name"},{"location":"reactor_type/#schema-source","title":"Schema Source","text":""},{"location":"reactor_type/#linkml-source","title":"LinkML Source","text":"
name: reactor_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: reactor type name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Anaerobic digesters can be designed and engineered to operate using a\n  number of different process configurations, as batch or continuous, mesophilic,\n  high solid or low solid, and single stage or multistage\ntitle: reactor type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reactor type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000350\nalias: reactor_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"read_qc_analysis_statistic/","title":"Slot: read_qc_analysis_statistic","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:read_qc_analysis_statistic

"},{"location":"read_qc_analysis_statistic/#inheritance","title":"Inheritance","text":""},{"location":"read_qc_analysis_statistic/#properties","title":"Properties","text":""},{"location":"read_qc_analysis_statistic/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"read_qc_analysis_statistic/#schema-source","title":"Schema Source","text":""},{"location":"read_qc_analysis_statistic/#linkml-source","title":"LinkML Source","text":"
name: read_qc_analysis_statistic\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: read_qc_analysis_statistic\nrange: string\n\n
"},{"location":"redox_potential/","title":"Slot: redox potential (redox_potential)","text":"

Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential

URI: MIXS:0000182

"},{"location":"redox_potential/#inheritance","title":"Inheritance","text":""},{"location":"redox_potential/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"redox_potential/#properties","title":"Properties","text":""},{"location":"redox_potential/#aliases","title":"Aliases","text":""},{"location":"redox_potential/#examples","title":"Examples","text":"Value 300 millivolt"},{"location":"redox_potential/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"redox_potential/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"redox_potential/#schema-source","title":"Schema Source","text":""},{"location":"redox_potential/#linkml-source","title":"LinkML Source","text":"
name: redox_potential\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millivolt\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Redox potential, measured relative to a hydrogen cell, indicating oxidation\n  or reduction potential\ntitle: redox potential\nexamples:\n- value: 300 millivolt\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- redox potential\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000182\nalias: redox_potential\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"rel_air_humidity/","title":"Slot: relative air humidity (rel_air_humidity)","text":"

Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air

URI: MIXS:0000121

"},{"location":"rel_air_humidity/#inheritance","title":"Inheritance","text":""},{"location":"rel_air_humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rel_air_humidity/#properties","title":"Properties","text":""},{"location":"rel_air_humidity/#aliases","title":"Aliases","text":""},{"location":"rel_air_humidity/#examples","title":"Examples","text":"Value 80%"},{"location":"rel_air_humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rel_air_humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"rel_air_humidity/#schema-source","title":"Schema Source","text":""},{"location":"rel_air_humidity/#linkml-source","title":"LinkML Source","text":"
name: rel_air_humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Partial vapor and air pressure, density of the vapor and air, or by the\n  actual mass of the vapor and air\ntitle: relative air humidity\nexamples:\n- value: 80%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000121\nalias: rel_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"rel_humidity_out/","title":"Slot: outside relative humidity (rel_humidity_out)","text":"

The recorded outside relative humidity value at the time of sampling

URI: MIXS:0000188

"},{"location":"rel_humidity_out/#inheritance","title":"Inheritance","text":""},{"location":"rel_humidity_out/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rel_humidity_out/#properties","title":"Properties","text":""},{"location":"rel_humidity_out/#aliases","title":"Aliases","text":""},{"location":"rel_humidity_out/#examples","title":"Examples","text":"Value 12 per kilogram of air"},{"location":"rel_humidity_out/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rel_humidity_out/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"rel_humidity_out/#schema-source","title":"Schema Source","text":""},{"location":"rel_humidity_out/#linkml-source","title":"LinkML Source","text":"
name: rel_humidity_out\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram of air, kilogram of air\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The recorded outside relative humidity value at the time of sampling\ntitle: outside relative humidity\nexamples:\n- value: 12 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- outside relative humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000188\nalias: rel_humidity_out\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"rel_samp_loc/","title":"Slot: relative sampling location (rel_samp_loc)","text":"

The sampling location within the train car

URI: MIXS:0000821

"},{"location":"rel_samp_loc/#inheritance","title":"Inheritance","text":""},{"location":"rel_samp_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rel_samp_loc/#properties","title":"Properties","text":""},{"location":"rel_samp_loc/#aliases","title":"Aliases","text":""},{"location":"rel_samp_loc/#examples","title":"Examples","text":"Value center of car"},{"location":"rel_samp_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rel_samp_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"rel_samp_loc/#schema-source","title":"Schema Source","text":""},{"location":"rel_samp_loc/#linkml-source","title":"LinkML Source","text":"
name: rel_samp_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The sampling location within the train car\ntitle: relative sampling location\nexamples:\n- value: center of car\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative sampling location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000821\nalias: rel_samp_loc\ndomain_of:\n- Biosample\nrange: rel_samp_loc_enum\nmultivalued: false\n\n
"},{"location":"related_identifiers/","title":"Slot: Related Identifiers (related_identifiers)","text":"

Identifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation.

URI: nmdc:related_identifiers

"},{"location":"related_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"related_identifiers/#properties","title":"Properties","text":""},{"location":"related_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"related_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"related_identifiers/#linkml-source","title":"LinkML Source","text":"
name: related_identifiers\ndescription: Identifiers assigned to a thing that is similar to that which is represented\n  in NMDC. Related identifier are not an identical match and may have some variation.\ntitle: Related Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: related_identifiers\ndomain_of:\n- Study\nrange: string\n\n
"},{"location":"replicate_number/","title":"Slot: replicate number (replicate_number)","text":"

If sending biological replicates, indicate the rep number here.

URI: nmdc:replicate_number

"},{"location":"replicate_number/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"replicate_number/#properties","title":"Properties","text":""},{"location":"replicate_number/#comments","title":"Comments","text":""},{"location":"replicate_number/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"replicate_number/#schema-source","title":"Schema Source","text":""},{"location":"replicate_number/#linkml-source","title":"LinkML Source","text":"
name: replicate_number\ndescription: If sending biological replicates, indicate the rep number here.\ntitle: replicate number\ncomments:\n- This will guide staff in ensuring your samples are blocked & randomized correctly\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{integer}'\nalias: replicate_number\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"reservoir/","title":"Slot: reservoir name (reservoir)","text":"

Name of the reservoir (e.g. Carapebus)

URI: MIXS:0000303

"},{"location":"reservoir/#inheritance","title":"Inheritance","text":""},{"location":"reservoir/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"reservoir/#properties","title":"Properties","text":""},{"location":"reservoir/#aliases","title":"Aliases","text":""},{"location":"reservoir/#examples","title":"Examples","text":"Value"},{"location":"reservoir/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"reservoir/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"reservoir/#schema-source","title":"Schema Source","text":""},{"location":"reservoir/#linkml-source","title":"LinkML Source","text":"
name: reservoir\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of the reservoir (e.g. Carapebus)\ntitle: reservoir name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reservoir name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000303\nalias: reservoir\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"resins_pc/","title":"Slot: resins wt% (resins_pc)","text":"

Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)

URI: MIXS:0000134

"},{"location":"resins_pc/#inheritance","title":"Inheritance","text":""},{"location":"resins_pc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"resins_pc/#properties","title":"Properties","text":""},{"location":"resins_pc/#aliases","title":"Aliases","text":""},{"location":"resins_pc/#examples","title":"Examples","text":"Value"},{"location":"resins_pc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"resins_pc/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"resins_pc/#schema-source","title":"Schema Source","text":""},{"location":"resins_pc/#linkml-source","title":"LinkML Source","text":"
name: resins_pc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n  that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n  There are three main methods to obtain SARA results. The most popular one is known\n  as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: resins wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- resins wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000134\nalias: resins_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"resolution_categories/","title":"Slot: resolution_categories","text":"

The relative resolution at which spectra were collected.

URI: nmdc:resolution_categories

"},{"location":"resolution_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"resolution_categories/#properties","title":"Properties","text":""},{"location":"resolution_categories/#examples","title":"Examples","text":"Value ['high', 'low']"},{"location":"resolution_categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"resolution_categories/#schema-source","title":"Schema Source","text":""},{"location":"resolution_categories/#linkml-source","title":"LinkML Source","text":"
name: resolution_categories\ndescription: The relative resolution at which spectra were collected.\nexamples:\n- value: '[''high'', ''low'']'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: resolution_categories\ndomain_of:\n- MassSpectrometryConfiguration\nrange: ResolutionCategoryEnum\nmultivalued: true\n\n
"},{"location":"rna_absorb1/","title":"Slot: RNA absorbance 260/280 (rna_absorb1)","text":"

260/280 measurement of RNA sample purity

URI: nmdc:rna_absorb1

"},{"location":"rna_absorb1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_absorb1/#properties","title":"Properties","text":""},{"location":"rna_absorb1/#examples","title":"Examples","text":"Value 2.02"},{"location":"rna_absorb1/#comments","title":"Comments","text":""},{"location":"rna_absorb1/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_absorb1/#schema-source","title":"Schema Source","text":""},{"location":"rna_absorb1/#linkml-source","title":"LinkML Source","text":"
name: rna_absorb1\ndescription: 260/280 measurement of RNA sample purity\ntitle: RNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nstring_serialization: '{float}'\nalias: rna_absorb1\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\n
"},{"location":"rna_absorb2/","title":"Slot: RNA absorbance 260/230 (rna_absorb2)","text":"

260/230 measurement of RNA sample purity

URI: nmdc:rna_absorb2

"},{"location":"rna_absorb2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_absorb2/#properties","title":"Properties","text":""},{"location":"rna_absorb2/#examples","title":"Examples","text":"Value 2.02"},{"location":"rna_absorb2/#comments","title":"Comments","text":""},{"location":"rna_absorb2/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_absorb2/#schema-source","title":"Schema Source","text":""},{"location":"rna_absorb2/#linkml-source","title":"LinkML Source","text":"
name: rna_absorb2\ndescription: 260/230 measurement of RNA sample purity\ntitle: RNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nstring_serialization: '{float}'\nalias: rna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\n
"},{"location":"rna_collect_site/","title":"Slot: RNA collection site (rna_collect_site)","text":"

Provide information on the site your RNA sample was collected from

URI: nmdc:rna_collect_site

"},{"location":"rna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_collect_site/#properties","title":"Properties","text":""},{"location":"rna_collect_site/#examples","title":"Examples","text":"Value untreated pond water"},{"location":"rna_collect_site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_collect_site/#schema-source","title":"Schema Source","text":""},{"location":"rna_collect_site/#linkml-source","title":"LinkML Source","text":"
name: rna_collect_site\ndescription: Provide information on the site your RNA sample was collected from\ntitle: RNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: rna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_concentration/","title":"Slot: RNA concentration in ng/ul (rna_concentration)","text":"

URI: nmdc:rna_concentration

"},{"location":"rna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_concentration/#properties","title":"Properties","text":""},{"location":"rna_concentration/#examples","title":"Examples","text":"Value 100"},{"location":"rna_concentration/#comments","title":"Comments","text":""},{"location":"rna_concentration/#see-also","title":"See Also","text":""},{"location":"rna_concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_concentration/#schema-source","title":"Schema Source","text":""},{"location":"rna_concentration/#linkml-source","title":"LinkML Source","text":"
name: rna_concentration\ntitle: RNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n  a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nstring_serialization: '{float}'\nalias: rna_concentration\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\n
"},{"location":"rna_cont_type/","title":"Slot: RNA container type (rna_cont_type)","text":"

Tube or plate (96-well)

URI: nmdc:rna_cont_type

"},{"location":"rna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_type/#properties","title":"Properties","text":""},{"location":"rna_cont_type/#examples","title":"Examples","text":"Value plate"},{"location":"rna_cont_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_cont_type/#schema-source","title":"Schema Source","text":""},{"location":"rna_cont_type/#linkml-source","title":"LinkML Source","text":"
name: rna_cont_type\ndescription: Tube or plate (96-well)\ntitle: RNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: rna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: JgiContTypeEnum\nrecommended: true\n\n
"},{"location":"rna_cont_well/","title":"Slot: RNA plate position (rna_cont_well)","text":"

URI: nmdc:rna_cont_well

"},{"location":"rna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_well/#properties","title":"Properties","text":""},{"location":"rna_cont_well/#examples","title":"Examples","text":"Value B2"},{"location":"rna_cont_well/#comments","title":"Comments","text":""},{"location":"rna_cont_well/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_cont_well/#schema-source","title":"Schema Source","text":""},{"location":"rna_cont_well/#linkml-source","title":"LinkML Source","text":"
name: rna_cont_well\ntitle: RNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n  validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: rna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\npattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n\n
"},{"location":"rna_container_id/","title":"Slot: RNA container label (rna_container_id)","text":"

URI: nmdc:rna_container_id

"},{"location":"rna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_container_id/#properties","title":"Properties","text":""},{"location":"rna_container_id/#examples","title":"Examples","text":"Value Pond_MT_041618"},{"location":"rna_container_id/#comments","title":"Comments","text":""},{"location":"rna_container_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_container_id/#schema-source","title":"Schema Source","text":""},{"location":"rna_container_id/#linkml-source","title":"LinkML Source","text":"
name: rna_container_id\ntitle: RNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n  plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: rna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_isolate_meth/","title":"Slot: RNA isolation method (rna_isolate_meth)","text":"

Describe the method/protocol/kit used to extract DNA/RNA.

URI: nmdc:rna_isolate_meth

"},{"location":"rna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_isolate_meth/#properties","title":"Properties","text":""},{"location":"rna_isolate_meth/#aliases","title":"Aliases","text":""},{"location":"rna_isolate_meth/#examples","title":"Examples","text":"Value phenol/chloroform extraction"},{"location":"rna_isolate_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_isolate_meth/#schema-source","title":"Schema Source","text":""},{"location":"rna_isolate_meth/#linkml-source","title":"LinkML Source","text":"
name: rna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: RNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Sample Isolation Method\nrank: 16\nstring_serialization: '{text}'\nalias: rna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_organisms/","title":"Slot: RNA expected organisms (rna_organisms)","text":"

List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.

URI: nmdc:rna_organisms

"},{"location":"rna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_organisms/#properties","title":"Properties","text":""},{"location":"rna_organisms/#examples","title":"Examples","text":"Value expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)"},{"location":"rna_organisms/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_organisms/#schema-source","title":"Schema Source","text":""},{"location":"rna_organisms/#linkml-source","title":"LinkML Source","text":"
name: rna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n  as estimated % of the organism in that culture.\ntitle: RNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: rna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_project_contact/","title":"Slot: RNA seq project contact (rna_project_contact)","text":"

URI: nmdc:rna_project_contact

"},{"location":"rna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_project_contact/#properties","title":"Properties","text":""},{"location":"rna_project_contact/#examples","title":"Examples","text":"Value John Jones"},{"location":"rna_project_contact/#comments","title":"Comments","text":""},{"location":"rna_project_contact/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_project_contact/#schema-source","title":"Schema Source","text":""},{"location":"rna_project_contact/#linkml-source","title":"LinkML Source","text":"
name: rna_project_contact\ntitle: RNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: rna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_samp_id/","title":"Slot: RNA sample ID (rna_samp_id)","text":"

URI: nmdc:rna_samp_id

"},{"location":"rna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_samp_id/#properties","title":"Properties","text":""},{"location":"rna_samp_id/#examples","title":"Examples","text":"Value 187654"},{"location":"rna_samp_id/#comments","title":"Comments","text":""},{"location":"rna_samp_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_samp_id/#schema-source","title":"Schema Source","text":""},{"location":"rna_samp_id/#linkml-source","title":"LinkML Source","text":"
name: rna_samp_id\ntitle: RNA sample ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: rna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_sample_format/","title":"Slot: RNA sample format (rna_sample_format)","text":"

Solution in which the RNA sample has been suspended

URI: nmdc:rna_sample_format

"},{"location":"rna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_format/#properties","title":"Properties","text":""},{"location":"rna_sample_format/#examples","title":"Examples","text":"Value Water"},{"location":"rna_sample_format/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_sample_format/#schema-source","title":"Schema Source","text":""},{"location":"rna_sample_format/#linkml-source","title":"LinkML Source","text":"
name: rna_sample_format\ndescription: Solution in which the RNA sample has been suspended\ntitle: RNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: rna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: RNASampleFormatEnum\nrecommended: true\n\n
"},{"location":"rna_sample_name/","title":"Slot: RNA sample name (rna_sample_name)","text":"

Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.

URI: nmdc:rna_sample_name

"},{"location":"rna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_name/#properties","title":"Properties","text":""},{"location":"rna_sample_name/#examples","title":"Examples","text":"Value JGI_pond_041618"},{"location":"rna_sample_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_sample_name/#schema-source","title":"Schema Source","text":""},{"location":"rna_sample_name/#linkml-source","title":"LinkML Source","text":"
name: rna_sample_name\ndescription: Give the RNA sample a name that is meaningful to you. Sample names must\n  be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: RNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: rna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\n
"},{"location":"rna_seq_project/","title":"Slot: RNA seq project ID (rna_seq_project)","text":"

URI: nmdc:rna_seq_project

"},{"location":"rna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project/#properties","title":"Properties","text":""},{"location":"rna_seq_project/#aliases","title":"Aliases","text":""},{"location":"rna_seq_project/#examples","title":"Examples","text":"Value 1191234"},{"location":"rna_seq_project/#comments","title":"Comments","text":""},{"location":"rna_seq_project/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_seq_project/#schema-source","title":"Schema Source","text":""},{"location":"rna_seq_project/#linkml-source","title":"LinkML Source","text":"
name: rna_seq_project\ntitle: RNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Seq Project ID\nrank: 1\nstring_serialization: '{text}'\nalias: rna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_seq_project_name/","title":"Slot: RNA seq project name (rna_seq_project_name)","text":"

URI: nmdc:rna_seq_project_name

"},{"location":"rna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_name/#properties","title":"Properties","text":""},{"location":"rna_seq_project_name/#examples","title":"Examples","text":"Value JGI Pond metatranscriptomics"},{"location":"rna_seq_project_name/#comments","title":"Comments","text":""},{"location":"rna_seq_project_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_seq_project_name/#schema-source","title":"Schema Source","text":""},{"location":"rna_seq_project_name/#linkml-source","title":"LinkML Source","text":"
name: rna_seq_project_name\ntitle: RNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: JGI Pond metatranscriptomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: rna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_seq_project_pi/","title":"Slot: RNA seq project PI (rna_seq_project_pi)","text":"

URI: nmdc:rna_seq_project_pi

"},{"location":"rna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_pi/#properties","title":"Properties","text":""},{"location":"rna_seq_project_pi/#examples","title":"Examples","text":"Value Jane Johnson"},{"location":"rna_seq_project_pi/#comments","title":"Comments","text":""},{"location":"rna_seq_project_pi/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_seq_project_pi/#schema-source","title":"Schema Source","text":""},{"location":"rna_seq_project_pi/#linkml-source","title":"LinkML Source","text":"
name: rna_seq_project_pi\ntitle: RNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n  have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: rna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\n
"},{"location":"rna_volume/","title":"Slot: RNA volume in ul (rna_volume)","text":"

URI: nmdc:rna_volume

"},{"location":"rna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_volume/#properties","title":"Properties","text":""},{"location":"rna_volume/#examples","title":"Examples","text":"Value 25"},{"location":"rna_volume/#comments","title":"Comments","text":""},{"location":"rna_volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"rna_volume/#schema-source","title":"Schema Source","text":""},{"location":"rna_volume/#linkml-source","title":"LinkML Source","text":"
name: rna_volume\ntitle: RNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n  accepts values < 25, but JGI may refuse to process them unless permission has been\n  granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: rna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\n
"},{"location":"room_air_exch_rate/","title":"Slot: room air exchange rate (room_air_exch_rate)","text":"

The rate at which outside air replaces indoor air in a given space

URI: MIXS:0000169

"},{"location":"room_air_exch_rate/#inheritance","title":"Inheritance","text":""},{"location":"room_air_exch_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_air_exch_rate/#properties","title":"Properties","text":""},{"location":"room_air_exch_rate/#aliases","title":"Aliases","text":""},{"location":"room_air_exch_rate/#examples","title":"Examples","text":"Value"},{"location":"room_air_exch_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_air_exch_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_air_exch_rate/#schema-source","title":"Schema Source","text":""},{"location":"room_air_exch_rate/#linkml-source","title":"LinkML Source","text":"
name: room_air_exch_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: liter per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The rate at which outside air replaces indoor air in a given space\ntitle: room air exchange rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room air exchange rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000169\nalias: room_air_exch_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"room_architec_elem/","title":"Slot: room architectural elements (room_architec_elem)","text":"

The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure

URI: MIXS:0000233

"},{"location":"room_architec_elem/#inheritance","title":"Inheritance","text":""},{"location":"room_architec_elem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_architec_elem/#properties","title":"Properties","text":""},{"location":"room_architec_elem/#aliases","title":"Aliases","text":""},{"location":"room_architec_elem/#examples","title":"Examples","text":"Value"},{"location":"room_architec_elem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_architec_elem/#annotations","title":"Annotations","text":"property value expected_value free text"},{"location":"room_architec_elem/#schema-source","title":"Schema Source","text":""},{"location":"room_architec_elem/#linkml-source","title":"LinkML Source","text":"
name: room_architec_elem\nannotations:\n  expected_value:\n    tag: expected_value\n    value: free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The unique details and component parts that, together, form the architecture\n  of a distinguisahable space within a built structure\ntitle: room architectural elements\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room architectural elements\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000233\nalias: room_architec_elem\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"room_condt/","title":"Slot: room condition (room_condt)","text":"

The condition of the room at the time of sampling

URI: MIXS:0000822

"},{"location":"room_condt/#inheritance","title":"Inheritance","text":""},{"location":"room_condt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_condt/#properties","title":"Properties","text":""},{"location":"room_condt/#aliases","title":"Aliases","text":""},{"location":"room_condt/#examples","title":"Examples","text":"Value new"},{"location":"room_condt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_condt/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_condt/#schema-source","title":"Schema Source","text":""},{"location":"room_condt/#linkml-source","title":"LinkML Source","text":"
name: room_condt\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The condition of the room at the time of sampling\ntitle: room condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000822\nalias: room_condt\ndomain_of:\n- Biosample\nrange: room_condt_enum\nmultivalued: false\n\n
"},{"location":"room_connected/","title":"Slot: rooms connected by a doorway (room_connected)","text":"

List of rooms connected to the sampling room by a doorway

URI: MIXS:0000826

"},{"location":"room_connected/#inheritance","title":"Inheritance","text":""},{"location":"room_connected/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_connected/#properties","title":"Properties","text":""},{"location":"room_connected/#aliases","title":"Aliases","text":""},{"location":"room_connected/#examples","title":"Examples","text":"Value office"},{"location":"room_connected/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_connected/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_connected/#schema-source","title":"Schema Source","text":""},{"location":"room_connected/#linkml-source","title":"LinkML Source","text":"
name: room_connected\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of rooms connected to the sampling room by a doorway\ntitle: rooms connected by a doorway\nexamples:\n- value: office\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms connected by a doorway\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000826\nalias: room_connected\ndomain_of:\n- Biosample\nrange: room_connected_enum\nmultivalued: false\n\n
"},{"location":"room_count/","title":"Slot: room count (room_count)","text":"

The total count of rooms in the built structure including all room types

URI: MIXS:0000234

"},{"location":"room_count/#inheritance","title":"Inheritance","text":""},{"location":"room_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_count/#properties","title":"Properties","text":""},{"location":"room_count/#aliases","title":"Aliases","text":""},{"location":"room_count/#examples","title":"Examples","text":"Value"},{"location":"room_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"room_count/#schema-source","title":"Schema Source","text":""},{"location":"room_count/#linkml-source","title":"LinkML Source","text":"
name: room_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The total count of rooms in the built structure including all room types\ntitle: room count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000234\nalias: room_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_dim/","title":"Slot: room dimensions (room_dim)","text":"

The length, width and height of sampling room

URI: MIXS:0000192

"},{"location":"room_dim/#inheritance","title":"Inheritance","text":""},{"location":"room_dim/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_dim/#properties","title":"Properties","text":""},{"location":"room_dim/#aliases","title":"Aliases","text":""},{"location":"room_dim/#examples","title":"Examples","text":"Value"},{"location":"room_dim/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_dim/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_dim/#schema-source","title":"Schema Source","text":""},{"location":"room_dim/#linkml-source","title":"LinkML Source","text":"
name: room_dim\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The length, width and height of sampling room\ntitle: room dimensions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room dimensions\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\nslot_uri: MIXS:0000192\nalias: room_dim\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_door_dist/","title":"Slot: room door distance (room_door_dist)","text":"

Distance between doors (meters) in the hallway between the sampling room and adjacent rooms

URI: MIXS:0000193

"},{"location":"room_door_dist/#inheritance","title":"Inheritance","text":""},{"location":"room_door_dist/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_door_dist/#properties","title":"Properties","text":""},{"location":"room_door_dist/#aliases","title":"Aliases","text":""},{"location":"room_door_dist/#examples","title":"Examples","text":"Value"},{"location":"room_door_dist/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_door_dist/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_door_dist/#schema-source","title":"Schema Source","text":""},{"location":"room_door_dist/#linkml-source","title":"LinkML Source","text":"
name: room_door_dist\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Distance between doors (meters) in the hallway between the sampling room\n  and adjacent rooms\ntitle: room door distance\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room door distance\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000193\nalias: room_door_dist\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_door_share/","title":"Slot: rooms that share a door with sampling room (room_door_share)","text":"

List of room(s) (room number, room name) sharing a door with the sampling room

URI: MIXS:0000242

"},{"location":"room_door_share/#inheritance","title":"Inheritance","text":""},{"location":"room_door_share/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_door_share/#properties","title":"Properties","text":""},{"location":"room_door_share/#aliases","title":"Aliases","text":""},{"location":"room_door_share/#examples","title":"Examples","text":"Value"},{"location":"room_door_share/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_door_share/#annotations","title":"Annotations","text":"property value expected_value room name;room number"},{"location":"room_door_share/#schema-source","title":"Schema Source","text":""},{"location":"room_door_share/#linkml-source","title":"LinkML Source","text":"
name: room_door_share\nannotations:\n  expected_value:\n    tag: expected_value\n    value: room name;room number\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of room(s) (room number, room name) sharing a door with the sampling\n  room\ntitle: rooms that share a door with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a door with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000242\nalias: room_door_share\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_hallway/","title":"Slot: rooms that are on the same hallway (room_hallway)","text":"

List of room(s) (room number, room name) located in the same hallway as sampling room

URI: MIXS:0000238

"},{"location":"room_hallway/#inheritance","title":"Inheritance","text":""},{"location":"room_hallway/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_hallway/#properties","title":"Properties","text":""},{"location":"room_hallway/#aliases","title":"Aliases","text":""},{"location":"room_hallway/#examples","title":"Examples","text":"Value"},{"location":"room_hallway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_hallway/#annotations","title":"Annotations","text":"property value expected_value room name;room number"},{"location":"room_hallway/#schema-source","title":"Schema Source","text":""},{"location":"room_hallway/#linkml-source","title":"LinkML Source","text":"
name: room_hallway\nannotations:\n  expected_value:\n    tag: expected_value\n    value: room name;room number\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of room(s) (room number, room name) located in the same hallway\n  as sampling room\ntitle: rooms that are on the same hallway\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that are on the same hallway\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000238\nalias: room_hallway\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_loc/","title":"Slot: room location in building (room_loc)","text":"

The position of the room within the building

URI: MIXS:0000823

"},{"location":"room_loc/#inheritance","title":"Inheritance","text":""},{"location":"room_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_loc/#properties","title":"Properties","text":""},{"location":"room_loc/#aliases","title":"Aliases","text":""},{"location":"room_loc/#examples","title":"Examples","text":"Value interior room"},{"location":"room_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_loc/#schema-source","title":"Schema Source","text":""},{"location":"room_loc/#linkml-source","title":"LinkML Source","text":"
name: room_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The position of the room within the building\ntitle: room location in building\nexamples:\n- value: interior room\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room location in building\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000823\nalias: room_loc\ndomain_of:\n- Biosample\nrange: room_loc_enum\nmultivalued: false\n\n
"},{"location":"room_moist_dam_hist/","title":"Slot: room moisture damage or mold history (room_moist_dam_hist)","text":"

The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed

URI: MIXS:0000235

"},{"location":"room_moist_dam_hist/#inheritance","title":"Inheritance","text":""},{"location":"room_moist_dam_hist/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_moist_dam_hist/#properties","title":"Properties","text":""},{"location":"room_moist_dam_hist/#aliases","title":"Aliases","text":""},{"location":"room_moist_dam_hist/#examples","title":"Examples","text":"Value"},{"location":"room_moist_dam_hist/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_moist_dam_hist/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"room_moist_dam_hist/#schema-source","title":"Schema Source","text":""},{"location":"room_moist_dam_hist/#linkml-source","title":"LinkML Source","text":"
name: room_moist_dam_hist\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The history of moisture damage or mold in the past 12 months. Number\n  of events of moisture damage or mold observed\ntitle: room moisture damage or mold history\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room moisture damage or mold history\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000235\nalias: room_moist_dam_hist\ndomain_of:\n- Biosample\nrange: integer\nmultivalued: false\n\n
"},{"location":"room_net_area/","title":"Slot: room net area (room_net_area)","text":"

The net floor area of sampling room. Net area excludes wall thicknesses

URI: MIXS:0000194

"},{"location":"room_net_area/#inheritance","title":"Inheritance","text":""},{"location":"room_net_area/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_net_area/#properties","title":"Properties","text":""},{"location":"room_net_area/#aliases","title":"Aliases","text":""},{"location":"room_net_area/#examples","title":"Examples","text":"Value"},{"location":"room_net_area/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_net_area/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_net_area/#schema-source","title":"Schema Source","text":""},{"location":"room_net_area/#linkml-source","title":"LinkML Source","text":"
name: room_net_area\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square feet, square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The net floor area of sampling room. Net area excludes wall thicknesses\ntitle: room net area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room net area\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000194\nalias: room_net_area\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_occup/","title":"Slot: room occupancy (room_occup)","text":"

Count of room occupancy at time of sampling

URI: MIXS:0000236

"},{"location":"room_occup/#inheritance","title":"Inheritance","text":""},{"location":"room_occup/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_occup/#properties","title":"Properties","text":""},{"location":"room_occup/#aliases","title":"Aliases","text":""},{"location":"room_occup/#examples","title":"Examples","text":"Value"},{"location":"room_occup/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_occup/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_occup/#schema-source","title":"Schema Source","text":""},{"location":"room_occup/#linkml-source","title":"LinkML Source","text":"
name: room_occup\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Count of room occupancy at time of sampling\ntitle: room occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000236\nalias: room_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"room_samp_pos/","title":"Slot: room sampling position (room_samp_pos)","text":"

The horizontal sampling position in the room relative to architectural elements

URI: MIXS:0000824

"},{"location":"room_samp_pos/#inheritance","title":"Inheritance","text":""},{"location":"room_samp_pos/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_samp_pos/#properties","title":"Properties","text":""},{"location":"room_samp_pos/#aliases","title":"Aliases","text":""},{"location":"room_samp_pos/#examples","title":"Examples","text":"Value south corner"},{"location":"room_samp_pos/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_samp_pos/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_samp_pos/#schema-source","title":"Schema Source","text":""},{"location":"room_samp_pos/#linkml-source","title":"LinkML Source","text":"
name: room_samp_pos\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The horizontal sampling position in the room relative to architectural\n  elements\ntitle: room sampling position\nexamples:\n- value: south corner\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room sampling position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000824\nalias: room_samp_pos\ndomain_of:\n- Biosample\nrange: room_samp_pos_enum\nmultivalued: false\n\n
"},{"location":"room_type/","title":"Slot: room type (room_type)","text":"

The main purpose or activity of the sampling room. A room is any distinguishable space within a structure

URI: MIXS:0000825

"},{"location":"room_type/#inheritance","title":"Inheritance","text":""},{"location":"room_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_type/#properties","title":"Properties","text":""},{"location":"room_type/#aliases","title":"Aliases","text":""},{"location":"room_type/#examples","title":"Examples","text":"Value bathroom"},{"location":"room_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"room_type/#schema-source","title":"Schema Source","text":""},{"location":"room_type/#linkml-source","title":"LinkML Source","text":"
name: room_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The main purpose or activity of the sampling room. A room is any distinguishable\n  space within a structure\ntitle: room type\nexamples:\n- value: bathroom\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000825\nalias: room_type\ndomain_of:\n- Biosample\nrange: room_type_enum\nmultivalued: false\n\n
"},{"location":"room_vol/","title":"Slot: room volume (room_vol)","text":"

Volume of sampling room

URI: MIXS:0000195

"},{"location":"room_vol/#inheritance","title":"Inheritance","text":""},{"location":"room_vol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_vol/#properties","title":"Properties","text":""},{"location":"room_vol/#aliases","title":"Aliases","text":""},{"location":"room_vol/#examples","title":"Examples","text":"Value"},{"location":"room_vol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_vol/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"room_vol/#schema-source","title":"Schema Source","text":""},{"location":"room_vol/#linkml-source","title":"LinkML Source","text":"
name: room_vol\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic feet, cubic meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Volume of sampling room\ntitle: room volume\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room volume\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000195\nalias: room_vol\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_wall_share/","title":"Slot: rooms that share a wall with sampling room (room_wall_share)","text":"

List of room(s) (room number, room name) sharing a wall with the sampling room

URI: MIXS:0000243

"},{"location":"room_wall_share/#inheritance","title":"Inheritance","text":""},{"location":"room_wall_share/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_wall_share/#properties","title":"Properties","text":""},{"location":"room_wall_share/#aliases","title":"Aliases","text":""},{"location":"room_wall_share/#examples","title":"Examples","text":"Value"},{"location":"room_wall_share/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_wall_share/#annotations","title":"Annotations","text":"property value expected_value room name;room number"},{"location":"room_wall_share/#schema-source","title":"Schema Source","text":""},{"location":"room_wall_share/#linkml-source","title":"LinkML Source","text":"
name: room_wall_share\nannotations:\n  expected_value:\n    tag: expected_value\n    value: room name;room number\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: List of room(s) (room number, room name) sharing a wall with the sampling\n  room\ntitle: rooms that share a wall with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a wall with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000243\nalias: room_wall_share\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"room_window_count/","title":"Slot: room window count (room_window_count)","text":"

Number of windows in the room

URI: MIXS:0000237

"},{"location":"room_window_count/#inheritance","title":"Inheritance","text":""},{"location":"room_window_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"room_window_count/#properties","title":"Properties","text":""},{"location":"room_window_count/#aliases","title":"Aliases","text":""},{"location":"room_window_count/#examples","title":"Examples","text":"Value"},{"location":"room_window_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"room_window_count/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"room_window_count/#schema-source","title":"Schema Source","text":""},{"location":"room_window_count/#linkml-source","title":"LinkML Source","text":"
name: room_window_count\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Number of windows in the room\ntitle: room window count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room window count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000237\nalias: room_window_count\ndomain_of:\n- Biosample\nrange: integer\nmultivalued: false\n\n
"},{"location":"root_cond/","title":"Slot: rooting conditions (root_cond)","text":"

Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.

URI: MIXS:0001061

"},{"location":"root_cond/#inheritance","title":"Inheritance","text":""},{"location":"root_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_cond/#properties","title":"Properties","text":""},{"location":"root_cond/#aliases","title":"Aliases","text":""},{"location":"root_cond/#examples","title":"Examples","text":"Value http://himedialabs.com/TD/PT158.pdf"},{"location":"root_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_cond/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url or free text"},{"location":"root_cond/#schema-source","title":"Schema Source","text":""},{"location":"root_cond/#linkml-source","title":"LinkML Source","text":"
name: root_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url or free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Relevant rooting conditions such as field plot size, sowing density,\n  container dimensions, number of plants per container.\ntitle: rooting conditions\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001061\nalias: root_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_carbon/","title":"Slot: rooting medium carbon (root_med_carbon)","text":"

Source of organic carbon in the culture rooting medium; e.g. sucrose.

URI: MIXS:0000577

"},{"location":"root_med_carbon/#inheritance","title":"Inheritance","text":""},{"location":"root_med_carbon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_carbon/#properties","title":"Properties","text":""},{"location":"root_med_carbon/#aliases","title":"Aliases","text":""},{"location":"root_med_carbon/#examples","title":"Examples","text":"Value sucrose"},{"location":"root_med_carbon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_carbon/#annotations","title":"Annotations","text":"property value expected_value carbon source name;measurement value"},{"location":"root_med_carbon/#schema-source","title":"Schema Source","text":""},{"location":"root_med_carbon/#linkml-source","title":"LinkML Source","text":"
name: root_med_carbon\nannotations:\n  expected_value:\n    tag: expected_value\n    value: carbon source name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Source of organic carbon in the culture rooting medium; e.g. sucrose.\ntitle: rooting medium carbon\nexamples:\n- value: sucrose\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium carbon\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000577\nalias: root_med_carbon\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_macronutr/","title":"Slot: rooting medium macronutrients (root_med_macronutr)","text":"

Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).

URI: MIXS:0000578

"},{"location":"root_med_macronutr/#inheritance","title":"Inheritance","text":""},{"location":"root_med_macronutr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_macronutr/#properties","title":"Properties","text":""},{"location":"root_med_macronutr/#aliases","title":"Aliases","text":""},{"location":"root_med_macronutr/#examples","title":"Examples","text":"Value KH2PO4;170\u00ac\u2020milligram per liter"},{"location":"root_med_macronutr/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_macronutr/#annotations","title":"Annotations","text":"property value expected_value macronutrient name;measurement value"},{"location":"root_med_macronutr/#schema-source","title":"Schema Source","text":""},{"location":"root_med_macronutr/#linkml-source","title":"LinkML Source","text":"
name: root_med_macronutr\nannotations:\n  expected_value:\n    tag: expected_value\n    value: macronutrient name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of the culture rooting medium macronutrients (N,P, K, Ca,\n  Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\ntitle: rooting medium macronutrients\nexamples:\n- value: KH2PO4;170\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium macronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000578\nalias: root_med_macronutr\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_micronutr/","title":"Slot: rooting medium micronutrients (root_med_micronutr)","text":"

Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).

URI: MIXS:0000579

"},{"location":"root_med_micronutr/#inheritance","title":"Inheritance","text":""},{"location":"root_med_micronutr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_micronutr/#properties","title":"Properties","text":""},{"location":"root_med_micronutr/#aliases","title":"Aliases","text":""},{"location":"root_med_micronutr/#examples","title":"Examples","text":"Value H3BO3;6.2\u00ac\u2020milligram per liter"},{"location":"root_med_micronutr/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_micronutr/#annotations","title":"Annotations","text":"property value expected_value micronutrient name;measurement value"},{"location":"root_med_micronutr/#schema-source","title":"Schema Source","text":""},{"location":"root_med_micronutr/#linkml-source","title":"LinkML Source","text":"
name: root_med_micronutr\nannotations:\n  expected_value:\n    tag: expected_value\n    value: micronutrient name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn,\n  B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\ntitle: rooting medium micronutrients\nexamples:\n- value: H3BO3;6.2\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium micronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000579\nalias: root_med_micronutr\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_ph/","title":"Slot: rooting medium pH (root_med_ph)","text":"

pH measurement of the culture rooting medium; e.g. 5.5.

URI: MIXS:0001062

"},{"location":"root_med_ph/#inheritance","title":"Inheritance","text":""},{"location":"root_med_ph/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_ph/#properties","title":"Properties","text":""},{"location":"root_med_ph/#aliases","title":"Aliases","text":""},{"location":"root_med_ph/#examples","title":"Examples","text":"Value 7.5"},{"location":"root_med_ph/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_ph/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"root_med_ph/#schema-source","title":"Schema Source","text":""},{"location":"root_med_ph/#linkml-source","title":"LinkML Source","text":"
name: root_med_ph\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: pH measurement of the culture rooting medium; e.g. 5.5.\ntitle: rooting medium pH\nexamples:\n- value: '7.5'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001062\nalias: root_med_ph\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"root_med_regl/","title":"Slot: rooting medium regulators (root_med_regl)","text":"

Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.

URI: MIXS:0000581

"},{"location":"root_med_regl/#inheritance","title":"Inheritance","text":""},{"location":"root_med_regl/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_regl/#properties","title":"Properties","text":""},{"location":"root_med_regl/#aliases","title":"Aliases","text":""},{"location":"root_med_regl/#examples","title":"Examples","text":"Value abscisic acid;0.75 milligram per liter"},{"location":"root_med_regl/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_regl/#annotations","title":"Annotations","text":"property value expected_value regulator name;measurement value"},{"location":"root_med_regl/#schema-source","title":"Schema Source","text":""},{"location":"root_med_regl/#linkml-source","title":"LinkML Source","text":"
name: root_med_regl\nannotations:\n  expected_value:\n    tag: expected_value\n    value: regulator name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Growth regulators in the culture rooting medium such as cytokinins, auxins,\n  gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\ntitle: rooting medium regulators\nexamples:\n- value: abscisic acid;0.75 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium regulators\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000581\nalias: root_med_regl\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_solid/","title":"Slot: rooting medium solidifier (root_med_solid)","text":"

Specification of the solidifying agent in the culture rooting medium; e.g. agar.

URI: MIXS:0001063

"},{"location":"root_med_solid/#inheritance","title":"Inheritance","text":""},{"location":"root_med_solid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_solid/#properties","title":"Properties","text":""},{"location":"root_med_solid/#aliases","title":"Aliases","text":""},{"location":"root_med_solid/#examples","title":"Examples","text":"Value agar"},{"location":"root_med_solid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_solid/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"root_med_solid/#schema-source","title":"Schema Source","text":""},{"location":"root_med_solid/#linkml-source","title":"LinkML Source","text":"
name: root_med_solid\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Specification of the solidifying agent in the culture rooting medium;\n  e.g. agar.\ntitle: rooting medium solidifier\nexamples:\n- value: agar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium solidifier\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001063\nalias: root_med_solid\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"root_med_suppl/","title":"Slot: rooting medium organic supplements (root_med_suppl)","text":"

Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5\u00ac\u2020mg/L).

URI: MIXS:0000580

"},{"location":"root_med_suppl/#inheritance","title":"Inheritance","text":""},{"location":"root_med_suppl/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"root_med_suppl/#properties","title":"Properties","text":""},{"location":"root_med_suppl/#aliases","title":"Aliases","text":""},{"location":"root_med_suppl/#examples","title":"Examples","text":"Value nicotinic acid;0.5 milligram per liter"},{"location":"root_med_suppl/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"root_med_suppl/#annotations","title":"Annotations","text":"property value expected_value supplement name;measurement value"},{"location":"root_med_suppl/#schema-source","title":"Schema Source","text":""},{"location":"root_med_suppl/#linkml-source","title":"LinkML Source","text":"
name: root_med_suppl\nannotations:\n  expected_value:\n    tag: expected_value\n    value: supplement name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Organic supplements of the culture rooting medium, such as vitamins,\n  amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n  (0.5\u00ac\u2020mg/L).\ntitle: rooting medium organic supplements\nexamples:\n- value: nicotinic acid;0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium organic supplements\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000580\nalias: root_med_suppl\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"salinity/","title":"Slot: salinity (salinity)","text":"

The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.

URI: MIXS:0000183

"},{"location":"salinity/#inheritance","title":"Inheritance","text":""},{"location":"salinity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salinity/#properties","title":"Properties","text":""},{"location":"salinity/#aliases","title":"Aliases","text":""},{"location":"salinity/#examples","title":"Examples","text":"Value 25 practical salinity unit"},{"location":"salinity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"salinity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"salinity/#schema-source","title":"Schema Source","text":""},{"location":"salinity/#linkml-source","title":"LinkML Source","text":"
name: salinity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: practical salinity unit, percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The total concentration of all dissolved salts in a liquid or solid sample.\n  While salinity can be measured by a complete chemical analysis, this method is difficult\n  and time consuming. More often, it is instead derived from the conductivity measurement.\n  This is known as practical salinity. These derivations compare the specific conductance\n  of the sample to a salinity standard such as seawater.\ntitle: salinity\nexamples:\n- value: 25 practical salinity unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000183\nalias: salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"salinity_category/","title":"Slot: salinity_category","text":"

Categorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline

URI: nmdc:salinity_category

"},{"location":"salinity_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salinity_category/#properties","title":"Properties","text":""},{"location":"salinity_category/#see-also","title":"See Also","text":""},{"location":"salinity_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"salinity_category/#schema-source","title":"Schema Source","text":""},{"location":"salinity_category/#linkml-source","title":"LinkML Source","text":"
name: salinity_category\ndescription: 'Categorical description of the sample''s salinity. Examples: halophile,\n  halotolerant, hypersaline, huryhaline'\nnotes:\n- maps to gold:salinity\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-metadata/pull/297\nrank: 1000\nalias: salinity_category\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"salinity_meth/","title":"Slot: salinity method (salinity_meth)","text":"

Reference or method used in determining salinity

URI: MIXS:0000341

"},{"location":"salinity_meth/#inheritance","title":"Inheritance","text":""},{"location":"salinity_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"salinity_meth/#properties","title":"Properties","text":""},{"location":"salinity_meth/#aliases","title":"Aliases","text":""},{"location":"salinity_meth/#examples","title":"Examples","text":"Value"},{"location":"salinity_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"salinity_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"salinity_meth/#schema-source","title":"Schema Source","text":""},{"location":"salinity_meth/#linkml-source","title":"LinkML Source","text":"
name: salinity_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining salinity\ntitle: salinity method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000341\nalias: salinity_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"salt_regm/","title":"Slot: salt regimen (salt_regm)","text":"

Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens

URI: MIXS:0000582

"},{"location":"salt_regm/#inheritance","title":"Inheritance","text":""},{"location":"salt_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salt_regm/#properties","title":"Properties","text":""},{"location":"salt_regm/#aliases","title":"Aliases","text":""},{"location":"salt_regm/#examples","title":"Examples","text":"Value NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"salt_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"salt_regm/#annotations","title":"Annotations","text":"property value expected_value salt name;salt amount;treatment interval and duration"},{"location":"salt_regm/#schema-source","title":"Schema Source","text":""},{"location":"salt_regm/#linkml-source","title":"LinkML Source","text":"
name: salt_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: salt name;salt amount;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, microgram, mole per liter, gram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving use of salts as supplement to liquid\n  and soil growth media; should include the name of salt, amount administered, treatment\n  regimen including how many times the treatment was repeated, how long each treatment\n  lasted, and the start and end time of the entire treatment; can include multiple\n  salt regimens\ntitle: salt regimen\nexamples:\n- value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salt regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000582\nalias: salt_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"samp_capt_status/","title":"Slot: sample capture status (samp_capt_status)","text":"

Reason for the sample

URI: MIXS:0000860

"},{"location":"samp_capt_status/#inheritance","title":"Inheritance","text":""},{"location":"samp_capt_status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_capt_status/#properties","title":"Properties","text":""},{"location":"samp_capt_status/#aliases","title":"Aliases","text":""},{"location":"samp_capt_status/#examples","title":"Examples","text":"Value farm sample"},{"location":"samp_capt_status/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_capt_status/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_capt_status/#schema-source","title":"Schema Source","text":""},{"location":"samp_capt_status/#linkml-source","title":"LinkML Source","text":"
name: samp_capt_status\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reason for the sample\ntitle: sample capture status\nexamples:\n- value: farm sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample capture status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000860\nalias: samp_capt_status\ndomain_of:\n- Biosample\nrange: samp_capt_status_enum\nmultivalued: false\n\n
"},{"location":"samp_collec_device/","title":"Slot: sample collection device (samp_collec_device)","text":"

The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).

URI: MIXS:0000002

"},{"location":"samp_collec_device/#inheritance","title":"Inheritance","text":""},{"location":"samp_collec_device/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_collec_device/#properties","title":"Properties","text":""},{"location":"samp_collec_device/#aliases","title":"Aliases","text":""},{"location":"samp_collec_device/#examples","title":"Examples","text":"Value swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]"},{"location":"samp_collec_device/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_collec_device/#annotations","title":"Annotations","text":"property value expected_value device name"},{"location":"samp_collec_device/#schema-source","title":"Schema Source","text":""},{"location":"samp_collec_device/#linkml-source","title":"LinkML Source","text":"
name: samp_collec_device\nannotations:\n  expected_value:\n    tag: expected_value\n    value: device name\ndescription: The device used to collect an environmental sample. This field accepts\n  terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n  This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\ntitle: sample collection device\nexamples:\n- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection device\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000002\nalias: samp_collec_device\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"samp_collec_method/","title":"Slot: sample collection method (samp_collec_method)","text":"

The method employed for collecting the sample.

URI: MIXS:0001225

"},{"location":"samp_collec_method/#inheritance","title":"Inheritance","text":""},{"location":"samp_collec_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_collec_method/#properties","title":"Properties","text":""},{"location":"samp_collec_method/#aliases","title":"Aliases","text":""},{"location":"samp_collec_method/#examples","title":"Examples","text":"Value swabbing"},{"location":"samp_collec_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_collec_method/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url , or text"},{"location":"samp_collec_method/#schema-source","title":"Schema Source","text":""},{"location":"samp_collec_method/#linkml-source","title":"LinkML Source","text":"
name: samp_collec_method\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url , or text\ndescription: The method employed for collecting the sample.\ntitle: sample collection method\nexamples:\n- value: swabbing\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection method\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001225\nalias: samp_collec_method\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"samp_collect_point/","title":"Slot: sample collection point (samp_collect_point)","text":"

Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0001015

"},{"location":"samp_collect_point/#inheritance","title":"Inheritance","text":""},{"location":"samp_collect_point/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_collect_point/#properties","title":"Properties","text":""},{"location":"samp_collect_point/#aliases","title":"Aliases","text":""},{"location":"samp_collect_point/#examples","title":"Examples","text":"Value well"},{"location":"samp_collect_point/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_collect_point/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_collect_point/#schema-source","title":"Schema Source","text":""},{"location":"samp_collect_point/#linkml-source","title":"LinkML Source","text":"
name: samp_collect_point\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sampling point on the asset were sample was collected (e.g. Wellhead,\n  storage tank, separator, etc). If \"other\" is specified, please propose entry in\n  \"additional info\" field\ntitle: sample collection point\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001015\nalias: samp_collect_point\ndomain_of:\n- Biosample\nrange: samp_collect_point_enum\nmultivalued: false\n\n
"},{"location":"samp_dis_stage/","title":"Slot: sample disease stage (samp_dis_stage)","text":"

Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.

URI: MIXS:0000249

"},{"location":"samp_dis_stage/#inheritance","title":"Inheritance","text":""},{"location":"samp_dis_stage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_dis_stage/#properties","title":"Properties","text":""},{"location":"samp_dis_stage/#aliases","title":"Aliases","text":""},{"location":"samp_dis_stage/#examples","title":"Examples","text":"Value infection"},{"location":"samp_dis_stage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_dis_stage/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_dis_stage/#schema-source","title":"Schema Source","text":""},{"location":"samp_dis_stage/#linkml-source","title":"LinkML Source","text":"
name: samp_dis_stage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Stage of the disease at the time of sample collection, e.g. inoculation,\n  penetration, infection, growth and reproduction, dissemination of pathogen.\ntitle: sample disease stage\nexamples:\n- value: infection\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample disease stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000249\nalias: samp_dis_stage\ndomain_of:\n- Biosample\nrange: samp_dis_stage_enum\nmultivalued: false\n\n
"},{"location":"samp_floor/","title":"Slot: sampling floor (samp_floor)","text":"

The floor of the building, where the sampling room is located

URI: MIXS:0000828

"},{"location":"samp_floor/#inheritance","title":"Inheritance","text":""},{"location":"samp_floor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_floor/#properties","title":"Properties","text":""},{"location":"samp_floor/#aliases","title":"Aliases","text":""},{"location":"samp_floor/#examples","title":"Examples","text":"Value 4th floor"},{"location":"samp_floor/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_floor/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_floor/#schema-source","title":"Schema Source","text":""},{"location":"samp_floor/#linkml-source","title":"LinkML Source","text":"
name: samp_floor\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The floor of the building, where the sampling room is located\ntitle: sampling floor\nexamples:\n- value: 4th floor\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling floor\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000828\nalias: samp_floor\ndomain_of:\n- Biosample\nrange: samp_floor_enum\nmultivalued: false\n\n
"},{"location":"samp_loc_corr_rate/","title":"Slot: corrosion rate at sample location (samp_loc_corr_rate)","text":"

Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays

URI: MIXS:0000136

"},{"location":"samp_loc_corr_rate/#inheritance","title":"Inheritance","text":""},{"location":"samp_loc_corr_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_loc_corr_rate/#properties","title":"Properties","text":""},{"location":"samp_loc_corr_rate/#aliases","title":"Aliases","text":""},{"location":"samp_loc_corr_rate/#examples","title":"Examples","text":"Value"},{"location":"samp_loc_corr_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_loc_corr_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value range"},{"location":"samp_loc_corr_rate/#schema-source","title":"Schema Source","text":""},{"location":"samp_loc_corr_rate/#linkml-source","title":"LinkML Source","text":"
name: samp_loc_corr_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter per year\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Metal corrosion rate is the speed of metal deterioration due to environmental\n  conditions. As environmental conditions change corrosion rates change accordingly.\n  Therefore, long term corrosion rates are generally more informative than short term\n  rates and for that reason they are preferred during reporting. In the case of suspected\n  MIC, corrosion rate measurements at the time of sampling might provide insights\n  into the involvement of certain microbial community members in MIC as well as potential\n  microbial interplays\ntitle: corrosion rate at sample location\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- corrosion rate at sample location\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000136\nalias: samp_loc_corr_rate\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_mat_process/","title":"Slot: sample material processing (samp_mat_process)","text":"

A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.

URI: MIXS:0000016

"},{"location":"samp_mat_process/#inheritance","title":"Inheritance","text":""},{"location":"samp_mat_process/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_mat_process/#properties","title":"Properties","text":""},{"location":"samp_mat_process/#aliases","title":"Aliases","text":""},{"location":"samp_mat_process/#examples","title":"Examples","text":"Value filtering of seawater, storing samples in ethanol"},{"location":"samp_mat_process/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_mat_process/#annotations","title":"Annotations","text":"property value expected_value text"},{"location":"samp_mat_process/#schema-source","title":"Schema Source","text":""},{"location":"samp_mat_process/#linkml-source","title":"LinkML Source","text":"
name: samp_mat_process\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text\ndescription: A brief description of any processing applied to the sample during or\n  after retrieving the sample from environment, or a link to the relevant protocol(s)\n  performed.\ntitle: sample material processing\nexamples:\n- value: filtering of seawater, storing samples in ethanol\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample material processing\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000016\nalias: samp_mat_process\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\n
"},{"location":"samp_md/","title":"Slot: sample measured depth (samp_md)","text":"

In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000413

"},{"location":"samp_md/#inheritance","title":"Inheritance","text":""},{"location":"samp_md/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_md/#properties","title":"Properties","text":""},{"location":"samp_md/#aliases","title":"Aliases","text":""},{"location":"samp_md/#examples","title":"Examples","text":"Value 1534 meter;MSL"},{"location":"samp_md/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_md/#annotations","title":"Annotations","text":"property value expected_value measurement value;enumeration"},{"location":"samp_md/#schema-source","title":"Schema Source","text":""},{"location":"samp_md/#linkml-source","title":"LinkML Source","text":"
name: samp_md\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;enumeration\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: In non deviated well, measured depth is equal to the true vertical depth,\n  TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the\n  MD is the length of trajectory of the borehole measured from the same reference\n  or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary\n  table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified,\n  please propose entry in \"additional info\" field\ntitle: sample measured depth\nexamples:\n- value: 1534 meter;MSL\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample measured depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000413\nalias: samp_md\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"samp_name/","title":"Slot: sample name (samp_name)","text":"

A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.

URI: MIXS:0001107

"},{"location":"samp_name/#inheritance","title":"Inheritance","text":""},{"location":"samp_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_name/#properties","title":"Properties","text":""},{"location":"samp_name/#aliases","title":"Aliases","text":""},{"location":"samp_name/#examples","title":"Examples","text":"Value ISDsoil1"},{"location":"samp_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_name/#annotations","title":"Annotations","text":"property value expected_value text"},{"location":"samp_name/#schema-source","title":"Schema Source","text":""},{"location":"samp_name/#linkml-source","title":"LinkML Source","text":"
name: samp_name\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text\ndescription: A local identifier or name that for the material sample used for extracting\n  nucleic acids, and subsequent sequencing. It can refer either to the original material\n  collected or to any derived sub-samples. It can have any format, but we suggest\n  that you make it concise, unique and consistent within your lab, and as informative\n  as possible. INSDC requires every sample name from a single Submitter to be unique.\n  Use of a globally unique identifier for the field source_mat_id is recommended in\n  addition to sample_name.\ntitle: sample name\nexamples:\n- value: ISDsoil1\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample name\nrank: 1000\nis_a: investigation field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001107\nalias: samp_name\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"samp_preserv/","title":"Slot: preservative added to sample (samp_preserv)","text":"

Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)

URI: MIXS:0000463

"},{"location":"samp_preserv/#inheritance","title":"Inheritance","text":""},{"location":"samp_preserv/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_preserv/#properties","title":"Properties","text":""},{"location":"samp_preserv/#aliases","title":"Aliases","text":""},{"location":"samp_preserv/#examples","title":"Examples","text":"Value"},{"location":"samp_preserv/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_preserv/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"samp_preserv/#schema-source","title":"Schema Source","text":""},{"location":"samp_preserv/#linkml-source","title":"LinkML Source","text":"
name: samp_preserv\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milliliter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n  etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\ntitle: preservative added to sample\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- preservative added to sample\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000463\nalias: samp_preserv\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_room_id/","title":"Slot: sampling room ID or name (samp_room_id)","text":"

Sampling room number. This ID should be consistent with the designations on the building floor plans

URI: MIXS:0000244

"},{"location":"samp_room_id/#inheritance","title":"Inheritance","text":""},{"location":"samp_room_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_room_id/#properties","title":"Properties","text":""},{"location":"samp_room_id/#aliases","title":"Aliases","text":""},{"location":"samp_room_id/#examples","title":"Examples","text":"Value"},{"location":"samp_room_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_room_id/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"samp_room_id/#schema-source","title":"Schema Source","text":""},{"location":"samp_room_id/#linkml-source","title":"LinkML Source","text":"
name: samp_room_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sampling room number. This ID should be consistent with the designations\n  on the building floor plans\ntitle: sampling room ID or name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling room ID or name\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000244\nalias: samp_room_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_size/","title":"Slot: amount or size of sample collected (samp_size)","text":"

The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.

URI: MIXS:0000001

"},{"location":"samp_size/#inheritance","title":"Inheritance","text":""},{"location":"samp_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_size/#properties","title":"Properties","text":""},{"location":"samp_size/#aliases","title":"Aliases","text":""},{"location":"samp_size/#examples","title":"Examples","text":"Value 5 liter"},{"location":"samp_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_size/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"samp_size/#schema-source","title":"Schema Source","text":""},{"location":"samp_size/#linkml-source","title":"LinkML Source","text":"
name: samp_size\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millliter, gram, milligram, liter\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n  collected.\ntitle: amount or size of sample collected\nexamples:\n- value: 5 liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount or size of sample collected\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000001\nalias: samp_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"samp_sort_meth/","title":"Slot: sample size sorting method (samp_sort_meth)","text":"

Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.

URI: MIXS:0000216

"},{"location":"samp_sort_meth/#inheritance","title":"Inheritance","text":""},{"location":"samp_sort_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_sort_meth/#properties","title":"Properties","text":""},{"location":"samp_sort_meth/#aliases","title":"Aliases","text":""},{"location":"samp_sort_meth/#examples","title":"Examples","text":"Value"},{"location":"samp_sort_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_sort_meth/#annotations","title":"Annotations","text":"property value expected_value description of method"},{"location":"samp_sort_meth/#schema-source","title":"Schema Source","text":""},{"location":"samp_sort_meth/#linkml-source","title":"LinkML Source","text":"
name: samp_sort_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: description of method\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Method by which samples are sorted; open face filter collecting total\n  suspended particles, prefilter to remove particles larger than X micrometers in\n  diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade\n  impactor.\ntitle: sample size sorting method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample size sorting method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000216\nalias: samp_sort_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"samp_store_dur/","title":"Slot: sample storage duration (samp_store_dur)","text":"

Duration for which the sample was stored

URI: MIXS:0000116

"},{"location":"samp_store_dur/#inheritance","title":"Inheritance","text":""},{"location":"samp_store_dur/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_store_dur/#properties","title":"Properties","text":""},{"location":"samp_store_dur/#aliases","title":"Aliases","text":""},{"location":"samp_store_dur/#examples","title":"Examples","text":"Value P1Y6M"},{"location":"samp_store_dur/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_store_dur/#annotations","title":"Annotations","text":"property value expected_value duration"},{"location":"samp_store_dur/#schema-source","title":"Schema Source","text":""},{"location":"samp_store_dur/#linkml-source","title":"LinkML Source","text":"
name: samp_store_dur\nannotations:\n  expected_value:\n    tag: expected_value\n    value: duration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Duration for which the sample was stored\ntitle: sample storage duration\nexamples:\n- value: P1Y6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage duration\nrank: 1000\nis_a: core field\nstring_serialization: '{duration}'\nslot_uri: MIXS:0000116\nalias: samp_store_dur\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_store_loc/","title":"Slot: sample storage location (samp_store_loc)","text":"

Location at which sample was stored, usually name of a specific freezer/room

URI: MIXS:0000755

"},{"location":"samp_store_loc/#inheritance","title":"Inheritance","text":""},{"location":"samp_store_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_store_loc/#properties","title":"Properties","text":""},{"location":"samp_store_loc/#aliases","title":"Aliases","text":""},{"location":"samp_store_loc/#examples","title":"Examples","text":"Value Freezer no:5"},{"location":"samp_store_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_store_loc/#annotations","title":"Annotations","text":"property value expected_value location name"},{"location":"samp_store_loc/#schema-source","title":"Schema Source","text":""},{"location":"samp_store_loc/#linkml-source","title":"LinkML Source","text":"
name: samp_store_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: location name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Location at which sample was stored, usually name of a specific freezer/room\ntitle: sample storage location\nexamples:\n- value: Freezer no:5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage location\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000755\nalias: samp_store_loc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_store_temp/","title":"Slot: sample storage temperature (samp_store_temp)","text":"

Temperature at which sample was stored, e.g. -80 degree Celsius

URI: MIXS:0000110

"},{"location":"samp_store_temp/#inheritance","title":"Inheritance","text":""},{"location":"samp_store_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_store_temp/#properties","title":"Properties","text":""},{"location":"samp_store_temp/#aliases","title":"Aliases","text":""},{"location":"samp_store_temp/#examples","title":"Examples","text":"Value -80 degree Celsius"},{"location":"samp_store_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_store_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"samp_store_temp/#schema-source","title":"Schema Source","text":""},{"location":"samp_store_temp/#linkml-source","title":"LinkML Source","text":"
name: samp_store_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Temperature at which sample was stored, e.g. -80 degree Celsius\ntitle: sample storage temperature\nexamples:\n- value: -80 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000110\nalias: samp_store_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"samp_subtype/","title":"Slot: sample subtype (samp_subtype)","text":"

Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000999

"},{"location":"samp_subtype/#inheritance","title":"Inheritance","text":""},{"location":"samp_subtype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_subtype/#properties","title":"Properties","text":""},{"location":"samp_subtype/#aliases","title":"Aliases","text":""},{"location":"samp_subtype/#examples","title":"Examples","text":"Value biofilm"},{"location":"samp_subtype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_subtype/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_subtype/#schema-source","title":"Schema Source","text":""},{"location":"samp_subtype/#linkml-source","title":"LinkML Source","text":"
name: samp_subtype\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of sample sub-type. For example if \"sample type\" is \"Produced Water\"\n  then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please\n  propose entry in \"additional info\" field\ntitle: sample subtype\nexamples:\n- value: biofilm\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample subtype\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000999\nalias: samp_subtype\ndomain_of:\n- Biosample\nrange: samp_subtype_enum\nmultivalued: false\n\n
"},{"location":"samp_taxon_id/","title":"Slot: Taxonomy ID of DNA sample (samp_taxon_id)","text":"

NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample' for negative controls.

URI: MIXS:0001320

"},{"location":"samp_taxon_id/#inheritance","title":"Inheritance","text":""},{"location":"samp_taxon_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_taxon_id/#properties","title":"Properties","text":""},{"location":"samp_taxon_id/#aliases","title":"Aliases","text":""},{"location":"samp_taxon_id/#comments","title":"Comments","text":""},{"location":"samp_taxon_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_taxon_id/#annotations","title":"Annotations","text":"property value expected_value Taxonomy ID"},{"location":"samp_taxon_id/#schema-source","title":"Schema Source","text":""},{"location":"samp_taxon_id/#linkml-source","title":"LinkML Source","text":"
name: samp_taxon_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: Taxonomy ID\ndescription: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa sample.\n  Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample'\n  for negative controls.\ntitle: Taxonomy ID of DNA sample\ncomments:\n- coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Taxonomy ID of DNA sample\nrank: 1000\nis_a: investigation field\nslot_uri: MIXS:0001320\nalias: samp_taxon_id\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\n
"},{"location":"samp_time_out/","title":"Slot: sampling time outside (samp_time_out)","text":"

The recent and long term history of outside sampling

URI: MIXS:0000196

"},{"location":"samp_time_out/#inheritance","title":"Inheritance","text":""},{"location":"samp_time_out/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_time_out/#properties","title":"Properties","text":""},{"location":"samp_time_out/#aliases","title":"Aliases","text":""},{"location":"samp_time_out/#examples","title":"Examples","text":"Value"},{"location":"samp_time_out/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_time_out/#annotations","title":"Annotations","text":"property value expected_value time"},{"location":"samp_time_out/#schema-source","title":"Schema Source","text":""},{"location":"samp_time_out/#linkml-source","title":"LinkML Source","text":"
name: samp_time_out\nannotations:\n  expected_value:\n    tag: expected_value\n    value: time\n  preferred_unit:\n    tag: preferred_unit\n    value: hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The recent and long term history of outside sampling\ntitle: sampling time outside\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling time outside\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000196\nalias: samp_time_out\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_transport_cond/","title":"Slot: sample transport conditions (samp_transport_cond)","text":"

Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)

URI: MIXS:0000410

"},{"location":"samp_transport_cond/#inheritance","title":"Inheritance","text":""},{"location":"samp_transport_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_transport_cond/#properties","title":"Properties","text":""},{"location":"samp_transport_cond/#aliases","title":"Aliases","text":""},{"location":"samp_transport_cond/#examples","title":"Examples","text":"Value 5 days;-20 degree Celsius"},{"location":"samp_transport_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_transport_cond/#annotations","title":"Annotations","text":"property value expected_value measurement value;measurement value"},{"location":"samp_transport_cond/#schema-source","title":"Schema Source","text":""},{"location":"samp_transport_cond/#linkml-source","title":"LinkML Source","text":"
name: samp_transport_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: days;degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sample transport duration (in days or hrs) and temperature the sample\n  was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\ntitle: sample transport conditions\nexamples:\n- value: 5 days;-20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample transport conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000410\nalias: samp_transport_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_tvdss/","title":"Slot: sample true vertical depth subsea (samp_tvdss)","text":"

Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m

URI: MIXS:0000409

"},{"location":"samp_tvdss/#inheritance","title":"Inheritance","text":""},{"location":"samp_tvdss/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_tvdss/#properties","title":"Properties","text":""},{"location":"samp_tvdss/#aliases","title":"Aliases","text":""},{"location":"samp_tvdss/#examples","title":"Examples","text":"Value"},{"location":"samp_tvdss/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_tvdss/#annotations","title":"Annotations","text":"property value expected_value measurement value or measurement value range"},{"location":"samp_tvdss/#schema-source","title":"Schema Source","text":""},{"location":"samp_tvdss/#linkml-source","title":"LinkML Source","text":"
name: samp_tvdss\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value or measurement value range\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Depth of the sample i.e. The vertical distance between the sea level\n  and the sampled position in the subsurface. Depth can be reported as an interval\n  for subsurface samples e.g. 1325.75-1362.25 m\ntitle: sample true vertical depth subsea\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample true vertical depth subsea\nrank: 1000\nis_a: core field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000409\nalias: samp_tvdss\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_type/","title":"Slot: sample type (samp_type)","text":"

The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).

URI: MIXS:0000998

"},{"location":"samp_type/#inheritance","title":"Inheritance","text":""},{"location":"samp_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_type/#properties","title":"Properties","text":""},{"location":"samp_type/#aliases","title":"Aliases","text":""},{"location":"samp_type/#examples","title":"Examples","text":"Value built environment sample [GENEPIO:0001248]"},{"location":"samp_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_type/#annotations","title":"Annotations","text":"property value expected_value GENEPIO:0001246"},{"location":"samp_type/#schema-source","title":"Schema Source","text":""},{"location":"samp_type/#linkml-source","title":"LinkML Source","text":"
name: samp_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: GENEPIO:0001246\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of material from which the sample was obtained. For the Hydrocarbon\n  package, samples include types like core, rock trimmings, drill cuttings, piping\n  section, coupon, pigging debris, solid deposit, produced fluid, produced water,\n  injected water, swabs, etc. For the Food Package, samples are usually categorized\n  as food, body products or tissues, or environmental material. This field accepts\n  terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\ntitle: sample type\nexamples:\n- value: built environment sample [GENEPIO:0001248]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000998\nalias: samp_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"samp_vol_we_dna_ext/","title":"Slot: sample volume or weight for DNA extraction (samp_vol_we_dna_ext)","text":"

Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).

URI: MIXS:0000111

"},{"location":"samp_vol_we_dna_ext/#inheritance","title":"Inheritance","text":""},{"location":"samp_vol_we_dna_ext/#properties","title":"Properties","text":""},{"location":"samp_vol_we_dna_ext/#aliases","title":"Aliases","text":""},{"location":"samp_vol_we_dna_ext/#examples","title":"Examples","text":"Value 1500 milliliter"},{"location":"samp_vol_we_dna_ext/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_vol_we_dna_ext/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"samp_vol_we_dna_ext/#schema-source","title":"Schema Source","text":""},{"location":"samp_vol_we_dna_ext/#linkml-source","title":"LinkML Source","text":"
name: samp_vol_we_dna_ext\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millliter, gram, milligram, square centimeter\ndescription: 'Volume (ml) or mass (g) of total collected sample processed for DNA\n  extraction. Note: total sample collected should be entered under the term Sample\n  Size (MIXS:0000001).'\ntitle: sample volume or weight for DNA extraction\nexamples:\n- value: 1500 milliliter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample volume or weight for DNA extraction\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000111\nalias: samp_vol_we_dna_ext\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"samp_weather/","title":"Slot: sampling day weather (samp_weather)","text":"

The weather on the sampling day

URI: MIXS:0000827

"},{"location":"samp_weather/#inheritance","title":"Inheritance","text":""},{"location":"samp_weather/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_weather/#properties","title":"Properties","text":""},{"location":"samp_weather/#aliases","title":"Aliases","text":""},{"location":"samp_weather/#examples","title":"Examples","text":"Value foggy"},{"location":"samp_weather/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_weather/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"samp_weather/#schema-source","title":"Schema Source","text":""},{"location":"samp_weather/#linkml-source","title":"LinkML Source","text":"
name: samp_weather\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The weather on the sampling day\ntitle: sampling day weather\nexamples:\n- value: foggy\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling day weather\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000827\nalias: samp_weather\ndomain_of:\n- Biosample\nrange: samp_weather_enum\nmultivalued: false\n\n
"},{"location":"samp_well_name/","title":"Slot: sample well name (samp_well_name)","text":"

Name of the well (e.g. BXA1123) where sample was taken

URI: MIXS:0000296

"},{"location":"samp_well_name/#inheritance","title":"Inheritance","text":""},{"location":"samp_well_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"samp_well_name/#properties","title":"Properties","text":""},{"location":"samp_well_name/#aliases","title":"Aliases","text":""},{"location":"samp_well_name/#examples","title":"Examples","text":"Value"},{"location":"samp_well_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"samp_well_name/#annotations","title":"Annotations","text":"property value expected_value name"},{"location":"samp_well_name/#schema-source","title":"Schema Source","text":""},{"location":"samp_well_name/#linkml-source","title":"LinkML Source","text":"
name: samp_well_name\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Name of the well (e.g. BXA1123) where sample was taken\ntitle: sample well name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample well name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000296\nalias: samp_well_name\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"sample_collection_day/","title":"Slot: sample_collection_day","text":"

URI: nmdc:sample_collection_day

"},{"location":"sample_collection_day/#properties","title":"Properties","text":""},{"location":"sample_collection_day/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_day/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_day/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_day\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_day\nrange: integer\n\n
"},{"location":"sample_collection_hour/","title":"Slot: sample_collection_hour","text":"

URI: nmdc:sample_collection_hour

"},{"location":"sample_collection_hour/#properties","title":"Properties","text":""},{"location":"sample_collection_hour/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_hour/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_hour/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_hour\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_hour\nrange: integer\n\n
"},{"location":"sample_collection_minute/","title":"Slot: sample_collection_minute","text":"

URI: nmdc:sample_collection_minute

"},{"location":"sample_collection_minute/#properties","title":"Properties","text":""},{"location":"sample_collection_minute/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_minute/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_minute/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_minute\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_minute\nrange: integer\n\n
"},{"location":"sample_collection_month/","title":"Slot: sample_collection_month","text":"

URI: nmdc:sample_collection_month

"},{"location":"sample_collection_month/#properties","title":"Properties","text":""},{"location":"sample_collection_month/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_month/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_month/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_month\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_month\nrange: string\n\n
"},{"location":"sample_collection_site/","title":"Slot: sample_collection_site","text":"

URI: nmdc:sample_collection_site

"},{"location":"sample_collection_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_collection_site/#properties","title":"Properties","text":""},{"location":"sample_collection_site/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_site/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_site/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_site\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_site\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"sample_collection_year/","title":"Slot: sample_collection_year","text":"

URI: nmdc:sample_collection_year

"},{"location":"sample_collection_year/#properties","title":"Properties","text":""},{"location":"sample_collection_year/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_collection_year/#schema-source","title":"Schema Source","text":""},{"location":"sample_collection_year/#linkml-source","title":"LinkML Source","text":"
name: sample_collection_year\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_year\nrange: integer\n\n
"},{"location":"sample_link/","title":"Slot: sample linkage (sample_link)","text":"

A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.

URI: nmdc:sample_link

"},{"location":"sample_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_link/#properties","title":"Properties","text":""},{"location":"sample_link/#examples","title":"Examples","text":"Value IGSN:DSJ0284"},{"location":"sample_link/#comments","title":"Comments","text":""},{"location":"sample_link/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_link/#schema-source","title":"Schema Source","text":""},{"location":"sample_link/#linkml-source","title":"LinkML Source","text":"
name: sample_link\ndescription: A unique identifier to assign parent-child, subsample, or sibling samples.\n  This is relevant when a sample or other material was used to generate the new sample.\ntitle: sample linkage\ncomments:\n- 'This field allows multiple entries separated by ; (Examples: Soil collected from\n  the field will link with the soil used in an incubation. The soil a plant was grown\n  in links to the plant sample. An original culture sample was transferred to a new\n  vial and generated a new sample)'\nexamples:\n- value: IGSN:DSJ0284\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{text}:{text}'\nalias: sample_link\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: string\nrecommended: true\nmultivalued: true\n\n
"},{"location":"sample_shipped/","title":"Slot: sample shipped amount (sample_shipped)","text":"

The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.

URI: nmdc:sample_shipped

"},{"location":"sample_shipped/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_shipped/#properties","title":"Properties","text":""},{"location":"sample_shipped/#examples","title":"Examples","text":"Value 15 g 100 uL 5 mL"},{"location":"sample_shipped/#comments","title":"Comments","text":""},{"location":"sample_shipped/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_shipped/#schema-source","title":"Schema Source","text":""},{"location":"sample_shipped/#linkml-source","title":"LinkML Source","text":"
name: sample_shipped\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n  sent to EMSL.\ntitle: sample shipped amount\ncomments:\n- This field is only required when completing metadata for samples being submitted\n  to EMSL for analyses.\nexamples:\n- value: 15 g\n- value: 100 uL\n- value: 5 mL\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{float} {unit}'\nalias: sample_shipped\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"sample_state_information/","title":"Slot: sample_state_information","text":"

The chemical phase of a pure sample, or the state of a mixed sample

URI: nmdc:sample_state_information

"},{"location":"sample_state_information/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"sample_state_information/#properties","title":"Properties","text":""},{"location":"sample_state_information/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_state_information/#schema-source","title":"Schema Source","text":""},{"location":"sample_state_information/#linkml-source","title":"LinkML Source","text":"
name: sample_state_information\ndescription: The chemical phase of a pure sample, or the state of a mixed sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_state_information\ndomain_of:\n- PortionOfSubstance\nrange: SampleStateEnum\n\n
"},{"location":"sample_type/","title":"Slot: sample type (sample_type)","text":"

Type of sample being submitted

URI: nmdc:sample_type

"},{"location":"sample_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_type/#properties","title":"Properties","text":""},{"location":"sample_type/#examples","title":"Examples","text":"Value water extracted soil"},{"location":"sample_type/#comments","title":"Comments","text":""},{"location":"sample_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sample_type/#schema-source","title":"Schema Source","text":""},{"location":"sample_type/#linkml-source","title":"LinkML Source","text":"
name: sample_type\ndescription: Type of sample being submitted\ntitle: sample type\ncomments:\n- This can vary from 'environmental package' if the sample is an extraction.\nexamples:\n- value: water extracted soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nalias: sample_type\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: SampleTypeEnum\nrecommended: true\n\n
"},{"location":"sampled_portion/","title":"Slot: sampled_portion","text":"

The portion of the sample that is taken for downstream activity.

URI: nmdc:sampled_portion

"},{"location":"sampled_portion/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no"},{"location":"sampled_portion/#properties","title":"Properties","text":""},{"location":"sampled_portion/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sampled_portion/#schema-source","title":"Schema Source","text":""},{"location":"sampled_portion/#linkml-source","title":"LinkML Source","text":"
name: sampled_portion\ndescription: The portion of the sample that is taken for downstream activity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sampled_portion\ndomain_of:\n- SubSamplingProcess\nrange: SamplePortionEnum\nmultivalued: true\n\n
"},{"location":"saturates_pc/","title":"Slot: saturates wt% (saturates_pc)","text":"

Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)

URI: MIXS:0000131

"},{"location":"saturates_pc/#inheritance","title":"Inheritance","text":""},{"location":"saturates_pc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"saturates_pc/#properties","title":"Properties","text":""},{"location":"saturates_pc/#aliases","title":"Aliases","text":""},{"location":"saturates_pc/#examples","title":"Examples","text":"Value"},{"location":"saturates_pc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"saturates_pc/#annotations","title":"Annotations","text":"property value expected_value name;measurement value"},{"location":"saturates_pc/#schema-source","title":"Schema Source","text":""},{"location":"saturates_pc/#linkml-source","title":"LinkML Source","text":"
name: saturates_pc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n  that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n  There are three main methods to obtain SARA results. The most popular one is known\n  as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: saturates wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- saturates wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000131\nalias: saturates_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"scaf_bp/","title":"Slot: scaf_bp","text":"

Total size in bp of all scaffolds.

URI: nmdc:scaf_bp

"},{"location":"scaf_bp/#inheritance","title":"Inheritance","text":""},{"location":"scaf_bp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_bp/#properties","title":"Properties","text":""},{"location":"scaf_bp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_bp/#schema-source","title":"Schema Source","text":""},{"location":"scaf_bp/#linkml-source","title":"LinkML Source","text":"
name: scaf_bp\ndescription: Total size in bp of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_l50/","title":"Slot: scaf_l50","text":"

Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.

URI: nmdc:scaf_l50

"},{"location":"scaf_l50/#inheritance","title":"Inheritance","text":""},{"location":"scaf_l50/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_l50/#properties","title":"Properties","text":""},{"location":"scaf_l50/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_l50/#schema-source","title":"Schema Source","text":""},{"location":"scaf_l50/#linkml-source","title":"LinkML Source","text":"
name: scaf_l50\ndescription: Given a set of scaffolds, the L50 is defined as the sequence length of\n  the shortest scaffold at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_l90/","title":"Slot: scaf_l90","text":"

The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.

URI: nmdc:scaf_l90

"},{"location":"scaf_l90/#inheritance","title":"Inheritance","text":""},{"location":"scaf_l90/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_l90/#properties","title":"Properties","text":""},{"location":"scaf_l90/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_l90/#schema-source","title":"Schema Source","text":""},{"location":"scaf_l90/#linkml-source","title":"LinkML Source","text":"
name: scaf_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n  length for which the collection of all scaffolds of that length or longer contains\n  at least 90% of the sum of the lengths of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_l_gt50k/","title":"Slot: scaf_l_gt50k","text":"

Total size in bp of all scaffolds greater than 50 KB.

URI: nmdc:scaf_l_gt50k

"},{"location":"scaf_l_gt50k/#inheritance","title":"Inheritance","text":""},{"location":"scaf_l_gt50k/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_l_gt50k/#properties","title":"Properties","text":""},{"location":"scaf_l_gt50k/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_l_gt50k/#schema-source","title":"Schema Source","text":""},{"location":"scaf_l_gt50k/#linkml-source","title":"LinkML Source","text":"
name: scaf_l_gt50k\ndescription: Total size in bp of all scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_logsum/","title":"Slot: scaf_logsum","text":"

The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase

URI: nmdc:scaf_logsum

"},{"location":"scaf_logsum/#inheritance","title":"Inheritance","text":""},{"location":"scaf_logsum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_logsum/#properties","title":"Properties","text":""},{"location":"scaf_logsum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_logsum/#schema-source","title":"Schema Source","text":""},{"location":"scaf_logsum/#linkml-source","title":"LinkML Source","text":"
name: scaf_logsum\ndescription: The sum of the (length*log(length)) of all scaffolds, times some constant.  Increase\n  the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_max/","title":"Slot: scaf_max","text":"

Maximum scaffold length.

URI: nmdc:scaf_max

"},{"location":"scaf_max/#inheritance","title":"Inheritance","text":""},{"location":"scaf_max/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_max/#properties","title":"Properties","text":""},{"location":"scaf_max/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_max/#schema-source","title":"Schema Source","text":""},{"location":"scaf_max/#linkml-source","title":"LinkML Source","text":"
name: scaf_max\ndescription: Maximum scaffold length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_n50/","title":"Slot: scaf_n50","text":"

Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.

URI: nmdc:scaf_n50

"},{"location":"scaf_n50/#inheritance","title":"Inheritance","text":""},{"location":"scaf_n50/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_n50/#properties","title":"Properties","text":""},{"location":"scaf_n50/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_n50/#schema-source","title":"Schema Source","text":""},{"location":"scaf_n50/#linkml-source","title":"LinkML Source","text":"
name: scaf_n50\ndescription: Given a set of scaffolds, each with its own length, the N50 count is\n  defined as the smallest number of scaffolds whose length sum makes up half of genome\n  size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_n90/","title":"Slot: scaf_n90","text":"

Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.

URI: nmdc:scaf_n90

"},{"location":"scaf_n90/#inheritance","title":"Inheritance","text":""},{"location":"scaf_n90/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_n90/#properties","title":"Properties","text":""},{"location":"scaf_n90/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_n90/#schema-source","title":"Schema Source","text":""},{"location":"scaf_n90/#linkml-source","title":"LinkML Source","text":"
name: scaf_n90\ndescription: Given a set of scaffolds, each with its own length, the N90 count is\n  defined as the smallest number of scaffolds whose length sum makes up 90% of genome\n  size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_n_gt50k/","title":"Slot: scaf_n_gt50k","text":"

Total sequence count of scaffolds greater than 50 KB.

URI: nmdc:scaf_n_gt50k

"},{"location":"scaf_n_gt50k/#inheritance","title":"Inheritance","text":""},{"location":"scaf_n_gt50k/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_n_gt50k/#properties","title":"Properties","text":""},{"location":"scaf_n_gt50k/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_n_gt50k/#schema-source","title":"Schema Source","text":""},{"location":"scaf_n_gt50k/#linkml-source","title":"LinkML Source","text":"
name: scaf_n_gt50k\ndescription: Total sequence count of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_pct_gt50k/","title":"Slot: scaf_pct_gt50k","text":"

Total sequence size percentage of scaffolds greater than 50 KB.

URI: nmdc:scaf_pct_gt50k

"},{"location":"scaf_pct_gt50k/#inheritance","title":"Inheritance","text":""},{"location":"scaf_pct_gt50k/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_pct_gt50k/#properties","title":"Properties","text":""},{"location":"scaf_pct_gt50k/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_pct_gt50k/#schema-source","title":"Schema Source","text":""},{"location":"scaf_pct_gt50k/#linkml-source","title":"LinkML Source","text":"
name: scaf_pct_gt50k\ndescription: Total sequence size percentage of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_pct_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaf_powsum/","title":"Slot: scaf_powsum","text":"

Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).

URI: nmdc:scaf_powsum

"},{"location":"scaf_powsum/#inheritance","title":"Inheritance","text":""},{"location":"scaf_powsum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaf_powsum/#properties","title":"Properties","text":""},{"location":"scaf_powsum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaf_powsum/#schema-source","title":"Schema Source","text":""},{"location":"scaf_powsum/#linkml-source","title":"LinkML Source","text":"
name: scaf_powsum\ndescription: Powersum of all scaffolds is the same as logsum except that it uses the\n  sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"scaffolds/","title":"Slot: scaffolds","text":"

Total sequence count of all scaffolds.

URI: nmdc:scaffolds

"},{"location":"scaffolds/#inheritance","title":"Inheritance","text":""},{"location":"scaffolds/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAssembly no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no"},{"location":"scaffolds/#properties","title":"Properties","text":""},{"location":"scaffolds/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"scaffolds/#schema-source","title":"Schema Source","text":""},{"location":"scaffolds/#linkml-source","title":"LinkML Source","text":"
name: scaffolds\ndescription: Total sequence count of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaffolds\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\n
"},{"location":"schema-validation/","title":"Validating data against the nmdc-schema","text":"

The nmdc-schema's preferred on-disk data serializations are YAML, closely followed by JSON. Preferred databases are MongDB and any RDF triplestore.

The nmdc-schema Makefiles use the linkml-validate and linkml-run-examples CLIs for build-time validation of data file, both of which build upon JSON Schema validation. linkml-validate can even validate against TSV, as long as the schema classes that are instantiated can reasonably be expressed in a table. Programmers can learn more about the internals of these tools at https://linkml.io/linkml/data/validating-data.html

We can conceive of validating a data file at two levels

  1. The file should be syntactically correct
  2. The file should conform to the NMDC schema
"},{"location":"schema-validation/#syntactically-correct-yaml-or-json","title":"Syntactically correct YAML or JSON","text":"

All tools, libraries, or scripts generating NMDC data SHOULD instantiate Python data classes from the nmdc-schema PyPI package. It is strongly discouraged to generate Python dicts or JSON by any method other than object instantiation, even using high-quality, standard JSON libraries. That practice may generate valid data files when first tested but is likely to degrade over time. That degradation can be difficult to debug.

Mike Farrah's yq is a system dependency for the nmdc-schema. It can be used to validate legacy YAML and JSON data. If malformed YAML or JSON is presented to linkml-validate, the error messages may not be as helpful as the messages from yq or some other syntactical validator.

"},{"location":"schema-validation/#what-to-do-if-the-data-do-not-validate","title":"What to do if the data do not validate","text":"

Start by reflecting on whether your data may be ahead of what the schema can currently account for.

  1. The data are reasonable, but the schema needs to be extended or modified to account for it
  2. The schema really does provide support for your data, but you are just not adhering to it

For 1, you can make PR on the schema yaml. If you aren't comfortable editing LinkML YAML, then you can get help from one of the schema developers. We recommend filing a new ticket explaining the issue. Please include your error messages.

For 2, we suggest taking a minimal example approach. linkml-validate is very good at identifying schema violations in small, syntactically valid data files. Debugging can be aided in pulling out single data instances and first verifying that they are syntactically valid YAML or JSON. If you don't want to use yq, then you could paste one instance into a website like https://jsonlint.com/. A common issue in multi-instance files is using incorrect syntax for grouping the instances into a YAML or JSON array. Using a small subsample of your data and an online linter as above can aide in debugging this.

"},{"location":"schema-validation/#expectations-of-nmdc-data-producers","title":"Expectations of NMDC data producers","text":"

It is expected that data producers or transformers take the upfront initiative to validate their data.

Currently, not all providers of information to NMDC provide JSON - for example, GOLD is provided as database dumps, and an ETL process transforms this into JSON. In the future, we would like to move towards a situation where all information is provided as JSON.

"},{"location":"schema_element_deprecation_guide/","title":"Deprecating NMDC schema elements","text":"

By deprecating, rather than deleting, schema elements in the NMDC model, we ensure backward compatibility, extend user trust, and provide a valuable historical record, aiding in the understanding of the model's evolution. Therefore, 'deleting' a schema element in NMDC is instead, a two-step (and two-release) deprecation process.

"},{"location":"schema_element_deprecation_guide/#first-release-cycle","title":"First release cycle:","text":" Annotation Value One of: deprecated_element_has_exact_replacement OR deprecated_element_has_possible_replacement * uriorcurie value required deprecated A string explaining the reason for deprecation along with a link to the corresponding issue. last_updated_on modified_by With an ORCID value Deprecation Date Conforms to iso8601/international dates (e.g., # doi_awards deprecated on 2023-11-12 in a class's usage).

* note: If a replacement is not warranted, then using only the deprecated metadata tag with an explanation string and issue link is fine.

"},{"location":"schema_element_deprecation_guide/#second-release-cycle","title":"Second release cycle:","text":"

** note: For a deprecated class, references could be in the is_a or mixin elements of another class, or in the domain or range elements of an existing slot. For deprecated slots, check all classes that reference that slot, etc.

"},{"location":"schema_element_deprecation_guide/#todo-section-on-updating-the-portal-schema-in-the-context-of-deprecation","title":"TODO - section on updating the portal schema in the context of deprecation","text":""},{"location":"season/","title":"Slot: season (season)","text":"

The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).

URI: MIXS:0000829

"},{"location":"season/#inheritance","title":"Inheritance","text":""},{"location":"season/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"season/#properties","title":"Properties","text":""},{"location":"season/#aliases","title":"Aliases","text":""},{"location":"season/#examples","title":"Examples","text":"Value autumn [NCIT:C94733]"},{"location":"season/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season/#annotations","title":"Annotations","text":"property value expected_value NCIT:C94729"},{"location":"season/#schema-source","title":"Schema Source","text":""},{"location":"season/#linkml-source","title":"LinkML Source","text":"
name: season\nannotations:\n  expected_value:\n    tag: expected_value\n    value: NCIT:C94729\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The season when sampling occurred. Any of the four periods into which\n  the year is divided by the equinoxes and solstices. This field accepts terms listed\n  under season (http://purl.obolibrary.org/obo/NCIT_C94729).\ntitle: season\nexamples:\n- value: autumn [NCIT:C94733]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- season\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000829\nalias: season\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"season_environment/","title":"Slot: seasonal environment (season_environment)","text":"

Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment

URI: MIXS:0001068

"},{"location":"season_environment/#inheritance","title":"Inheritance","text":""},{"location":"season_environment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"season_environment/#properties","title":"Properties","text":""},{"location":"season_environment/#aliases","title":"Aliases","text":""},{"location":"season_environment/#examples","title":"Examples","text":"Value rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"season_environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season_environment/#annotations","title":"Annotations","text":"property value expected_value seasonal environment name;treatment interval and duration"},{"location":"season_environment/#schema-source","title":"Schema Source","text":""},{"location":"season_environment/#linkml-source","title":"LinkML Source","text":"
name: season_environment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: seasonal environment name;treatment interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Treatment involving an exposure to a particular season (e.g. Winter,\n  summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment\ntitle: seasonal environment\nexamples:\n- value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001068\nalias: season_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"season_precpt/","title":"Slot: mean seasonal precipitation (season_precpt)","text":"

The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.

URI: MIXS:0000645

"},{"location":"season_precpt/#inheritance","title":"Inheritance","text":""},{"location":"season_precpt/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"season_precpt/#properties","title":"Properties","text":""},{"location":"season_precpt/#aliases","title":"Aliases","text":""},{"location":"season_precpt/#examples","title":"Examples","text":"Value"},{"location":"season_precpt/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season_precpt/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"season_precpt/#schema-source","title":"Schema Source","text":""},{"location":"season_precpt/#linkml-source","title":"LinkML Source","text":"
name: season_precpt\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: millimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average of all seasonal precipitation values known, or an estimated\n  equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean seasonal precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000645\nalias: season_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"season_temp/","title":"Slot: mean seasonal temperature (season_temp)","text":"

Mean seasonal temperature

URI: MIXS:0000643

"},{"location":"season_temp/#inheritance","title":"Inheritance","text":""},{"location":"season_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"season_temp/#properties","title":"Properties","text":""},{"location":"season_temp/#aliases","title":"Aliases","text":""},{"location":"season_temp/#examples","title":"Examples","text":"Value 18 degree Celsius"},{"location":"season_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"season_temp/#schema-source","title":"Schema Source","text":""},{"location":"season_temp/#linkml-source","title":"LinkML Source","text":"
name: season_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Mean seasonal temperature\ntitle: mean seasonal temperature\nexamples:\n- value: 18 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000643\nalias: season_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"season_use/","title":"Slot: seasonal use (season_use)","text":"

The seasons the space is occupied

URI: MIXS:0000830

"},{"location":"season_use/#inheritance","title":"Inheritance","text":""},{"location":"season_use/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"season_use/#properties","title":"Properties","text":""},{"location":"season_use/#aliases","title":"Aliases","text":""},{"location":"season_use/#examples","title":"Examples","text":"Value Winter"},{"location":"season_use/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"season_use/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"season_use/#schema-source","title":"Schema Source","text":""},{"location":"season_use/#linkml-source","title":"LinkML Source","text":"
name: season_use\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The seasons the space is occupied\ntitle: seasonal use\nexamples:\n- value: Winter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000830\nalias: season_use\ndomain_of:\n- Biosample\nrange: season_use_enum\nmultivalued: false\n\n
"},{"location":"secondary_treatment/","title":"Slot: secondary treatment (secondary_treatment)","text":"

The process for substantially degrading the biological content of the sewage

URI: MIXS:0000351

"},{"location":"secondary_treatment/#inheritance","title":"Inheritance","text":""},{"location":"secondary_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"secondary_treatment/#properties","title":"Properties","text":""},{"location":"secondary_treatment/#aliases","title":"Aliases","text":""},{"location":"secondary_treatment/#examples","title":"Examples","text":"Value"},{"location":"secondary_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"secondary_treatment/#annotations","title":"Annotations","text":"property value expected_value secondary treatment type"},{"location":"secondary_treatment/#schema-source","title":"Schema Source","text":""},{"location":"secondary_treatment/#linkml-source","title":"LinkML Source","text":"
name: secondary_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: secondary treatment type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The process for substantially degrading the biological content of the\n  sewage\ntitle: secondary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000351\nalias: secondary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"sediment_type/","title":"Slot: sediment type (sediment_type)","text":"

Information about the sediment type based on major constituents

URI: MIXS:0001078

"},{"location":"sediment_type/#inheritance","title":"Inheritance","text":""},{"location":"sediment_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sediment_type/#properties","title":"Properties","text":""},{"location":"sediment_type/#aliases","title":"Aliases","text":""},{"location":"sediment_type/#examples","title":"Examples","text":"Value biogenous"},{"location":"sediment_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sediment_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sediment_type/#schema-source","title":"Schema Source","text":""},{"location":"sediment_type/#linkml-source","title":"LinkML Source","text":"
name: sediment_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Information about the sediment type based on major constituents\ntitle: sediment type\nexamples:\n- value: biogenous\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sediment type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001078\nalias: sediment_type\ndomain_of:\n- Biosample\nrange: sediment_type_enum\nmultivalued: false\n\n
"},{"location":"separation_method/","title":"Slot: separation_method","text":"

The method that was used to separate a substance from a solution or mixture.

URI: nmdc:separation_method

"},{"location":"separation_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"separation_method/#properties","title":"Properties","text":""},{"location":"separation_method/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"separation_method/#schema-source","title":"Schema Source","text":""},{"location":"separation_method/#linkml-source","title":"LinkML Source","text":"
name: separation_method\ndescription: The method that was used to separate a substance from a solution or mixture.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: separation_method\ndomain_of:\n- FiltrationProcess\nrange: SeparationMethodEnum\n\n
"},{"location":"seq_meth/","title":"Slot: sequencing method (seq_meth)","text":"

Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).

URI: MIXS:0000050

"},{"location":"seq_meth/#inheritance","title":"Inheritance","text":""},{"location":"seq_meth/#properties","title":"Properties","text":""},{"location":"seq_meth/#aliases","title":"Aliases","text":""},{"location":"seq_meth/#examples","title":"Examples","text":"Value 454 Genome Sequencer FLX [OBI:0000702]"},{"location":"seq_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"seq_meth/#annotations","title":"Annotations","text":"property value expected_value Text or OBI"},{"location":"seq_meth/#schema-source","title":"Schema Source","text":""},{"location":"seq_meth/#linkml-source","title":"LinkML Source","text":"
name: seq_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: Text or OBI\ndescription: Sequencing machine used. Where possible the term should be taken from\n  the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\ntitle: sequencing method\nexamples:\n- value: 454 Genome Sequencer FLX [OBI:0000702]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequencing method\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000050\nalias: seq_meth\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"seq_quality_check/","title":"Slot: sequence quality check (seq_quality_check)","text":"

Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA

URI: MIXS:0000051

"},{"location":"seq_quality_check/#inheritance","title":"Inheritance","text":""},{"location":"seq_quality_check/#properties","title":"Properties","text":""},{"location":"seq_quality_check/#aliases","title":"Aliases","text":""},{"location":"seq_quality_check/#examples","title":"Examples","text":"Value none"},{"location":"seq_quality_check/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"seq_quality_check/#annotations","title":"Annotations","text":"property value expected_value none or manually edited"},{"location":"seq_quality_check/#schema-source","title":"Schema Source","text":""},{"location":"seq_quality_check/#linkml-source","title":"LinkML Source","text":"
name: seq_quality_check\nannotations:\n  expected_value:\n    tag: expected_value\n    value: none or manually edited\ndescription: Indicate if the sequence has been called by automatic systems (none)\n  or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms).\n  Applied only for sequences that are not submitted to SRA,ENA or DRA\ntitle: sequence quality check\nexamples:\n- value: none\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequence quality check\nrank: 1000\nis_a: sequencing field\nstring_serialization: '[none|manually edited]'\nslot_uri: MIXS:0000051\nalias: seq_quality_check\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"seqid/","title":"Slot: seqid","text":"

The ID of the landmark used to establish the coordinate system for the current feature.

URI: nmdc:seqid

"},{"location":"seqid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"seqid/#properties","title":"Properties","text":""},{"location":"seqid/#todos","title":"TODOs","text":""},{"location":"seqid/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"seqid/#schema-source","title":"Schema Source","text":""},{"location":"seqid/#linkml-source","title":"LinkML Source","text":"
name: seqid\ndescription: The ID of the landmark used to establish the coordinate system for the\n  current feature.\ntodos:\n- change range from string to object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: seqid\ndomain_of:\n- GenomeFeature\nrange: string\n\n
"},{"location":"sequencing_field/","title":"Slot: sequencing_field","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:sequencing_field

"},{"location":"sequencing_field/#inheritance","title":"Inheritance","text":""},{"location":"sequencing_field/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sequencing_field/#properties","title":"Properties","text":""},{"location":"sequencing_field/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sequencing_field/#schema-source","title":"Schema Source","text":""},{"location":"sequencing_field/#linkml-source","title":"LinkML Source","text":"
name: sequencing field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: sequencing_field\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"sewage_type/","title":"Slot: sewage type (sewage_type)","text":"

Type of wastewater treatment plant as municipial or industrial

URI: MIXS:0000215

"},{"location":"sewage_type/#inheritance","title":"Inheritance","text":""},{"location":"sewage_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sewage_type/#properties","title":"Properties","text":""},{"location":"sewage_type/#aliases","title":"Aliases","text":""},{"location":"sewage_type/#examples","title":"Examples","text":"Value"},{"location":"sewage_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sewage_type/#annotations","title":"Annotations","text":"property value expected_value sewage type name"},{"location":"sewage_type/#schema-source","title":"Schema Source","text":""},{"location":"sewage_type/#linkml-source","title":"LinkML Source","text":"
name: sewage_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: sewage type name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Type of wastewater treatment plant as municipial or industrial\ntitle: sewage type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sewage type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000215\nalias: sewage_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"shad_dev_water_mold/","title":"Slot: shading device signs of water/mold (shad_dev_water_mold)","text":"

Signs of the presence of mold or mildew on the shading device

URI: MIXS:0000834

"},{"location":"shad_dev_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"shad_dev_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shad_dev_water_mold/#properties","title":"Properties","text":""},{"location":"shad_dev_water_mold/#aliases","title":"Aliases","text":""},{"location":"shad_dev_water_mold/#examples","title":"Examples","text":"Value no presence of mold visible"},{"location":"shad_dev_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shad_dev_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"shad_dev_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"shad_dev_water_mold/#linkml-source","title":"LinkML Source","text":"
name: shad_dev_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on the shading device\ntitle: shading device signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000834\nalias: shad_dev_water_mold\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"shading_device_cond/","title":"Slot: shading device condition (shading_device_cond)","text":"

The physical condition of the shading device at the time of sampling

URI: MIXS:0000831

"},{"location":"shading_device_cond/#inheritance","title":"Inheritance","text":""},{"location":"shading_device_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shading_device_cond/#properties","title":"Properties","text":""},{"location":"shading_device_cond/#aliases","title":"Aliases","text":""},{"location":"shading_device_cond/#examples","title":"Examples","text":"Value new"},{"location":"shading_device_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shading_device_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"shading_device_cond/#schema-source","title":"Schema Source","text":""},{"location":"shading_device_cond/#linkml-source","title":"LinkML Source","text":"
name: shading_device_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the shading device at the time of sampling\ntitle: shading device condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000831\nalias: shading_device_cond\ndomain_of:\n- Biosample\nrange: shading_device_cond_enum\nmultivalued: false\n\n
"},{"location":"shading_device_loc/","title":"Slot: shading device location (shading_device_loc)","text":"

The location of the shading device in relation to the built structure

URI: MIXS:0000832

"},{"location":"shading_device_loc/#inheritance","title":"Inheritance","text":""},{"location":"shading_device_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shading_device_loc/#properties","title":"Properties","text":""},{"location":"shading_device_loc/#aliases","title":"Aliases","text":""},{"location":"shading_device_loc/#examples","title":"Examples","text":"Value exterior"},{"location":"shading_device_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shading_device_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"shading_device_loc/#schema-source","title":"Schema Source","text":""},{"location":"shading_device_loc/#linkml-source","title":"LinkML Source","text":"
name: shading_device_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The location of the shading device in relation to the built structure\ntitle: shading device location\nexamples:\n- value: exterior\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device location\nrank: 1000\nis_a: core field\nstring_serialization: '[exterior|interior]'\nslot_uri: MIXS:0000832\nalias: shading_device_loc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"shading_device_mat/","title":"Slot: shading device material (shading_device_mat)","text":"

The material the shading device is composed of

URI: MIXS:0000245

"},{"location":"shading_device_mat/#inheritance","title":"Inheritance","text":""},{"location":"shading_device_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shading_device_mat/#properties","title":"Properties","text":""},{"location":"shading_device_mat/#aliases","title":"Aliases","text":""},{"location":"shading_device_mat/#examples","title":"Examples","text":"Value"},{"location":"shading_device_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shading_device_mat/#annotations","title":"Annotations","text":"property value expected_value material name"},{"location":"shading_device_mat/#schema-source","title":"Schema Source","text":""},{"location":"shading_device_mat/#linkml-source","title":"LinkML Source","text":"
name: shading_device_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: material name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The material the shading device is composed of\ntitle: shading device material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device material\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000245\nalias: shading_device_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"shading_device_type/","title":"Slot: shading device type (shading_device_type)","text":"

The type of shading device

URI: MIXS:0000835

"},{"location":"shading_device_type/#inheritance","title":"Inheritance","text":""},{"location":"shading_device_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"shading_device_type/#properties","title":"Properties","text":""},{"location":"shading_device_type/#aliases","title":"Aliases","text":""},{"location":"shading_device_type/#examples","title":"Examples","text":"Value slatted aluminum awning"},{"location":"shading_device_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"shading_device_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"shading_device_type/#schema-source","title":"Schema Source","text":""},{"location":"shading_device_type/#linkml-source","title":"LinkML Source","text":"
name: shading_device_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of shading device\ntitle: shading device type\nexamples:\n- value: slatted aluminum awning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000835\nalias: shading_device_type\ndomain_of:\n- Biosample\nrange: shading_device_type_enum\nmultivalued: false\n\n
"},{"location":"sieving/","title":"Slot: composite design/sieving (sieving)","text":"

Collection design of pooled samples and/or sieve size and amount of sample sieved

URI: MIXS:0000322

"},{"location":"sieving/#inheritance","title":"Inheritance","text":""},{"location":"sieving/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"sieving/#properties","title":"Properties","text":""},{"location":"sieving/#aliases","title":"Aliases","text":""},{"location":"sieving/#examples","title":"Examples","text":"Value"},{"location":"sieving/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sieving/#annotations","title":"Annotations","text":"property value expected_value design name and/or size;amount"},{"location":"sieving/#schema-source","title":"Schema Source","text":""},{"location":"sieving/#linkml-source","title":"LinkML Source","text":"
name: sieving\nannotations:\n  expected_value:\n    tag: expected_value\n    value: design name and/or size;amount\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Collection design of pooled samples and/or sieve size and amount of sample\n  sieved\ntitle: composite design/sieving\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- composite design/sieving\nrank: 1000\nis_a: core field\nstring_serialization: '{{text}|{float} {unit}};{float} {unit}'\nslot_uri: MIXS:0000322\nalias: sieving\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"silicate/","title":"Slot: silicate (silicate)","text":"

Concentration of silicate

URI: MIXS:0000184

"},{"location":"silicate/#inheritance","title":"Inheritance","text":""},{"location":"silicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"silicate/#properties","title":"Properties","text":""},{"location":"silicate/#aliases","title":"Aliases","text":""},{"location":"silicate/#examples","title":"Examples","text":"Value 0.05 micromole per liter"},{"location":"silicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"silicate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"silicate/#schema-source","title":"Schema Source","text":""},{"location":"silicate/#linkml-source","title":"LinkML Source","text":"
name: silicate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of silicate\ntitle: silicate\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- silicate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000184\nalias: silicate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"size_frac/","title":"Slot: size fraction selected (size_frac)","text":"

Filtering pore size used in sample preparation

URI: MIXS:0000017

"},{"location":"size_frac/#inheritance","title":"Inheritance","text":""},{"location":"size_frac/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"size_frac/#properties","title":"Properties","text":""},{"location":"size_frac/#aliases","title":"Aliases","text":""},{"location":"size_frac/#examples","title":"Examples","text":"Value 0-0.22 micrometer"},{"location":"size_frac/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"size_frac/#annotations","title":"Annotations","text":"property value expected_value filter size value range"},{"location":"size_frac/#schema-source","title":"Schema Source","text":""},{"location":"size_frac/#linkml-source","title":"LinkML Source","text":"
name: size_frac\nannotations:\n  expected_value:\n    tag: expected_value\n    value: filter size value range\ndescription: Filtering pore size used in sample preparation\ntitle: size fraction selected\nexamples:\n- value: 0-0.22 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size fraction selected\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000017\nalias: size_frac\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"size_frac_low/","title":"Slot: size-fraction lower threshold (size_frac_low)","text":"

Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample

URI: MIXS:0000735

"},{"location":"size_frac_low/#inheritance","title":"Inheritance","text":""},{"location":"size_frac_low/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"size_frac_low/#properties","title":"Properties","text":""},{"location":"size_frac_low/#aliases","title":"Aliases","text":""},{"location":"size_frac_low/#examples","title":"Examples","text":"Value 0.2 micrometer"},{"location":"size_frac_low/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"size_frac_low/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"size_frac_low/#schema-source","title":"Schema Source","text":""},{"location":"size_frac_low/#linkml-source","title":"LinkML Source","text":"
name: size_frac_low\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: micrometer\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n  Materials larger than the size threshold are excluded from the sample\ntitle: size-fraction lower threshold\nexamples:\n- value: 0.2 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction lower threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000735\nalias: size_frac_low\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"size_frac_up/","title":"Slot: size-fraction upper threshold (size_frac_up)","text":"

Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample

URI: MIXS:0000736

"},{"location":"size_frac_up/#inheritance","title":"Inheritance","text":""},{"location":"size_frac_up/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"size_frac_up/#properties","title":"Properties","text":""},{"location":"size_frac_up/#aliases","title":"Aliases","text":""},{"location":"size_frac_up/#examples","title":"Examples","text":"Value 20 micrometer"},{"location":"size_frac_up/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"size_frac_up/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"size_frac_up/#schema-source","title":"Schema Source","text":""},{"location":"size_frac_up/#linkml-source","title":"LinkML Source","text":"
name: size_frac_up\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: micrometer\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Refers to the mesh/pore size used to retain the sample. Materials smaller\n  than the size threshold are excluded from the sample\ntitle: size-fraction upper threshold\nexamples:\n- value: 20 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction upper threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000736\nalias: size_frac_up\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"slope_aspect/","title":"Slot: slope aspect (slope_aspect)","text":"

The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.

URI: MIXS:0000647

"},{"location":"slope_aspect/#inheritance","title":"Inheritance","text":""},{"location":"slope_aspect/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"slope_aspect/#properties","title":"Properties","text":""},{"location":"slope_aspect/#aliases","title":"Aliases","text":""},{"location":"slope_aspect/#examples","title":"Examples","text":"Value"},{"location":"slope_aspect/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"slope_aspect/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"slope_aspect/#schema-source","title":"Schema Source","text":""},{"location":"slope_aspect/#linkml-source","title":"LinkML Source","text":"
name: slope_aspect\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The direction a slope faces. While looking down a slope use a compass\n  to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees.\n  This measure provides an indication of sun and wind exposure that will influence\n  soil temperature and evapotranspiration.\ntitle: slope aspect\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope aspect\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000647\nalias: slope_aspect\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"slope_gradient/","title":"Slot: slope gradient (slope_gradient)","text":"

Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer

URI: MIXS:0000646

"},{"location":"slope_gradient/#inheritance","title":"Inheritance","text":""},{"location":"slope_gradient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"slope_gradient/#properties","title":"Properties","text":""},{"location":"slope_gradient/#aliases","title":"Aliases","text":""},{"location":"slope_gradient/#examples","title":"Examples","text":"Value"},{"location":"slope_gradient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"slope_gradient/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"slope_gradient/#schema-source","title":"Schema Source","text":""},{"location":"slope_gradient/#linkml-source","title":"LinkML Source","text":"
name: slope_gradient\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Commonly called 'slope'. The angle between ground surface and a horizontal\n  line (in percent). This is the direction that overland water would flow. This measure\n  is usually taken with a hand level meter or clinometer\ntitle: slope gradient\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope gradient\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000646\nalias: slope_gradient\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"sludge_retent_time/","title":"Slot: sludge retention time (sludge_retent_time)","text":"

The time activated sludge remains in reactor

URI: MIXS:0000669

"},{"location":"sludge_retent_time/#inheritance","title":"Inheritance","text":""},{"location":"sludge_retent_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sludge_retent_time/#properties","title":"Properties","text":""},{"location":"sludge_retent_time/#aliases","title":"Aliases","text":""},{"location":"sludge_retent_time/#examples","title":"Examples","text":"Value"},{"location":"sludge_retent_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sludge_retent_time/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sludge_retent_time/#schema-source","title":"Schema Source","text":""},{"location":"sludge_retent_time/#linkml-source","title":"LinkML Source","text":"
name: sludge_retent_time\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: hours\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The time activated sludge remains in reactor\ntitle: sludge retention time\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sludge retention time\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000669\nalias: sludge_retent_time\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"smiles/","title":"Slot: smiles","text":"

A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.

URI: nmdc:smiles

"},{"location":"smiles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"smiles/#properties","title":"Properties","text":""},{"location":"smiles/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"smiles/#schema-source","title":"Schema Source","text":""},{"location":"smiles/#linkml-source","title":"LinkML Source","text":"
name: smiles\ndescription: A string encoding of a molecular graph, no chiral or isotopic information.\n  There are usually a large number of valid SMILES which represent a given structure.\n  For example, CCO, OCC and C(O)C all specify the structure of ethanol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: smiles\ndomain_of:\n- ChemicalEntity\nrange: string\nmultivalued: true\n\n
"},{"location":"sodium/","title":"Slot: sodium (sodium)","text":"

Sodium concentration in the sample

URI: MIXS:0000428

"},{"location":"sodium/#inheritance","title":"Inheritance","text":""},{"location":"sodium/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sodium/#properties","title":"Properties","text":""},{"location":"sodium/#aliases","title":"Aliases","text":""},{"location":"sodium/#examples","title":"Examples","text":"Value 10.5 milligram per liter"},{"location":"sodium/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sodium/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sodium/#schema-source","title":"Schema Source","text":""},{"location":"sodium/#linkml-source","title":"LinkML Source","text":"
name: sodium\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Sodium concentration in the sample\ntitle: sodium\nexamples:\n- value: 10.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sodium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000428\nalias: sodium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"soil_annual_season_temp/","title":"Slot: soil_annual_season_temp","text":"

URI: nmdc:soil_annual_season_temp

"},{"location":"soil_annual_season_temp/#properties","title":"Properties","text":""},{"location":"soil_annual_season_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_annual_season_temp/#schema-source","title":"Schema Source","text":""},{"location":"soil_annual_season_temp/#linkml-source","title":"LinkML Source","text":"
name: soil_annual_season_temp\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soil_annual_season_temp\nrange: string\n\n
"},{"location":"soil_horizon/","title":"Slot: soil horizon (soil_horizon)","text":"

Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath

URI: MIXS:0001082

"},{"location":"soil_horizon/#inheritance","title":"Inheritance","text":""},{"location":"soil_horizon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soil_horizon/#properties","title":"Properties","text":""},{"location":"soil_horizon/#aliases","title":"Aliases","text":""},{"location":"soil_horizon/#examples","title":"Examples","text":"Value A horizon"},{"location":"soil_horizon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_horizon/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"soil_horizon/#schema-source","title":"Schema Source","text":""},{"location":"soil_horizon/#linkml-source","title":"LinkML Source","text":"
name: soil_horizon\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Specific layer in the land area which measures parallel to the soil surface\n  and possesses physical characteristics which differ from the layers above and beneath\ntitle: soil horizon\nexamples:\n- value: A horizon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001082\nalias: soil_horizon\ndomain_of:\n- Biosample\nrange: soil_horizon_enum\nmultivalued: false\n\n
"},{"location":"soil_text_measure/","title":"Slot: soil texture measurement (soil_text_measure)","text":"

The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.

URI: MIXS:0000335

"},{"location":"soil_text_measure/#inheritance","title":"Inheritance","text":""},{"location":"soil_text_measure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soil_text_measure/#properties","title":"Properties","text":""},{"location":"soil_text_measure/#aliases","title":"Aliases","text":""},{"location":"soil_text_measure/#examples","title":"Examples","text":"Value"},{"location":"soil_text_measure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_text_measure/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"soil_text_measure/#schema-source","title":"Schema Source","text":""},{"location":"soil_text_measure/#linkml-source","title":"LinkML Source","text":"
name: soil_text_measure\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The relative proportion of different grain sizes of mineral particles\n  in a soil, as described using a standard system; express as % sand (50 um to 2 mm),\n  silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam)\n  optional.\ntitle: soil texture measurement\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture measurement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000335\nalias: soil_text_measure\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"soil_texture_meth/","title":"Slot: soil texture method (soil_texture_meth)","text":"

Reference or method used in determining soil texture

URI: MIXS:0000336

"},{"location":"soil_texture_meth/#inheritance","title":"Inheritance","text":""},{"location":"soil_texture_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soil_texture_meth/#properties","title":"Properties","text":""},{"location":"soil_texture_meth/#aliases","title":"Aliases","text":""},{"location":"soil_texture_meth/#examples","title":"Examples","text":"Value"},{"location":"soil_texture_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_texture_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"soil_texture_meth/#schema-source","title":"Schema Source","text":""},{"location":"soil_texture_meth/#linkml-source","title":"LinkML Source","text":"
name: soil_texture_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining soil texture\ntitle: soil texture method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000336\nalias: soil_texture_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"soil_type/","title":"Slot: soil type (soil_type)","text":"

Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.

URI: MIXS:0000332

"},{"location":"soil_type/#inheritance","title":"Inheritance","text":""},{"location":"soil_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no"},{"location":"soil_type/#properties","title":"Properties","text":""},{"location":"soil_type/#aliases","title":"Aliases","text":""},{"location":"soil_type/#examples","title":"Examples","text":"Value plinthosol [ENVO:00002250]"},{"location":"soil_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_type/#annotations","title":"Annotations","text":"property value expected_value ENVO_00001998"},{"location":"soil_type/#schema-source","title":"Schema Source","text":""},{"location":"soil_type/#linkml-source","title":"LinkML Source","text":"
name: soil_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: ENVO_00001998\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Description of the soil type or classification. This field accepts terms\n  under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms can be\n  separated by pipes.\ntitle: soil type\nexamples:\n- value: plinthosol [ENVO:00002250]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000332\nalias: soil_type\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"soil_type_meth/","title":"Slot: soil type method (soil_type_meth)","text":"

Reference or method used in determining soil series name or other lower-level classification

URI: MIXS:0000334

"},{"location":"soil_type_meth/#inheritance","title":"Inheritance","text":""},{"location":"soil_type_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soil_type_meth/#properties","title":"Properties","text":""},{"location":"soil_type_meth/#aliases","title":"Aliases","text":""},{"location":"soil_type_meth/#examples","title":"Examples","text":"Value"},{"location":"soil_type_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soil_type_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"soil_type_meth/#schema-source","title":"Schema Source","text":""},{"location":"soil_type_meth/#linkml-source","title":"LinkML Source","text":"
name: soil_type_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining soil series name or other lower-level\n  classification\ntitle: soil type method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000334\nalias: soil_type_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"solar_irradiance/","title":"Slot: solar irradiance (solar_irradiance)","text":"

The amount of solar energy that arrives at a specific area of a surface during a specific time interval

URI: MIXS:0000112

"},{"location":"solar_irradiance/#inheritance","title":"Inheritance","text":""},{"location":"solar_irradiance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"solar_irradiance/#properties","title":"Properties","text":""},{"location":"solar_irradiance/#aliases","title":"Aliases","text":""},{"location":"solar_irradiance/#examples","title":"Examples","text":"Value 1.36 kilowatts per square meter per day"},{"location":"solar_irradiance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"solar_irradiance/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"solar_irradiance/#schema-source","title":"Schema Source","text":""},{"location":"solar_irradiance/#linkml-source","title":"LinkML Source","text":"
name: solar_irradiance\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: kilowatts per square meter per day, ergs per square centimeter per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The amount of solar energy that arrives at a specific area of a surface\n  during a specific time interval\ntitle: solar irradiance\nexamples:\n- value: 1.36 kilowatts per square meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- solar irradiance\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000112\nalias: solar_irradiance\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"soluble_inorg_mat/","title":"Slot: soluble inorganic material (soluble_inorg_mat)","text":"

Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.

URI: MIXS:0000672

"},{"location":"soluble_inorg_mat/#inheritance","title":"Inheritance","text":""},{"location":"soluble_inorg_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_inorg_mat/#properties","title":"Properties","text":""},{"location":"soluble_inorg_mat/#aliases","title":"Aliases","text":""},{"location":"soluble_inorg_mat/#examples","title":"Examples","text":"Value"},{"location":"soluble_inorg_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soluble_inorg_mat/#annotations","title":"Annotations","text":"property value expected_value soluble inorganic material name;measurement value"},{"location":"soluble_inorg_mat/#schema-source","title":"Schema Source","text":""},{"location":"soluble_inorg_mat/#linkml-source","title":"LinkML Source","text":"
name: soluble_inorg_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: soluble inorganic material name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, microgram, mole per liter, gram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide,\n  hydrogen sulfide, thiocyanates, thiosulfates, etc.\ntitle: soluble inorganic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble inorganic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000672\nalias: soluble_inorg_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"soluble_iron_micromol/","title":"Slot: soluble_iron_micromol","text":"

URI: nmdc:soluble_iron_micromol

"},{"location":"soluble_iron_micromol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_iron_micromol/#properties","title":"Properties","text":""},{"location":"soluble_iron_micromol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soluble_iron_micromol/#schema-source","title":"Schema Source","text":""},{"location":"soluble_iron_micromol/#linkml-source","title":"LinkML Source","text":"
name: soluble_iron_micromol\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soluble_iron_micromol\ndomain_of:\n- Biosample\nrange: string\n\n
"},{"location":"soluble_org_mat/","title":"Slot: soluble organic material (soluble_org_mat)","text":"

Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.

URI: MIXS:0000673

"},{"location":"soluble_org_mat/#inheritance","title":"Inheritance","text":""},{"location":"soluble_org_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_org_mat/#properties","title":"Properties","text":""},{"location":"soluble_org_mat/#aliases","title":"Aliases","text":""},{"location":"soluble_org_mat/#examples","title":"Examples","text":"Value"},{"location":"soluble_org_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soluble_org_mat/#annotations","title":"Annotations","text":"property value expected_value soluble organic material name;measurement value"},{"location":"soluble_org_mat/#schema-source","title":"Schema Source","text":""},{"location":"soluble_org_mat/#linkml-source","title":"LinkML Source","text":"
name: soluble_org_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: soluble organic material name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, microgram, mole per liter, gram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of substances such as urea, fruit sugars, soluble proteins,\n  drugs, pharmaceuticals, etc.\ntitle: soluble organic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble organic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000673\nalias: soluble_org_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"soluble_react_phosp/","title":"Slot: soluble reactive phosphorus (soluble_react_phosp)","text":"

Concentration of soluble reactive phosphorus

URI: MIXS:0000738

"},{"location":"soluble_react_phosp/#inheritance","title":"Inheritance","text":""},{"location":"soluble_react_phosp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_react_phosp/#properties","title":"Properties","text":""},{"location":"soluble_react_phosp/#aliases","title":"Aliases","text":""},{"location":"soluble_react_phosp/#examples","title":"Examples","text":"Value 0.1 milligram per liter"},{"location":"soluble_react_phosp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"soluble_react_phosp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"soluble_react_phosp/#schema-source","title":"Schema Source","text":""},{"location":"soluble_react_phosp/#linkml-source","title":"LinkML Source","text":"
name: soluble_react_phosp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of soluble reactive phosphorus\ntitle: soluble reactive phosphorus\nexamples:\n- value: 0.1 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble reactive phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000738\nalias: soluble_react_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"source_concentration/","title":"Slot: source_concentration","text":"

When solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in solution A

URI: nmdc:source_concentration

"},{"location":"source_concentration/#inheritance","title":"Inheritance","text":""},{"location":"source_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"source_concentration/#properties","title":"Properties","text":""},{"location":"source_concentration/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"source_concentration/#schema-source","title":"Schema Source","text":""},{"location":"source_concentration/#linkml-source","title":"LinkML Source","text":"
name: source_concentration\ndescription: When solutions A (containing substance X) and B are combined together,\n  this slot captures the concentration of X in solution A\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: concentration\nalias: source_concentration\ndomain_of:\n- PortionOfSubstance\nrange: QuantityValue\n\n
"},{"location":"source_mat_id/","title":"Slot: source material identifiers (source_mat_id)","text":"

A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).

URI: MIXS:0000026

"},{"location":"source_mat_id/#inheritance","title":"Inheritance","text":""},{"location":"source_mat_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"source_mat_id/#properties","title":"Properties","text":""},{"location":"source_mat_id/#aliases","title":"Aliases","text":""},{"location":"source_mat_id/#examples","title":"Examples","text":"Value MPI012345"},{"location":"source_mat_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"source_mat_id/#annotations","title":"Annotations","text":"property value expected_value for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer"},{"location":"source_mat_id/#schema-source","title":"Schema Source","text":""},{"location":"source_mat_id/#linkml-source","title":"LinkML Source","text":"
name: source_mat_id\nannotations:\n  expected_value:\n    tag: expected_value\n    value: 'for cultures of microorganisms: identifiers for two culture collections;\n      for other material a unique arbitrary identifer'\ndescription: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID,\n  and as opposed to a particular digital record of a material sample) used for extracting\n  nucleic acids, and subsequent sequencing. The identifier can refer either to the\n  original material collected or to any derived sub-samples. The INSDC qualifiers\n  /specimen_voucher, /bio_material, or /culture_collection may or may not share the\n  same value as the source_mat_id field. For instance, the /specimen_voucher qualifier\n  and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen\n  voucher and sampled tissue with the same identifier. However, the /culture_collection\n  qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id\n  would refer to an identifier from some derived culture from which the nucleic acids\n  were extracted (e.g. xatc123 or ark:/2154/R2).\ntitle: source material identifiers\nexamples:\n- value: MPI012345\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source material identifiers\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000026\nalias: source_mat_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"space_typ_state/","title":"Slot: space typical state (space_typ_state)","text":"

Customary or normal state of the space

URI: MIXS:0000770

"},{"location":"space_typ_state/#inheritance","title":"Inheritance","text":""},{"location":"space_typ_state/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"space_typ_state/#properties","title":"Properties","text":""},{"location":"space_typ_state/#aliases","title":"Aliases","text":""},{"location":"space_typ_state/#examples","title":"Examples","text":"Value typically occupied"},{"location":"space_typ_state/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"space_typ_state/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"space_typ_state/#schema-source","title":"Schema Source","text":""},{"location":"space_typ_state/#linkml-source","title":"LinkML Source","text":"
name: space_typ_state\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Customary or normal state of the space\ntitle: space typical state\nexamples:\n- value: typically occupied\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- space typical state\nrank: 1000\nis_a: core field\nstring_serialization: '[typically occupied|typically unoccupied]'\nslot_uri: MIXS:0000770\nalias: space_typ_state\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"specific/","title":"Slot: specifications (specific)","text":"

The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents

URI: MIXS:0000836

"},{"location":"specific/#inheritance","title":"Inheritance","text":""},{"location":"specific/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"specific/#properties","title":"Properties","text":""},{"location":"specific/#aliases","title":"Aliases","text":""},{"location":"specific/#examples","title":"Examples","text":"Value construction"},{"location":"specific/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"specific/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"specific/#schema-source","title":"Schema Source","text":""},{"location":"specific/#linkml-source","title":"LinkML Source","text":"
name: specific\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'The building specifications. If design is chosen, indicate phase: conceptual,\n  schematic, design development, construction documents'\ntitle: specifications\nexamples:\n- value: construction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specifications\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000836\nalias: specific\ndomain_of:\n- Biosample\nrange: specific_enum\nmultivalued: false\n\n
"},{"location":"specific_ecosystem/","title":"Slot: specific_ecosystem","text":"

Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.

URI: nmdc:specific_ecosystem

"},{"location":"specific_ecosystem/#inheritance","title":"Inheritance","text":""},{"location":"specific_ecosystem/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"specific_ecosystem/#properties","title":"Properties","text":""},{"location":"specific_ecosystem/#comments","title":"Comments","text":""},{"location":"specific_ecosystem/#see-also","title":"See Also","text":""},{"location":"specific_ecosystem/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"specific_ecosystem/#schema-source","title":"Schema Source","text":""},{"location":"specific_ecosystem/#linkml-source","title":"LinkML Source","text":"
name: specific_ecosystem\ndescription: Specific ecosystems represent specific features of the environment like\n  aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific\n  ecosystem is in position 5/5 in a GOLD path.\ncomments:\n- Specific ecosystems help to define samples based on very specific characteristics\n  of an environment under the five-level classification system.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: specific_ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\n
"},{"location":"specific_humidity/","title":"Slot: specific humidity (specific_humidity)","text":"

The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.

URI: MIXS:0000214

"},{"location":"specific_humidity/#inheritance","title":"Inheritance","text":""},{"location":"specific_humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"specific_humidity/#properties","title":"Properties","text":""},{"location":"specific_humidity/#aliases","title":"Aliases","text":""},{"location":"specific_humidity/#examples","title":"Examples","text":"Value 15 per kilogram of air"},{"location":"specific_humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"specific_humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"specific_humidity/#schema-source","title":"Schema Source","text":""},{"location":"specific_humidity/#linkml-source","title":"LinkML Source","text":"
name: specific_humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram of air, kilogram of air\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The mass of water vapour in a unit mass of moist air, usually expressed\n  as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.\ntitle: specific humidity\nexamples:\n- value: 15 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specific humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000214\nalias: specific_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"sr_dep_env/","title":"Slot: source rock depositional environment (sr_dep_env)","text":"

Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000996

"},{"location":"sr_dep_env/#inheritance","title":"Inheritance","text":""},{"location":"sr_dep_env/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sr_dep_env/#properties","title":"Properties","text":""},{"location":"sr_dep_env/#aliases","title":"Aliases","text":""},{"location":"sr_dep_env/#examples","title":"Examples","text":"Value Marine"},{"location":"sr_dep_env/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sr_dep_env/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sr_dep_env/#schema-source","title":"Schema Source","text":""},{"location":"sr_dep_env/#linkml-source","title":"LinkML Source","text":"
name: sr_dep_env\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n  If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock depositional environment\nexamples:\n- value: Marine\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000996\nalias: sr_dep_env\ndomain_of:\n- Biosample\nrange: sr_dep_env_enum\nmultivalued: false\n\n
"},{"location":"sr_geol_age/","title":"Slot: source rock geological age (sr_geol_age)","text":"

Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000997

"},{"location":"sr_geol_age/#inheritance","title":"Inheritance","text":""},{"location":"sr_geol_age/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sr_geol_age/#properties","title":"Properties","text":""},{"location":"sr_geol_age/#aliases","title":"Aliases","text":""},{"location":"sr_geol_age/#examples","title":"Examples","text":"Value Silurian"},{"location":"sr_geol_age/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sr_geol_age/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sr_geol_age/#schema-source","title":"Schema Source","text":""},{"location":"sr_geol_age/#linkml-source","title":"LinkML Source","text":"
name: sr_geol_age\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n  If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: source rock geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000997\nalias: sr_geol_age\ndomain_of:\n- Biosample\nrange: sr_geol_age_enum\nmultivalued: false\n\n
"},{"location":"sr_kerog_type/","title":"Slot: source rock kerogen type (sr_kerog_type)","text":"

Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000994

"},{"location":"sr_kerog_type/#inheritance","title":"Inheritance","text":""},{"location":"sr_kerog_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sr_kerog_type/#properties","title":"Properties","text":""},{"location":"sr_kerog_type/#aliases","title":"Aliases","text":""},{"location":"sr_kerog_type/#examples","title":"Examples","text":"Value Type IV"},{"location":"sr_kerog_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sr_kerog_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sr_kerog_type/#schema-source","title":"Schema Source","text":""},{"location":"sr_kerog_type/#linkml-source","title":"LinkML Source","text":"
name: sr_kerog_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and\n  soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous\n  plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial)\n  (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified,\n  please propose entry in \"additional info\" field'\ntitle: source rock kerogen type\nexamples:\n- value: Type IV\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock kerogen type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000994\nalias: sr_kerog_type\ndomain_of:\n- Biosample\nrange: sr_kerog_type_enum\nmultivalued: false\n\n
"},{"location":"sr_lithology/","title":"Slot: source rock lithology (sr_lithology)","text":"

Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field

URI: MIXS:0000995

"},{"location":"sr_lithology/#inheritance","title":"Inheritance","text":""},{"location":"sr_lithology/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sr_lithology/#properties","title":"Properties","text":""},{"location":"sr_lithology/#aliases","title":"Aliases","text":""},{"location":"sr_lithology/#examples","title":"Examples","text":"Value Coal"},{"location":"sr_lithology/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sr_lithology/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"sr_lithology/#schema-source","title":"Schema Source","text":""},{"location":"sr_lithology/#linkml-source","title":"LinkML Source","text":"
name: sr_lithology\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n  If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock lithology\nexamples:\n- value: Coal\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000995\nalias: sr_lithology\ndomain_of:\n- Biosample\nrange: sr_lithology_enum\nmultivalued: false\n\n
"},{"location":"standing_water_regm/","title":"Slot: standing water regimen (standing_water_regm)","text":"

Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0001069

"},{"location":"standing_water_regm/#inheritance","title":"Inheritance","text":""},{"location":"standing_water_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"standing_water_regm/#properties","title":"Properties","text":""},{"location":"standing_water_regm/#aliases","title":"Aliases","text":""},{"location":"standing_water_regm/#examples","title":"Examples","text":"Value standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"standing_water_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"standing_water_regm/#annotations","title":"Annotations","text":"property value expected_value standing water type;treatment interval and duration"},{"location":"standing_water_regm/#schema-source","title":"Schema Source","text":""},{"location":"standing_water_regm/#linkml-source","title":"LinkML Source","text":"
name: standing_water_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: standing water type;treatment interval and duration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Treatment involving an exposure to standing water during a plant's life\n  span, types can be flood water or standing water, treatment regimen including how\n  many times the treatment was repeated, how long each treatment lasted, and the start\n  and end time of the entire treatment; can include multiple regimens\ntitle: standing water regimen\nexamples:\n- value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- standing water regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001069\nalias: standing_water_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"start/","title":"Slot: start","text":"

The start of the feature in positive 1-based integer coordinates

URI: nmdc:start

"},{"location":"start/#inheritance","title":"Inheritance","text":""},{"location":"start/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"start/#properties","title":"Properties","text":""},{"location":"start/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"start/#schema-source","title":"Schema Source","text":""},{"location":"start/#linkml-source","title":"LinkML Source","text":"
name: start\ndescription: The start of the feature in positive 1-based integer coordinates\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:start_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: start\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\n
"},{"location":"start_date/","title":"Slot: start_date","text":"

The date on which any process or activity was started

URI: nmdc:start_date

"},{"location":"start_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAnnotation no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetatranscriptomeAssembly no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no PlannedProcess no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FiltrationProcess The process of segregation of phases; e no MetabolomicsAnalysis no ProtocolExecution A PlannedProces that has PlannedProcess parts no LibraryPreparation no"},{"location":"start_date/#properties","title":"Properties","text":""},{"location":"start_date/#comments","title":"Comments","text":""},{"location":"start_date/#todos","title":"TODOs","text":""},{"location":"start_date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"start_date/#schema-source","title":"Schema Source","text":""},{"location":"start_date/#linkml-source","title":"LinkML Source","text":"
name: start_date\ndescription: The date on which any process or activity was started\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n  can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: start_date\ndomain_of:\n- PlannedProcess\nrange: string\n\n
"},{"location":"start_date_inc/","title":"Slot: incubation start date (start_date_inc)","text":"

Date the incubation was started. Only relevant for incubation samples.

URI: nmdc:start_date_inc

"},{"location":"start_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_date_inc/#properties","title":"Properties","text":""},{"location":"start_date_inc/#examples","title":"Examples","text":"Value 2021-04-15, 2021-04 and 2021 are all acceptable."},{"location":"start_date_inc/#comments","title":"Comments","text":""},{"location":"start_date_inc/#see-also","title":"See Also","text":""},{"location":"start_date_inc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"start_date_inc/#schema-source","title":"Schema Source","text":""},{"location":"start_date_inc/#linkml-source","title":"LinkML Source","text":"
name: start_date_inc\ndescription: Date the incubation was started. Only relevant for incubation samples.\ntitle: incubation start date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n  date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n  all acceptable.\nexamples:\n- value: 2021-04-15, 2021-04 and 2021 are all acceptable.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 4\nstring_serialization: '{date, arbitrary precision}'\nalias: start_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"start_time_inc/","title":"Slot: incubation start time, GMT (start_time_inc)","text":"

Time the incubation was started. Only relevant for incubation samples.

URI: nmdc:start_time_inc

"},{"location":"start_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_time_inc/#properties","title":"Properties","text":""},{"location":"start_time_inc/#examples","title":"Examples","text":"Value 13:33 or 13:33:55"},{"location":"start_time_inc/#comments","title":"Comments","text":""},{"location":"start_time_inc/#see-also","title":"See Also","text":""},{"location":"start_time_inc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"start_time_inc/#schema-source","title":"Schema Source","text":""},{"location":"start_time_inc/#linkml-source","title":"LinkML Source","text":"
name: start_time_inc\ndescription: Time the incubation was started. Only relevant for incubation samples.\ntitle: incubation start time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n  only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 5\nstring_serialization: '{time, seconds optional}'\nalias: start_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\n
"},{"location":"started_at_time/","title":"Slot: started_at_time","text":"

URI: nmdc:started_at_time

"},{"location":"started_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetatranscriptomeAssembly no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetabolomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetaproteomicsAnalysis no"},{"location":"started_at_time/#properties","title":"Properties","text":""},{"location":"started_at_time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"started_at_time/#schema-source","title":"Schema Source","text":""},{"location":"started_at_time/#linkml-source","title":"LinkML Source","text":"
name: started_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n  It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:startedAtTime\nrank: 1000\nalias: started_at_time\ndomain_of:\n- WorkflowExecution\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\n
"},{"location":"stationary_phase/","title":"Slot: stationary_phase","text":"

The material the stationary phase is comprised of used in chromatography.

URI: nmdc:stationary_phase

"},{"location":"stationary_phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no"},{"location":"stationary_phase/#properties","title":"Properties","text":""},{"location":"stationary_phase/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"stationary_phase/#schema-source","title":"Schema Source","text":""},{"location":"stationary_phase/#linkml-source","title":"LinkML Source","text":"
name: stationary_phase\ndescription: The material the stationary phase is comprised of used in chromatography.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stationary_phase\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: StationaryPhaseEnum\n\n
"},{"location":"storage_process_set/","title":"Slot: storage_process_set","text":"

This property links a database object to the set of storage processes within it.

URI: nmdc:storage_process_set

"},{"location":"storage_process_set/#inheritance","title":"Inheritance","text":""},{"location":"storage_process_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"storage_process_set/#properties","title":"Properties","text":""},{"location":"storage_process_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"storage_process_set/#schema-source","title":"Schema Source","text":""},{"location":"storage_process_set/#linkml-source","title":"LinkML Source","text":"
name: storage_process_set\ndescription: This property links a database object to the set of storage processes\n  within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: storage_process_set\ndomain_of:\n- Database\nrange: StorageProcess\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"store_cond/","title":"Slot: storage conditions (store_cond)","text":"

Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).

URI: MIXS:0000327

"},{"location":"store_cond/#inheritance","title":"Inheritance","text":""},{"location":"store_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"store_cond/#properties","title":"Properties","text":""},{"location":"store_cond/#aliases","title":"Aliases","text":""},{"location":"store_cond/#examples","title":"Examples","text":"Value -20 degree Celsius freezer;P2Y10D"},{"location":"store_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"store_cond/#annotations","title":"Annotations","text":"property value expected_value storage condition type;duration"},{"location":"store_cond/#schema-source","title":"Schema Source","text":""},{"location":"store_cond/#linkml-source","title":"LinkML Source","text":"
name: store_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: storage condition type;duration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Explain how and for how long the soil sample was stored before DNA extraction\n  (fresh/frozen/other).\ntitle: storage conditions\nexamples:\n- value: -20 degree Celsius freezer;P2Y10D\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- storage conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000327\nalias: store_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"strand/","title":"Slot: strand","text":"

The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).

URI: nmdc:strand

"},{"location":"strand/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"strand/#properties","title":"Properties","text":""},{"location":"strand/#todos","title":"TODOs","text":""},{"location":"strand/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"strand/#schema-source","title":"Schema Source","text":""},{"location":"strand/#linkml-source","title":"LinkML Source","text":"
name: strand\ndescription: The strand on which a feature is located. Has a value of '+' (sense strand\n  or forward strand) or  '-' (anti-sense strand or reverse strand).\ntodos:\n- set the range to an enum?\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:strand\nrank: 1000\nalias: strand\ndomain_of:\n- GenomeFeature\nrange: string\n\n
"},{"location":"stranded_orientation/","title":"Slot: stranded_orientation","text":"

Lists the strand orientiation for a stranded RNA library preparation.

URI: nmdc:stranded_orientation

"},{"location":"stranded_orientation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"stranded_orientation/#properties","title":"Properties","text":""},{"location":"stranded_orientation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"stranded_orientation/#schema-source","title":"Schema Source","text":""},{"location":"stranded_orientation/#linkml-source","title":"LinkML Source","text":"
name: stranded_orientation\ndescription: Lists the strand orientiation for a stranded RNA library preparation.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stranded_orientation\ndomain_of:\n- LibraryPreparation\nrange: StrandedOrientationEnum\n\n
"},{"location":"study_category/","title":"Slot: study_category","text":"

The type of research initiative

URI: nmdc:study_category

"},{"location":"study_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_category/#properties","title":"Properties","text":""},{"location":"study_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"study_category/#schema-source","title":"Schema Source","text":""},{"location":"study_category/#linkml-source","title":"LinkML Source","text":"
name: study_category\ndescription: The type of research initiative\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_category\ndomain_of:\n- Study\nrange: StudyCategoryEnum\nrequired: true\n\n
"},{"location":"study_identifiers/","title":"Slot: study_identifiers","text":"

Note

This is an abstract slot and should not be populated directly.

URI: nmdc:study_identifiers

"},{"location":"study_identifiers/#inheritance","title":"Inheritance","text":""},{"location":"study_identifiers/#properties","title":"Properties","text":""},{"location":"study_identifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"study_identifiers/#schema-source","title":"Schema Source","text":""},{"location":"study_identifiers/#linkml-source","title":"LinkML Source","text":"
name: study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: study_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\n
"},{"location":"study_image/","title":"Slot: study_image","text":"

Links a study to one or more images.

URI: nmdc:study_image

"},{"location":"study_image/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_image/#properties","title":"Properties","text":""},{"location":"study_image/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"study_image/#schema-source","title":"Schema Source","text":""},{"location":"study_image/#linkml-source","title":"LinkML Source","text":"
name: study_image\ndescription: Links a study to one or more images.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_image\ndomain_of:\n- Study\nrange: ImageValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"study_set/","title":"Slot: study_set","text":"

This property links a database object to the set of studies within it.

URI: nmdc:study_set

"},{"location":"study_set/#inheritance","title":"Inheritance","text":""},{"location":"study_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"study_set/#properties","title":"Properties","text":""},{"location":"study_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"study_set/#schema-source","title":"Schema Source","text":""},{"location":"study_set/#linkml-source","title":"LinkML Source","text":"
name: study_set\ndescription: This property links a database object to the set of studies within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: study_set\ndomain_of:\n- Database\nrange: Study\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"subject/","title":"Slot: subject","text":"

URI: nmdc:subject

"},{"location":"subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e no"},{"location":"subject/#properties","title":"Properties","text":""},{"location":"subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"subject/#schema-source","title":"Schema Source","text":""},{"location":"subject/#linkml-source","title":"LinkML Source","text":"
name: subject\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subject\ndomain_of:\n- FunctionalAnnotation\nrange: GeneProduct\n\n
"},{"location":"substance_role/","title":"Slot: substance_role","text":"

The role of a substance in a process

URI: nmdc:substance_role

"},{"location":"substance_role/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"substance_role/#properties","title":"Properties","text":""},{"location":"substance_role/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"substance_role/#schema-source","title":"Schema Source","text":""},{"location":"substance_role/#linkml-source","title":"LinkML Source","text":"
name: substance_role\ndescription: The role of a substance in a process\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substance_role\ndomain_of:\n- PortionOfSubstance\nrange: SubstanceRoleEnum\n\n
"},{"location":"substances_used/","title":"Slot: substances_used","text":"

The substances that are combined to enable a ChemicalConversionProcess.

URI: nmdc:substances_used

"},{"location":"substances_used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Extraction A material separation in which a desired component of an input material is se... no StorageProcess A planned process with the objective to preserve and protect material entitie... yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no"},{"location":"substances_used/#properties","title":"Properties","text":""},{"location":"substances_used/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"substances_used/#schema-source","title":"Schema Source","text":""},{"location":"substances_used/#linkml-source","title":"LinkML Source","text":"
name: substances_used\ndescription: The substances that are combined to enable a ChemicalConversionProcess.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substances_used\ndomain_of:\n- Extraction\n- StorageProcess\n- DissolvingProcess\n- ChemicalConversionProcess\n- MobilePhaseSegment\nrange: PortionOfSubstance\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"substances_volume/","title":"Slot: substances_volume","text":"

The volume of the combined substances that was included in a ChemicalConversionProcess.

URI: nmdc:substances_volume

"},{"location":"substances_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no"},{"location":"substances_volume/#properties","title":"Properties","text":""},{"location":"substances_volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"substances_volume/#schema-source","title":"Schema Source","text":""},{"location":"substances_volume/#linkml-source","title":"LinkML Source","text":"
name: substances_volume\ndescription: The volume of the combined substances that was included in a ChemicalConversionProcess.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substances_volume\ndomain_of:\n- ChemicalConversionProcess\nrange: QuantityValue\n\n
"},{"location":"substructure_type/","title":"Slot: substructure type (substructure_type)","text":"

The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level

URI: MIXS:0000767

"},{"location":"substructure_type/#inheritance","title":"Inheritance","text":""},{"location":"substructure_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"substructure_type/#properties","title":"Properties","text":""},{"location":"substructure_type/#aliases","title":"Aliases","text":""},{"location":"substructure_type/#examples","title":"Examples","text":"Value basement"},{"location":"substructure_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"substructure_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"substructure_type/#schema-source","title":"Schema Source","text":""},{"location":"substructure_type/#linkml-source","title":"LinkML Source","text":"
name: substructure_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: The substructure or under building is that largely hidden section of\n  the building which is built off the foundations to the ground floor level\ntitle: substructure type\nexamples:\n- value: basement\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- substructure type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000767\nalias: substructure_type\ndomain_of:\n- Biosample\nrange: substructure_type_enum\nmultivalued: true\n\n
"},{"location":"subsurface_depth/","title":"Slot: subsurface_depth","text":"

URI: nmdc:subsurface_depth

"},{"location":"subsurface_depth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"subsurface_depth/#properties","title":"Properties","text":""},{"location":"subsurface_depth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"subsurface_depth/#schema-source","title":"Schema Source","text":""},{"location":"subsurface_depth/#linkml-source","title":"LinkML Source","text":"
name: subsurface_depth\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subsurface_depth\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"},{"location":"sulfate/","title":"Slot: sulfate (sulfate)","text":"

Concentration of sulfate in the sample

URI: MIXS:0000423

"},{"location":"sulfate/#inheritance","title":"Inheritance","text":""},{"location":"sulfate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sulfate/#properties","title":"Properties","text":""},{"location":"sulfate/#aliases","title":"Aliases","text":""},{"location":"sulfate/#examples","title":"Examples","text":"Value 5 micromole per liter"},{"location":"sulfate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sulfate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sulfate/#schema-source","title":"Schema Source","text":""},{"location":"sulfate/#linkml-source","title":"LinkML Source","text":"
name: sulfate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of sulfate in the sample\ntitle: sulfate\nexamples:\n- value: 5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000423\nalias: sulfate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"sulfate_fw/","title":"Slot: sulfate in formation water (sulfate_fw)","text":"

Original sulfate concentration in the hydrocarbon resource

URI: MIXS:0000407

"},{"location":"sulfate_fw/#inheritance","title":"Inheritance","text":""},{"location":"sulfate_fw/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sulfate_fw/#properties","title":"Properties","text":""},{"location":"sulfate_fw/#aliases","title":"Aliases","text":""},{"location":"sulfate_fw/#examples","title":"Examples","text":"Value"},{"location":"sulfate_fw/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sulfate_fw/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sulfate_fw/#schema-source","title":"Schema Source","text":""},{"location":"sulfate_fw/#linkml-source","title":"LinkML Source","text":"
name: sulfate_fw\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original sulfate concentration in the hydrocarbon resource\ntitle: sulfate in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000407\nalias: sulfate_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"sulfide/","title":"Slot: sulfide (sulfide)","text":"

Concentration of sulfide in the sample

URI: MIXS:0000424

"},{"location":"sulfide/#inheritance","title":"Inheritance","text":""},{"location":"sulfide/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sulfide/#properties","title":"Properties","text":""},{"location":"sulfide/#aliases","title":"Aliases","text":""},{"location":"sulfide/#examples","title":"Examples","text":"Value 2 micromole per liter"},{"location":"sulfide/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"sulfide/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"sulfide/#schema-source","title":"Schema Source","text":""},{"location":"sulfide/#linkml-source","title":"LinkML Source","text":"
name: sulfide\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of sulfide in the sample\ntitle: sulfide\nexamples:\n- value: 2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000424\nalias: sulfide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"surf_air_cont/","title":"Slot: surface-air contaminant (surf_air_cont)","text":"

Contaminant identified on surface

URI: MIXS:0000759

"},{"location":"surf_air_cont/#inheritance","title":"Inheritance","text":""},{"location":"surf_air_cont/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_air_cont/#properties","title":"Properties","text":""},{"location":"surf_air_cont/#aliases","title":"Aliases","text":""},{"location":"surf_air_cont/#examples","title":"Examples","text":"Value radon"},{"location":"surf_air_cont/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_air_cont/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"surf_air_cont/#schema-source","title":"Schema Source","text":""},{"location":"surf_air_cont/#linkml-source","title":"LinkML Source","text":"
name: surf_air_cont\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Contaminant identified on surface\ntitle: surface-air contaminant\nexamples:\n- value: radon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface-air contaminant\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000759\nalias: surf_air_cont\ndomain_of:\n- Biosample\nrange: surf_air_cont_enum\nmultivalued: true\n\n
"},{"location":"surf_humidity/","title":"Slot: surface humidity (surf_humidity)","text":"

Surfaces: water activity as a function of air and material moisture

URI: MIXS:0000123

"},{"location":"surf_humidity/#inheritance","title":"Inheritance","text":""},{"location":"surf_humidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_humidity/#properties","title":"Properties","text":""},{"location":"surf_humidity/#aliases","title":"Aliases","text":""},{"location":"surf_humidity/#examples","title":"Examples","text":"Value 10%"},{"location":"surf_humidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_humidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"surf_humidity/#schema-source","title":"Schema Source","text":""},{"location":"surf_humidity/#linkml-source","title":"LinkML Source","text":"
name: surf_humidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percentage\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Surfaces: water activity as a function of air and material moisture'\ntitle: surface humidity\nexamples:\n- value: 10%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000123\nalias: surf_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"surf_material/","title":"Slot: surface material (surf_material)","text":"

Surface materials at the point of sampling

URI: MIXS:0000758

"},{"location":"surf_material/#inheritance","title":"Inheritance","text":""},{"location":"surf_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_material/#properties","title":"Properties","text":""},{"location":"surf_material/#aliases","title":"Aliases","text":""},{"location":"surf_material/#examples","title":"Examples","text":"Value wood"},{"location":"surf_material/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_material/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"surf_material/#schema-source","title":"Schema Source","text":""},{"location":"surf_material/#linkml-source","title":"LinkML Source","text":"
name: surf_material\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Surface materials at the point of sampling\ntitle: surface material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000758\nalias: surf_material\ndomain_of:\n- Biosample\nrange: surf_material_enum\nmultivalued: false\n\n
"},{"location":"surf_moisture/","title":"Slot: surface moisture (surf_moisture)","text":"

Water held on a surface

URI: MIXS:0000128

"},{"location":"surf_moisture/#inheritance","title":"Inheritance","text":""},{"location":"surf_moisture/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_moisture/#properties","title":"Properties","text":""},{"location":"surf_moisture/#aliases","title":"Aliases","text":""},{"location":"surf_moisture/#examples","title":"Examples","text":"Value 0.01 gram per square meter"},{"location":"surf_moisture/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_moisture/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"surf_moisture/#schema-source","title":"Schema Source","text":""},{"location":"surf_moisture/#linkml-source","title":"LinkML Source","text":"
name: surf_moisture\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: parts per million, gram per cubic meter, gram per square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Water held on a surface\ntitle: surface moisture\nexamples:\n- value: 0.01 gram per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000128\nalias: surf_moisture\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"surf_moisture_ph/","title":"Slot: surface moisture pH (surf_moisture_ph)","text":"

ph measurement of surface

URI: MIXS:0000760

"},{"location":"surf_moisture_ph/#inheritance","title":"Inheritance","text":""},{"location":"surf_moisture_ph/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_moisture_ph/#properties","title":"Properties","text":""},{"location":"surf_moisture_ph/#aliases","title":"Aliases","text":""},{"location":"surf_moisture_ph/#examples","title":"Examples","text":"Value 7"},{"location":"surf_moisture_ph/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_moisture_ph/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"surf_moisture_ph/#schema-source","title":"Schema Source","text":""},{"location":"surf_moisture_ph/#linkml-source","title":"LinkML Source","text":"
name: surf_moisture_ph\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: ph measurement of surface\ntitle: surface moisture pH\nexamples:\n- value: '7'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000760\nalias: surf_moisture_ph\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\n
"},{"location":"surf_temp/","title":"Slot: surface temperature (surf_temp)","text":"

Temperature of the surface at the time of sampling

URI: MIXS:0000125

"},{"location":"surf_temp/#inheritance","title":"Inheritance","text":""},{"location":"surf_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"surf_temp/#properties","title":"Properties","text":""},{"location":"surf_temp/#aliases","title":"Aliases","text":""},{"location":"surf_temp/#examples","title":"Examples","text":"Value 15 degree Celsius"},{"location":"surf_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"surf_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"surf_temp/#schema-source","title":"Schema Source","text":""},{"location":"surf_temp/#linkml-source","title":"LinkML Source","text":"
name: surf_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Temperature of the surface at the time of sampling\ntitle: surface temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000125\nalias: surf_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"suspend_part_matter/","title":"Slot: suspended particulate matter (suspend_part_matter)","text":"

Concentration of suspended particulate matter

URI: MIXS:0000741

"},{"location":"suspend_part_matter/#inheritance","title":"Inheritance","text":""},{"location":"suspend_part_matter/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"suspend_part_matter/#properties","title":"Properties","text":""},{"location":"suspend_part_matter/#aliases","title":"Aliases","text":""},{"location":"suspend_part_matter/#examples","title":"Examples","text":"Value 0.5 milligram per liter"},{"location":"suspend_part_matter/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"suspend_part_matter/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"suspend_part_matter/#schema-source","title":"Schema Source","text":""},{"location":"suspend_part_matter/#linkml-source","title":"LinkML Source","text":"
name: suspend_part_matter\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of suspended particulate matter\ntitle: suspended particulate matter\nexamples:\n- value: 0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended particulate matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000741\nalias: suspend_part_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"suspend_solids/","title":"Slot: suspended solids (suspend_solids)","text":"

Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances

URI: MIXS:0000150

"},{"location":"suspend_solids/#inheritance","title":"Inheritance","text":""},{"location":"suspend_solids/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"suspend_solids/#properties","title":"Properties","text":""},{"location":"suspend_solids/#aliases","title":"Aliases","text":""},{"location":"suspend_solids/#examples","title":"Examples","text":"Value"},{"location":"suspend_solids/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"suspend_solids/#annotations","title":"Annotations","text":"property value expected_value suspended solid name;measurement value"},{"location":"suspend_solids/#schema-source","title":"Schema Source","text":""},{"location":"suspend_solids/#linkml-source","title":"LinkML Source","text":"
name: suspend_solids\nannotations:\n  expected_value:\n    tag: expected_value\n    value: suspended solid name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram, microgram, milligram per liter, mole per liter, gram per liter, part\n      per million\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of substances including a wide variety of material, such\n  as silt, decaying plant and animal matter; can include multiple substances\ntitle: suspended solids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended solids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000150\nalias: suspend_solids\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"tan/","title":"Slot: total acid number (tan)","text":"

Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)

URI: MIXS:0000120

"},{"location":"tan/#inheritance","title":"Inheritance","text":""},{"location":"tan/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tan/#properties","title":"Properties","text":""},{"location":"tan/#aliases","title":"Aliases","text":""},{"location":"tan/#examples","title":"Examples","text":"Value"},{"location":"tan/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tan/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tan/#schema-source","title":"Schema Source","text":""},{"location":"tan/#linkml-source","title":"LinkML Source","text":"
name: tan\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n  by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n  the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n  oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\ntitle: total acid number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total acid number\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000120\nalias: tan\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"target_gene/","title":"Slot: target gene (target_gene)","text":"

Targeted gene or locus name for marker gene studies

URI: MIXS:0000044

"},{"location":"target_gene/#inheritance","title":"Inheritance","text":""},{"location":"target_gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"target_gene/#properties","title":"Properties","text":""},{"location":"target_gene/#aliases","title":"Aliases","text":""},{"location":"target_gene/#examples","title":"Examples","text":"Value 16S rRNA, 18S rRNA, nif, amoA, rpo"},{"location":"target_gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"target_gene/#annotations","title":"Annotations","text":"property value expected_value gene name"},{"location":"target_gene/#schema-source","title":"Schema Source","text":""},{"location":"target_gene/#linkml-source","title":"LinkML Source","text":"
name: target_gene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gene name\ndescription: Targeted gene or locus name for marker gene studies\ntitle: target gene\nexamples:\n- value: 16S rRNA, 18S rRNA, nif, amoA, rpo\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target gene\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000044\nalias: target_gene\ndomain_of:\n- NucleotideSequencing\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"target_subfragment/","title":"Slot: target subfragment (target_subfragment)","text":"

Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA

URI: MIXS:0000045

"},{"location":"target_subfragment/#inheritance","title":"Inheritance","text":""},{"location":"target_subfragment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"target_subfragment/#properties","title":"Properties","text":""},{"location":"target_subfragment/#aliases","title":"Aliases","text":""},{"location":"target_subfragment/#examples","title":"Examples","text":"Value V6, V9, ITS"},{"location":"target_subfragment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"target_subfragment/#annotations","title":"Annotations","text":"property value expected_value gene fragment name"},{"location":"target_subfragment/#schema-source","title":"Schema Source","text":""},{"location":"target_subfragment/#linkml-source","title":"LinkML Source","text":"
name: target_subfragment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: gene fragment name\ndescription: Name of subfragment of a gene or locus. Important to e.g. identify special\n  regions on marker genes like V6 on 16S rRNA\ntitle: target subfragment\nexamples:\n- value: V6, V9, ITS\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target subfragment\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000045\nalias: target_subfragment\ndomain_of:\n- NucleotideSequencing\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"technical_reps/","title":"Slot: number technical replicate (technical_reps)","text":"

If sending technical replicates of the same sample, indicate the replicate count.

URI: nmdc:technical_reps

"},{"location":"technical_reps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"technical_reps/#properties","title":"Properties","text":""},{"location":"technical_reps/#examples","title":"Examples","text":"Value 2"},{"location":"technical_reps/#comments","title":"Comments","text":""},{"location":"technical_reps/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"technical_reps/#schema-source","title":"Schema Source","text":""},{"location":"technical_reps/#linkml-source","title":"LinkML Source","text":"
name: technical_reps\ndescription: If sending technical replicates of the same sample, indicate the replicate\n  count.\ntitle: number technical replicate\ncomments:\n- This field is only required when completing metadata for samples being submitted\n  to EMSL for analyses.\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{integer}'\nalias: technical_reps\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\n
"},{"location":"temp/","title":"Slot: temperature (temp)","text":"

Temperature of the sample at the time of sampling.

URI: MIXS:0000113

"},{"location":"temp/#inheritance","title":"Inheritance","text":""},{"location":"temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"temp/#properties","title":"Properties","text":""},{"location":"temp/#aliases","title":"Aliases","text":""},{"location":"temp/#examples","title":"Examples","text":"Value 25 degree Celsius"},{"location":"temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"temp/#schema-source","title":"Schema Source","text":""},{"location":"temp/#linkml-source","title":"LinkML Source","text":"
name: temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\ndescription: Temperature of the sample at the time of sampling.\ntitle: temperature\nexamples:\n- value: 25 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000113\nalias: temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"temp_out/","title":"Slot: temperature outside house (temp_out)","text":"

The recorded temperature value at sampling time outside

URI: MIXS:0000197

"},{"location":"temp_out/#inheritance","title":"Inheritance","text":""},{"location":"temp_out/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"temp_out/#properties","title":"Properties","text":""},{"location":"temp_out/#aliases","title":"Aliases","text":""},{"location":"temp_out/#examples","title":"Examples","text":"Value 5 degree Celsius"},{"location":"temp_out/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"temp_out/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"temp_out/#schema-source","title":"Schema Source","text":""},{"location":"temp_out/#linkml-source","title":"LinkML Source","text":"
name: temp_out\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The recorded temperature value at sampling time outside\ntitle: temperature outside house\nexamples:\n- value: 5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature outside house\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000197\nalias: temp_out\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"temperature/","title":"Slot: temperature","text":"

The value of a temperature measurement or temperature used in a process.

URI: nmdc:temperature

"},{"location":"temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no StorageProcess A planned process with the objective to preserve and protect material entitie... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no"},{"location":"temperature/#properties","title":"Properties","text":""},{"location":"temperature/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"temperature/#schema-source","title":"Schema Source","text":""},{"location":"temperature/#linkml-source","title":"LinkML Source","text":"
name: temperature\ndescription: The value of a temperature measurement or temperature used in a process.\nnotes:\n- Not to be confused with the MIXS:0000113\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: temperature\ndomain_of:\n- ChromatographyConfiguration\n- SubSamplingProcess\n- StorageProcess\n- ChromatographicSeparationProcess\n- DissolvingProcess\n- ChemicalConversionProcess\nrange: QuantityValue\n\n
"},{"location":"term/","title":"Slot: term","text":"

pointer to an ontology class

URI: nmdc:term

"},{"location":"term/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ControlledTermValue A controlled term or class from an ontology no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... yes"},{"location":"term/#properties","title":"Properties","text":""},{"location":"term/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"term/#schema-source","title":"Schema Source","text":""},{"location":"term/#linkml-source","title":"LinkML Source","text":"
name: term\ndescription: pointer to an ontology class\nnotes:\n- 'removed ''slot_uri: rdf:type'''\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: term\ndomain_of:\n- ControlledTermValue\nrange: OntologyClass\ninlined: true\n\n
"},{"location":"tertiary_treatment/","title":"Slot: tertiary treatment (tertiary_treatment)","text":"

The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment

URI: MIXS:0000352

"},{"location":"tertiary_treatment/#inheritance","title":"Inheritance","text":""},{"location":"tertiary_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tertiary_treatment/#properties","title":"Properties","text":""},{"location":"tertiary_treatment/#aliases","title":"Aliases","text":""},{"location":"tertiary_treatment/#examples","title":"Examples","text":"Value"},{"location":"tertiary_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tertiary_treatment/#annotations","title":"Annotations","text":"property value expected_value tertiary treatment type"},{"location":"tertiary_treatment/#schema-source","title":"Schema Source","text":""},{"location":"tertiary_treatment/#linkml-source","title":"LinkML Source","text":"
name: tertiary_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: tertiary treatment type\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The process providing a final treatment stage to raise the effluent quality\n  before it is discharged to the receiving environment\ntitle: tertiary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tertiary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000352\nalias: tertiary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"tidal_stage/","title":"Slot: tidal stage (tidal_stage)","text":"

Stage of tide

URI: MIXS:0000750

"},{"location":"tidal_stage/#inheritance","title":"Inheritance","text":""},{"location":"tidal_stage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tidal_stage/#properties","title":"Properties","text":""},{"location":"tidal_stage/#aliases","title":"Aliases","text":""},{"location":"tidal_stage/#examples","title":"Examples","text":"Value high tide"},{"location":"tidal_stage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tidal_stage/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"tidal_stage/#schema-source","title":"Schema Source","text":""},{"location":"tidal_stage/#linkml-source","title":"LinkML Source","text":"
name: tidal_stage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Stage of tide\ntitle: tidal stage\nexamples:\n- value: high tide\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tidal stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000750\nalias: tidal_stage\ndomain_of:\n- Biosample\nrange: tidal_stage_enum\nmultivalued: false\n\n
"},{"location":"tillage/","title":"Slot: history/tillage (tillage)","text":"

Note method(s) used for tilling

URI: MIXS:0001081

"},{"location":"tillage/#inheritance","title":"Inheritance","text":""},{"location":"tillage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tillage/#properties","title":"Properties","text":""},{"location":"tillage/#aliases","title":"Aliases","text":""},{"location":"tillage/#examples","title":"Examples","text":"Value chisel"},{"location":"tillage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tillage/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"tillage/#schema-source","title":"Schema Source","text":""},{"location":"tillage/#linkml-source","title":"LinkML Source","text":"
name: tillage\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Note method(s) used for tilling\ntitle: history/tillage\nexamples:\n- value: chisel\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/tillage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001081\nalias: tillage\ndomain_of:\n- Biosample\nrange: tillage_enum\nmultivalued: true\n\n
"},{"location":"tiss_cult_growth_med/","title":"Slot: tissue culture growth media (tiss_cult_growth_med)","text":"

Description of plant tissue culture growth media used

URI: MIXS:0001070

"},{"location":"tiss_cult_growth_med/#inheritance","title":"Inheritance","text":""},{"location":"tiss_cult_growth_med/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tiss_cult_growth_med/#properties","title":"Properties","text":""},{"location":"tiss_cult_growth_med/#aliases","title":"Aliases","text":""},{"location":"tiss_cult_growth_med/#examples","title":"Examples","text":"Value https://link.springer.com/content/pdf/10.1007/BF02796489.pdf"},{"location":"tiss_cult_growth_med/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tiss_cult_growth_med/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI,url or free text"},{"location":"tiss_cult_growth_med/#schema-source","title":"Schema Source","text":""},{"location":"tiss_cult_growth_med/#linkml-source","title":"LinkML Source","text":"
name: tiss_cult_growth_med\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI,url or free text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Description of plant tissue culture growth media used\ntitle: tissue culture growth media\nexamples:\n- value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tissue culture growth media\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001070\nalias: tiss_cult_growth_med\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"title/","title":"Slot: title","text":"

A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.

URI: nmdc:title

"},{"location":"title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"title/#properties","title":"Properties","text":""},{"location":"title/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"title/#schema-source","title":"Schema Source","text":""},{"location":"title/#linkml-source","title":"LinkML Source","text":"
name: title\ndescription: A name given to the entity that differs from the name/label programmatically\n  assigned to it. For example, when extracting study information for GOLD, the GOLD\n  system has assigned a name/label. However, for display purposes, we may also wish\n  the capture the title of the proposal that was used to fund the study.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:title\nrank: 1000\nalias: title\ndomain_of:\n- Study\nrange: string\n\n
"},{"location":"toluene/","title":"Slot: toluene (toluene)","text":"

Concentration of toluene in the sample

URI: MIXS:0000154

"},{"location":"toluene/#inheritance","title":"Inheritance","text":""},{"location":"toluene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"toluene/#properties","title":"Properties","text":""},{"location":"toluene/#aliases","title":"Aliases","text":""},{"location":"toluene/#examples","title":"Examples","text":"Value"},{"location":"toluene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"toluene/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"toluene/#schema-source","title":"Schema Source","text":""},{"location":"toluene/#linkml-source","title":"LinkML Source","text":"
name: toluene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of toluene in the sample\ntitle: toluene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- toluene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000154\nalias: toluene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"too_short_contig_num/","title":"Slot: too_short_contig_num","text":"

URI: nmdc:too_short_contig_num

"},{"location":"too_short_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"too_short_contig_num/#properties","title":"Properties","text":""},{"location":"too_short_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"too_short_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"too_short_contig_num/#linkml-source","title":"LinkML Source","text":"
name: too_short_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: too_short_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"tot_carb/","title":"Slot: total carbon (tot_carb)","text":"

Total carbon content

URI: MIXS:0000525

"},{"location":"tot_carb/#inheritance","title":"Inheritance","text":""},{"location":"tot_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_carb/#properties","title":"Properties","text":""},{"location":"tot_carb/#aliases","title":"Aliases","text":""},{"location":"tot_carb/#examples","title":"Examples","text":"Value"},{"location":"tot_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_carb/#schema-source","title":"Schema Source","text":""},{"location":"tot_carb/#linkml-source","title":"LinkML Source","text":"
name: tot_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total carbon content\ntitle: total carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000525\nalias: tot_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_depth_water_col/","title":"Slot: total depth of water column (tot_depth_water_col)","text":"

Measurement of total depth of water column

URI: MIXS:0000634

"},{"location":"tot_depth_water_col/#inheritance","title":"Inheritance","text":""},{"location":"tot_depth_water_col/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_depth_water_col/#properties","title":"Properties","text":""},{"location":"tot_depth_water_col/#aliases","title":"Aliases","text":""},{"location":"tot_depth_water_col/#examples","title":"Examples","text":"Value 500 meter"},{"location":"tot_depth_water_col/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_depth_water_col/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_depth_water_col/#schema-source","title":"Schema Source","text":""},{"location":"tot_depth_water_col/#linkml-source","title":"LinkML Source","text":"
name: tot_depth_water_col\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of total depth of water column\ntitle: total depth of water column\nexamples:\n- value: 500 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total depth of water column\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000634\nalias: tot_depth_water_col\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_diss_nitro/","title":"Slot: total dissolved nitrogen (tot_diss_nitro)","text":"

Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen

URI: MIXS:0000744

"},{"location":"tot_diss_nitro/#inheritance","title":"Inheritance","text":""},{"location":"tot_diss_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_diss_nitro/#properties","title":"Properties","text":""},{"location":"tot_diss_nitro/#aliases","title":"Aliases","text":""},{"location":"tot_diss_nitro/#examples","title":"Examples","text":"Value 40 microgram per liter"},{"location":"tot_diss_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_diss_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_diss_nitro/#schema-source","title":"Schema Source","text":""},{"location":"tot_diss_nitro/#linkml-source","title":"LinkML Source","text":"
name: tot_diss_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n  by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\ntitle: total dissolved nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total dissolved nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000744\nalias: tot_diss_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_inorg_nitro/","title":"Slot: total inorganic nitrogen (tot_inorg_nitro)","text":"

Total inorganic nitrogen content

URI: MIXS:0000745

"},{"location":"tot_inorg_nitro/#inheritance","title":"Inheritance","text":""},{"location":"tot_inorg_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_inorg_nitro/#properties","title":"Properties","text":""},{"location":"tot_inorg_nitro/#aliases","title":"Aliases","text":""},{"location":"tot_inorg_nitro/#examples","title":"Examples","text":"Value 40 microgram per liter"},{"location":"tot_inorg_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_inorg_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_inorg_nitro/#schema-source","title":"Schema Source","text":""},{"location":"tot_inorg_nitro/#linkml-source","title":"LinkML Source","text":"
name: tot_inorg_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total inorganic nitrogen content\ntitle: total inorganic nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000745\nalias: tot_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_iron/","title":"Slot: total iron (tot_iron)","text":"

Concentration of total iron in the sample

URI: MIXS:0000105

"},{"location":"tot_iron/#inheritance","title":"Inheritance","text":""},{"location":"tot_iron/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_iron/#properties","title":"Properties","text":""},{"location":"tot_iron/#aliases","title":"Aliases","text":""},{"location":"tot_iron/#examples","title":"Examples","text":"Value"},{"location":"tot_iron/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_iron/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_iron/#schema-source","title":"Schema Source","text":""},{"location":"tot_iron/#linkml-source","title":"LinkML Source","text":"
name: tot_iron\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, milligram per kilogram\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of total iron in the sample\ntitle: total iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000105\nalias: tot_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_nitro/","title":"Slot: total nitrogen concentration (tot_nitro)","text":"

Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen

URI: MIXS:0000102

"},{"location":"tot_nitro/#inheritance","title":"Inheritance","text":""},{"location":"tot_nitro/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_nitro/#properties","title":"Properties","text":""},{"location":"tot_nitro/#aliases","title":"Aliases","text":""},{"location":"tot_nitro/#examples","title":"Examples","text":"Value 50 micromole per liter"},{"location":"tot_nitro/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_nitro/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_nitro/#schema-source","title":"Schema Source","text":""},{"location":"tot_nitro/#linkml-source","title":"LinkML Source","text":"
name: tot_nitro\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Total nitrogen concentration of water samples, calculated by: total\n  nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n  without filtering, reported as nitrogen'\ntitle: total nitrogen concentration\nexamples:\n- value: 50 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen concentration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000102\nalias: tot_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_nitro_cont_meth/","title":"Slot: total nitrogen content method (tot_nitro_cont_meth)","text":"

Reference or method used in determining the total nitrogen

URI: MIXS:0000338

"},{"location":"tot_nitro_cont_meth/#inheritance","title":"Inheritance","text":""},{"location":"tot_nitro_cont_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_nitro_cont_meth/#properties","title":"Properties","text":""},{"location":"tot_nitro_cont_meth/#aliases","title":"Aliases","text":""},{"location":"tot_nitro_cont_meth/#examples","title":"Examples","text":"Value"},{"location":"tot_nitro_cont_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_nitro_cont_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"tot_nitro_cont_meth/#schema-source","title":"Schema Source","text":""},{"location":"tot_nitro_cont_meth/#linkml-source","title":"LinkML Source","text":"
name: tot_nitro_cont_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining the total nitrogen\ntitle: total nitrogen content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000338\nalias: tot_nitro_cont_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"tot_nitro_content/","title":"Slot: total nitrogen content (tot_nitro_content)","text":"

Total nitrogen content of the sample

URI: MIXS:0000530

"},{"location":"tot_nitro_content/#inheritance","title":"Inheritance","text":""},{"location":"tot_nitro_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_nitro_content/#properties","title":"Properties","text":""},{"location":"tot_nitro_content/#aliases","title":"Aliases","text":""},{"location":"tot_nitro_content/#examples","title":"Examples","text":"Value"},{"location":"tot_nitro_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_nitro_content/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_nitro_content/#schema-source","title":"Schema Source","text":""},{"location":"tot_nitro_content/#linkml-source","title":"LinkML Source","text":"
name: tot_nitro_content\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter, milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total nitrogen content of the sample\ntitle: total nitrogen content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000530\nalias: tot_nitro_content\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_org_c_meth/","title":"Slot: total organic carbon method (tot_org_c_meth)","text":"

Reference or method used in determining total organic carbon

URI: MIXS:0000337

"},{"location":"tot_org_c_meth/#inheritance","title":"Inheritance","text":""},{"location":"tot_org_c_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_org_c_meth/#properties","title":"Properties","text":""},{"location":"tot_org_c_meth/#aliases","title":"Aliases","text":""},{"location":"tot_org_c_meth/#examples","title":"Examples","text":"Value"},{"location":"tot_org_c_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_org_c_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"tot_org_c_meth/#schema-source","title":"Schema Source","text":""},{"location":"tot_org_c_meth/#linkml-source","title":"LinkML Source","text":"
name: tot_org_c_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining total organic carbon\ntitle: total organic carbon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000337\nalias: tot_org_c_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"tot_org_carb/","title":"Slot: total organic carbon (tot_org_carb)","text":"

Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content

URI: MIXS:0000533

"},{"location":"tot_org_carb/#inheritance","title":"Inheritance","text":""},{"location":"tot_org_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"tot_org_carb/#properties","title":"Properties","text":""},{"location":"tot_org_carb/#aliases","title":"Aliases","text":""},{"location":"tot_org_carb/#examples","title":"Examples","text":"Value"},{"location":"tot_org_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_org_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_org_carb/#schema-source","title":"Schema Source","text":""},{"location":"tot_org_carb/#linkml-source","title":"LinkML Source","text":"
name: tot_org_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram Carbon per kilogram sample material\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Definition for soil: total organic carbon content of the soil, definition\n  otherwise: total organic carbon content'\ntitle: total organic carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000533\nalias: tot_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_part_carb/","title":"Slot: total particulate carbon (tot_part_carb)","text":"

Total particulate carbon content

URI: MIXS:0000747

"},{"location":"tot_part_carb/#inheritance","title":"Inheritance","text":""},{"location":"tot_part_carb/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_part_carb/#properties","title":"Properties","text":""},{"location":"tot_part_carb/#aliases","title":"Aliases","text":""},{"location":"tot_part_carb/#examples","title":"Examples","text":"Value 35 micromole per liter"},{"location":"tot_part_carb/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_part_carb/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_part_carb/#schema-source","title":"Schema Source","text":""},{"location":"tot_part_carb/#linkml-source","title":"LinkML Source","text":"
name: tot_part_carb\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total particulate carbon content\ntitle: total particulate carbon\nexamples:\n- value: 35 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total particulate carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000747\nalias: tot_part_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_phosp/","title":"Slot: total phosphorus (tot_phosp)","text":"

Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus

URI: MIXS:0000117

"},{"location":"tot_phosp/#inheritance","title":"Inheritance","text":""},{"location":"tot_phosp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_phosp/#properties","title":"Properties","text":""},{"location":"tot_phosp/#aliases","title":"Aliases","text":""},{"location":"tot_phosp/#examples","title":"Examples","text":"Value 0.03 milligram per liter"},{"location":"tot_phosp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_phosp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_phosp/#schema-source","title":"Schema Source","text":""},{"location":"tot_phosp/#linkml-source","title":"LinkML Source","text":"
name: tot_phosp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: micromole per liter, milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'Total phosphorus concentration in the sample, calculated by: total phosphorus\n  = total dissolved phosphorus + particulate phosphorus'\ntitle: total phosphorus\nexamples:\n- value: 0.03 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000117\nalias: tot_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_phosphate/","title":"Slot: total phosphate (tot_phosphate)","text":"

Total amount or concentration of phosphate

URI: MIXS:0000689

"},{"location":"tot_phosphate/#inheritance","title":"Inheritance","text":""},{"location":"tot_phosphate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_phosphate/#properties","title":"Properties","text":""},{"location":"tot_phosphate/#aliases","title":"Aliases","text":""},{"location":"tot_phosphate/#examples","title":"Examples","text":"Value"},{"location":"tot_phosphate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_phosphate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_phosphate/#schema-source","title":"Schema Source","text":""},{"location":"tot_phosphate/#linkml-source","title":"LinkML Source","text":"
name: tot_phosphate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per liter, micromole per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Total amount or concentration of phosphate\ntitle: total phosphate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000689\nalias: tot_phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tot_sulfur/","title":"Slot: total sulfur (tot_sulfur)","text":"

Concentration of total sulfur in the sample

URI: MIXS:0000419

"},{"location":"tot_sulfur/#inheritance","title":"Inheritance","text":""},{"location":"tot_sulfur/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tot_sulfur/#properties","title":"Properties","text":""},{"location":"tot_sulfur/#aliases","title":"Aliases","text":""},{"location":"tot_sulfur/#examples","title":"Examples","text":"Value"},{"location":"tot_sulfur/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tot_sulfur/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tot_sulfur/#schema-source","title":"Schema Source","text":""},{"location":"tot_sulfur/#linkml-source","title":"LinkML Source","text":"
name: tot_sulfur\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of total sulfur in the sample\ntitle: total sulfur\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total sulfur\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000419\nalias: tot_sulfur\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"total_bases/","title":"Slot: total_bases","text":"

URI: nmdc:total_bases

"},{"location":"total_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"total_bases/#properties","title":"Properties","text":""},{"location":"total_bases/#todos","title":"TODOs","text":""},{"location":"total_bases/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"total_bases/#schema-source","title":"Schema Source","text":""},{"location":"total_bases/#linkml-source","title":"LinkML Source","text":"
name: total_bases\ntodos:\n- this slot needs some basic textual annotations and constraints\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: total_bases\ndomain_of:\n- MagBin\nrange: integer\n\n
"},{"location":"train_line/","title":"Slot: train line (train_line)","text":"

The subway line name

URI: MIXS:0000837

"},{"location":"train_line/#inheritance","title":"Inheritance","text":""},{"location":"train_line/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"train_line/#properties","title":"Properties","text":""},{"location":"train_line/#aliases","title":"Aliases","text":""},{"location":"train_line/#examples","title":"Examples","text":"Value red"},{"location":"train_line/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"train_line/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"train_line/#schema-source","title":"Schema Source","text":""},{"location":"train_line/#linkml-source","title":"LinkML Source","text":"
name: train_line\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The subway line name\ntitle: train line\nexamples:\n- value: red\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train line\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000837\nalias: train_line\ndomain_of:\n- Biosample\nrange: train_line_enum\nmultivalued: false\n\n
"},{"location":"train_stat_loc/","title":"Slot: train station collection location (train_stat_loc)","text":"

The train station collection location

URI: MIXS:0000838

"},{"location":"train_stat_loc/#inheritance","title":"Inheritance","text":""},{"location":"train_stat_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"train_stat_loc/#properties","title":"Properties","text":""},{"location":"train_stat_loc/#aliases","title":"Aliases","text":""},{"location":"train_stat_loc/#examples","title":"Examples","text":"Value forest hills"},{"location":"train_stat_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"train_stat_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"train_stat_loc/#schema-source","title":"Schema Source","text":""},{"location":"train_stat_loc/#linkml-source","title":"LinkML Source","text":"
name: train_stat_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The train station collection location\ntitle: train station collection location\nexamples:\n- value: forest hills\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train station collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000838\nalias: train_stat_loc\ndomain_of:\n- Biosample\nrange: train_stat_loc_enum\nmultivalued: false\n\n
"},{"location":"train_stop_loc/","title":"Slot: train stop collection location (train_stop_loc)","text":"

The train stop collection location

URI: MIXS:0000839

"},{"location":"train_stop_loc/#inheritance","title":"Inheritance","text":""},{"location":"train_stop_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"train_stop_loc/#properties","title":"Properties","text":""},{"location":"train_stop_loc/#aliases","title":"Aliases","text":""},{"location":"train_stop_loc/#examples","title":"Examples","text":"Value end"},{"location":"train_stop_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"train_stop_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"train_stop_loc/#schema-source","title":"Schema Source","text":""},{"location":"train_stop_loc/#linkml-source","title":"LinkML Source","text":"
name: train_stop_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The train stop collection location\ntitle: train stop collection location\nexamples:\n- value: end\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train stop collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000839\nalias: train_stop_loc\ndomain_of:\n- Biosample\nrange: train_stop_loc_enum\nmultivalued: false\n\n
"},{"location":"turbidity/","title":"Slot: turbidity (turbidity)","text":"

Measure of the amount of cloudiness or haziness in water caused by individual particles

URI: MIXS:0000191

"},{"location":"turbidity/#inheritance","title":"Inheritance","text":""},{"location":"turbidity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"turbidity/#properties","title":"Properties","text":""},{"location":"turbidity/#aliases","title":"Aliases","text":""},{"location":"turbidity/#examples","title":"Examples","text":"Value 0.3 nephelometric turbidity units"},{"location":"turbidity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"turbidity/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"turbidity/#schema-source","title":"Schema Source","text":""},{"location":"turbidity/#linkml-source","title":"LinkML Source","text":"
name: turbidity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: formazin turbidity unit, formazin nephelometric units\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measure of the amount of cloudiness or haziness in water caused by individual\n  particles\ntitle: turbidity\nexamples:\n- value: 0.3 nephelometric turbidity units\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- turbidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000191\nalias: turbidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tvdss_of_hcr_press/","title":"Slot: depth (TVDSS) of hydrocarbon resource pressure (tvdss_of_hcr_press)","text":"

True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).

URI: MIXS:0000397

"},{"location":"tvdss_of_hcr_press/#inheritance","title":"Inheritance","text":""},{"location":"tvdss_of_hcr_press/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tvdss_of_hcr_press/#properties","title":"Properties","text":""},{"location":"tvdss_of_hcr_press/#aliases","title":"Aliases","text":""},{"location":"tvdss_of_hcr_press/#examples","title":"Examples","text":"Value"},{"location":"tvdss_of_hcr_press/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tvdss_of_hcr_press/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tvdss_of_hcr_press/#schema-source","title":"Schema Source","text":""},{"location":"tvdss_of_hcr_press/#linkml-source","title":"LinkML Source","text":"
name: tvdss_of_hcr_press\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n  the original pressure was measured (e.g. 1578 m).\ntitle: depth (TVDSS) of hydrocarbon resource pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000397\nalias: tvdss_of_hcr_press\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"tvdss_of_hcr_temp/","title":"Slot: depth (TVDSS) of hydrocarbon resource temperature (tvdss_of_hcr_temp)","text":"

True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).

URI: MIXS:0000394

"},{"location":"tvdss_of_hcr_temp/#inheritance","title":"Inheritance","text":""},{"location":"tvdss_of_hcr_temp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"tvdss_of_hcr_temp/#properties","title":"Properties","text":""},{"location":"tvdss_of_hcr_temp/#aliases","title":"Aliases","text":""},{"location":"tvdss_of_hcr_temp/#examples","title":"Examples","text":"Value"},{"location":"tvdss_of_hcr_temp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"tvdss_of_hcr_temp/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"tvdss_of_hcr_temp/#schema-source","title":"Schema Source","text":""},{"location":"tvdss_of_hcr_temp/#linkml-source","title":"LinkML Source","text":"
name: tvdss_of_hcr_temp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n  the original temperature was measured (e.g. 1345 m).\ntitle: depth (TVDSS) of hydrocarbon resource temperature\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000394\nalias: tvdss_of_hcr_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"typ_occup_density/","title":"Slot: typical occupant density (typ_occup_density)","text":"

Customary or normal density of occupants

URI: MIXS:0000771

"},{"location":"typ_occup_density/#inheritance","title":"Inheritance","text":""},{"location":"typ_occup_density/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"typ_occup_density/#properties","title":"Properties","text":""},{"location":"typ_occup_density/#aliases","title":"Aliases","text":""},{"location":"typ_occup_density/#examples","title":"Examples","text":"Value 25"},{"location":"typ_occup_density/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"typ_occup_density/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"typ_occup_density/#schema-source","title":"Schema Source","text":""},{"location":"typ_occup_density/#linkml-source","title":"LinkML Source","text":"
name: typ_occup_density\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Customary or normal density of occupants\ntitle: typical occupant density\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- typical occupant density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000771\nalias: typ_occup_density\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\n
"},{"location":"type/","title":"Slot: type","text":"

the class_uri of the class that has been instantiated

URI: rdf:type

"},{"location":"type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no QuantityValue A simple quantity, e no MetatranscriptomeAnnotation no PersonValue An attribute value representing a person no GenomeFeature A feature localized to an interval along a genome no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no FunctionalAnnotation An assignment of a function term (e no CreditAssociation This class supports binding associated researchers to studies no Site no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no FailureCategorization no MaterialEntity no MetatranscriptomeAssembly no Configuration A set of parameters that define the actions of a process and is shared among ... no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DataObject An object that primarily consists of symbols that represent information no PlannedProcess no ControlledTermValue A controlled term or class from an ontology no EnvironmentalMaterialTerm no NamedThing a databased entity or concept/class no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no ProcessedSample no TimestampValue A value that is a timestamp no ChemicalEntity An atom or molecule that can be represented with a chemical formula no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no CollectingBiosamplesFromSite no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NomAnalysis no Instrument A material entity that is designed to perform a function in a scientific inve... no TextValue A basic string value no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no MagBin no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no GeneProduct A molecule encoded by a gene that has an evolved function no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no Study A study summarizes the overall goal of a research initiative and outlines the... no PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no Extraction A material separation in which a desired component of an input material is se... no ImageValue An attribute value representing an image no CalibrationInformation A calibration object that is associated with a process no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Protocol no Pooling physical combination of several instances of like material no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no OntologyClass no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no GeolocationValue A normalized value for a location on the earth's surface no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetaproteomicsAnalysis no FunctionalAnnotationAggMember no FiltrationProcess The process of segregation of phases; e no Doi A centrally registered identifier symbol used to uniquely identify objects gi... no MetabolomicsAnalysis no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ProtocolExecution A PlannedProces that has PlannedProcess parts no Manifest no OrthologyGroup A set of genes or gene products in which all members are orthologous no AttributeValue The value for any value of a attribute for a sample no Biosample Biological source material which can be characterized by an experiment no LibraryPreparation no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no"},{"location":"type/#properties","title":"Properties","text":""},{"location":"type/#examples","title":"Examples","text":"Value nmdc:Biosample nmdc:Study"},{"location":"type/#see-also","title":"See Also","text":""},{"location":"type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"type/#schema-source","title":"Schema Source","text":""},{"location":"type/#linkml-source","title":"LinkML Source","text":"
name: type\ndescription: the class_uri of the class that has been instantiated\nnotes:\n- replaces legacy nmdc:type slot\n- makes it easier to read example data files\n- required for polymorphic MongoDB collections\nexamples:\n- value: nmdc:Biosample\n- value: nmdc:Study\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-schema/issues/1048\n- https://github.com/microbiomedata/nmdc-schema/issues/1233\n- https://github.com/microbiomedata/nmdc-schema/issues/248\nrank: 1000\nslot_uri: rdf:type\ndesignates_type: true\nalias: type\ndomain_of:\n- EukEval\n- FunctionalAnnotationAggMember\n- MobilePhaseSegment\n- PortionOfSubstance\n- MagBin\n- MetaboliteIdentification\n- PeptideQuantification\n- ProteinQuantification\n- GenomeFeature\n- FunctionalAnnotation\n- AttributeValue\n- NamedThing\n- FailureCategorization\n- Protocol\n- CreditAssociation\n- Doi\nrange: uriorcurie\nrequired: true\n\n
"},{"location":"unbinned_contig_num/","title":"Slot: unbinned_contig_num","text":"

URI: nmdc:unbinned_contig_num

"},{"location":"unbinned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"unbinned_contig_num/#properties","title":"Properties","text":""},{"location":"unbinned_contig_num/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"unbinned_contig_num/#schema-source","title":"Schema Source","text":""},{"location":"unbinned_contig_num/#linkml-source","title":"LinkML Source","text":"
name: unbinned_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: unbinned_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\n\n
"},{"location":"url/","title":"Slot: url","text":"

URI: nmdc:url

"},{"location":"url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ImageValue An attribute value representing an image no DataObject An object that primarily consists of symbols that represent information no Protocol no"},{"location":"url/#properties","title":"Properties","text":""},{"location":"url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"url/#schema-source","title":"Schema Source","text":""},{"location":"url/#linkml-source","title":"LinkML Source","text":"
name: url\nnotes:\n- See issue 207 - this clashes with the mixs field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: url\ndomain_of:\n- ImageValue\n- Protocol\n- DataObject\nrange: string\n\n
"},{"location":"value/","title":"Slot: value","text":"

URI: nmdc:value

"},{"location":"value/#properties","title":"Properties","text":""},{"location":"value/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"value/#schema-source","title":"Schema Source","text":""},{"location":"value/#linkml-source","title":"LinkML Source","text":"
name: value\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: value\nrange: QuantityValue\n\n
"},{"location":"vendor/","title":"Slot: vendor","text":"

URI: nmdc:vendor

"},{"location":"vendor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Instrument A material entity that is designed to perform a function in a scientific inve... no"},{"location":"vendor/#properties","title":"Properties","text":""},{"location":"vendor/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"vendor/#schema-source","title":"Schema Source","text":""},{"location":"vendor/#linkml-source","title":"LinkML Source","text":"
name: vendor\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: vendor\ndomain_of:\n- Instrument\nrange: InstrumentVendorEnum\n\n
"},{"location":"ventilation_rate/","title":"Slot: ventilation rate (ventilation_rate)","text":"

Ventilation rate of the system in the sampled premises

URI: MIXS:0000114

"},{"location":"ventilation_rate/#inheritance","title":"Inheritance","text":""},{"location":"ventilation_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ventilation_rate/#properties","title":"Properties","text":""},{"location":"ventilation_rate/#aliases","title":"Aliases","text":""},{"location":"ventilation_rate/#examples","title":"Examples","text":"Value 750 cubic meter per minute"},{"location":"ventilation_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ventilation_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"ventilation_rate/#schema-source","title":"Schema Source","text":""},{"location":"ventilation_rate/#linkml-source","title":"LinkML Source","text":"
name: ventilation_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic meter per minute, liters per second\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Ventilation rate of the system in the sampled premises\ntitle: ventilation rate\nexamples:\n- value: 750 cubic meter per minute\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000114\nalias: ventilation_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"ventilation_type/","title":"Slot: ventilation type (ventilation_type)","text":"

Ventilation system used in the sampled premises

URI: MIXS:0000756

"},{"location":"ventilation_type/#inheritance","title":"Inheritance","text":""},{"location":"ventilation_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ventilation_type/#properties","title":"Properties","text":""},{"location":"ventilation_type/#aliases","title":"Aliases","text":""},{"location":"ventilation_type/#examples","title":"Examples","text":"Value Operable windows"},{"location":"ventilation_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ventilation_type/#annotations","title":"Annotations","text":"property value expected_value ventilation type name"},{"location":"ventilation_type/#schema-source","title":"Schema Source","text":""},{"location":"ventilation_type/#linkml-source","title":"LinkML Source","text":"
name: ventilation_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: ventilation type name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Ventilation system used in the sampled premises\ntitle: ventilation type\nexamples:\n- value: Operable windows\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000756\nalias: ventilation_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"version/","title":"Slot: version","text":"

URI: nmdc:version

"},{"location":"version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetatranscriptomeAssembly no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetabolomicsAnalysis no NomAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetaproteomicsAnalysis no"},{"location":"version/#properties","title":"Properties","text":""},{"location":"version/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"version/#schema-source","title":"Schema Source","text":""},{"location":"version/#linkml-source","title":"LinkML Source","text":"
name: version\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: version\ndomain_of:\n- WorkflowExecution\nrange: string\n\n
"},{"location":"vfa/","title":"Slot: volatile fatty acids (vfa)","text":"

Concentration of Volatile Fatty Acids in the sample

URI: MIXS:0000152

"},{"location":"vfa/#inheritance","title":"Inheritance","text":""},{"location":"vfa/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"vfa/#properties","title":"Properties","text":""},{"location":"vfa/#aliases","title":"Aliases","text":""},{"location":"vfa/#examples","title":"Examples","text":"Value"},{"location":"vfa/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"vfa/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"vfa/#schema-source","title":"Schema Source","text":""},{"location":"vfa/#linkml-source","title":"LinkML Source","text":"
name: vfa\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of Volatile Fatty Acids in the sample\ntitle: volatile fatty acids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile fatty acids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000152\nalias: vfa\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"vfa_fw/","title":"Slot: vfa in formation water (vfa_fw)","text":"

Original volatile fatty acid concentration in the hydrocarbon resource

URI: MIXS:0000408

"},{"location":"vfa_fw/#inheritance","title":"Inheritance","text":""},{"location":"vfa_fw/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"vfa_fw/#properties","title":"Properties","text":""},{"location":"vfa_fw/#aliases","title":"Aliases","text":""},{"location":"vfa_fw/#examples","title":"Examples","text":"Value"},{"location":"vfa_fw/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"vfa_fw/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"vfa_fw/#schema-source","title":"Schema Source","text":""},{"location":"vfa_fw/#linkml-source","title":"LinkML Source","text":"
name: vfa_fw\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Original volatile fatty acid concentration in the hydrocarbon resource\ntitle: vfa in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- vfa in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000408\nalias: vfa_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"vis_media/","title":"Slot: visual media (vis_media)","text":"

The building visual media

URI: MIXS:0000840

"},{"location":"vis_media/#inheritance","title":"Inheritance","text":""},{"location":"vis_media/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"vis_media/#properties","title":"Properties","text":""},{"location":"vis_media/#aliases","title":"Aliases","text":""},{"location":"vis_media/#examples","title":"Examples","text":"Value 3D scans"},{"location":"vis_media/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"vis_media/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"vis_media/#schema-source","title":"Schema Source","text":""},{"location":"vis_media/#linkml-source","title":"LinkML Source","text":"
name: vis_media\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The building visual media\ntitle: visual media\nexamples:\n- value: 3D scans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- visual media\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000840\nalias: vis_media\ndomain_of:\n- Biosample\nrange: vis_media_enum\nmultivalued: false\n\n
"},{"location":"viscosity/","title":"Slot: viscosity (viscosity)","text":"

A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)

URI: MIXS:0000126

"},{"location":"viscosity/#inheritance","title":"Inheritance","text":""},{"location":"viscosity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"viscosity/#properties","title":"Properties","text":""},{"location":"viscosity/#aliases","title":"Aliases","text":""},{"location":"viscosity/#examples","title":"Examples","text":"Value"},{"location":"viscosity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"viscosity/#annotations","title":"Annotations","text":"property value expected_value measurement value;measurement value"},{"location":"viscosity/#schema-source","title":"Schema Source","text":""},{"location":"viscosity/#linkml-source","title":"LinkML Source","text":"
name: viscosity\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cP at degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n  stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\ntitle: viscosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- viscosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000126\nalias: viscosity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"volatile_org_comp/","title":"Slot: volatile organic compounds (volatile_org_comp)","text":"

Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound

URI: MIXS:0000115

"},{"location":"volatile_org_comp/#inheritance","title":"Inheritance","text":""},{"location":"volatile_org_comp/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"volatile_org_comp/#properties","title":"Properties","text":""},{"location":"volatile_org_comp/#aliases","title":"Aliases","text":""},{"location":"volatile_org_comp/#examples","title":"Examples","text":"Value formaldehyde;500 nanogram per liter"},{"location":"volatile_org_comp/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"volatile_org_comp/#annotations","title":"Annotations","text":"property value expected_value volatile organic compound name;measurement value"},{"location":"volatile_org_comp/#schema-source","title":"Schema Source","text":""},{"location":"volatile_org_comp/#linkml-source","title":"LinkML Source","text":"
name: volatile_org_comp\nannotations:\n  expected_value:\n    tag: expected_value\n    value: volatile organic compound name;measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: microgram per cubic meter, parts per million, nanogram per liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Concentration of carbon-based chemicals that easily evaporate at room\n  temperature; can report multiple volatile organic compounds by entering numeric\n  values preceded by name of compound\ntitle: volatile organic compounds\nexamples:\n- value: formaldehyde;500 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile organic compounds\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000115\nalias: volatile_org_comp\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"volume/","title":"Slot: volume","text":"

The volume of a substance.

URI: nmdc:volume

"},{"location":"volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes FiltrationProcess The process of segregation of phases; e yes Extraction A material separation in which a desired component of an input material is se... yes PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no"},{"location":"volume/#properties","title":"Properties","text":""},{"location":"volume/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"volume/#schema-source","title":"Schema Source","text":""},{"location":"volume/#linkml-source","title":"LinkML Source","text":"
name: volume\ndescription: The volume of a substance.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: volume\ndomain_of:\n- Extraction\n- SubSamplingProcess\n- FiltrationProcess\n- MobilePhaseSegment\n- PortionOfSubstance\nrange: QuantityValue\n\n
"},{"location":"wall_area/","title":"Slot: wall area (wall_area)","text":"

The total area of the sampled room's walls

URI: MIXS:0000198

"},{"location":"wall_area/#inheritance","title":"Inheritance","text":""},{"location":"wall_area/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_area/#properties","title":"Properties","text":""},{"location":"wall_area/#aliases","title":"Aliases","text":""},{"location":"wall_area/#examples","title":"Examples","text":"Value"},{"location":"wall_area/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_area/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"wall_area/#schema-source","title":"Schema Source","text":""},{"location":"wall_area/#linkml-source","title":"LinkML Source","text":"
name: wall_area\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The total area of the sampled room's walls\ntitle: wall area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000198\nalias: wall_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"wall_const_type/","title":"Slot: wall construction type (wall_const_type)","text":"

The building class of the wall defined by the composition of the building elements and fire-resistance rating.

URI: MIXS:0000841

"},{"location":"wall_const_type/#inheritance","title":"Inheritance","text":""},{"location":"wall_const_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_const_type/#properties","title":"Properties","text":""},{"location":"wall_const_type/#aliases","title":"Aliases","text":""},{"location":"wall_const_type/#examples","title":"Examples","text":"Value fire resistive"},{"location":"wall_const_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_const_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_const_type/#schema-source","title":"Schema Source","text":""},{"location":"wall_const_type/#linkml-source","title":"LinkML Source","text":"
name: wall_const_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The building class of the wall defined by the composition of the building\n  elements and fire-resistance rating.\ntitle: wall construction type\nexamples:\n- value: fire resistive\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall construction type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000841\nalias: wall_const_type\ndomain_of:\n- Biosample\nrange: wall_const_type_enum\nmultivalued: false\n\n
"},{"location":"wall_finish_mat/","title":"Slot: wall finish material (wall_finish_mat)","text":"

The material utilized to finish the outer most layer of the wall

URI: MIXS:0000842

"},{"location":"wall_finish_mat/#inheritance","title":"Inheritance","text":""},{"location":"wall_finish_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_finish_mat/#properties","title":"Properties","text":""},{"location":"wall_finish_mat/#aliases","title":"Aliases","text":""},{"location":"wall_finish_mat/#examples","title":"Examples","text":"Value wood"},{"location":"wall_finish_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_finish_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_finish_mat/#schema-source","title":"Schema Source","text":""},{"location":"wall_finish_mat/#linkml-source","title":"LinkML Source","text":"
name: wall_finish_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The material utilized to finish the outer most layer of the wall\ntitle: wall finish material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000842\nalias: wall_finish_mat\ndomain_of:\n- Biosample\nrange: wall_finish_mat_enum\nmultivalued: false\n\n
"},{"location":"wall_height/","title":"Slot: wall height (wall_height)","text":"

The average height of the walls in the sampled room

URI: MIXS:0000221

"},{"location":"wall_height/#inheritance","title":"Inheritance","text":""},{"location":"wall_height/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_height/#properties","title":"Properties","text":""},{"location":"wall_height/#aliases","title":"Aliases","text":""},{"location":"wall_height/#examples","title":"Examples","text":"Value"},{"location":"wall_height/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_height/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"wall_height/#schema-source","title":"Schema Source","text":""},{"location":"wall_height/#linkml-source","title":"LinkML Source","text":"
name: wall_height\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  preferred_unit:\n    tag: preferred_unit\n    value: centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The average height of the walls in the sampled room\ntitle: wall height\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000221\nalias: wall_height\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"wall_loc/","title":"Slot: wall location (wall_loc)","text":"

The relative location of the wall within the room

URI: MIXS:0000843

"},{"location":"wall_loc/#inheritance","title":"Inheritance","text":""},{"location":"wall_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_loc/#properties","title":"Properties","text":""},{"location":"wall_loc/#aliases","title":"Aliases","text":""},{"location":"wall_loc/#examples","title":"Examples","text":"Value north"},{"location":"wall_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_loc/#schema-source","title":"Schema Source","text":""},{"location":"wall_loc/#linkml-source","title":"LinkML Source","text":"
name: wall_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The relative location of the wall within the room\ntitle: wall location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000843\nalias: wall_loc\ndomain_of:\n- Biosample\nrange: wall_loc_enum\nmultivalued: false\n\n
"},{"location":"wall_surf_treatment/","title":"Slot: wall surface treatment (wall_surf_treatment)","text":"

The surface treatment of interior wall

URI: MIXS:0000845

"},{"location":"wall_surf_treatment/#inheritance","title":"Inheritance","text":""},{"location":"wall_surf_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_surf_treatment/#properties","title":"Properties","text":""},{"location":"wall_surf_treatment/#aliases","title":"Aliases","text":""},{"location":"wall_surf_treatment/#examples","title":"Examples","text":"Value paneling"},{"location":"wall_surf_treatment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_surf_treatment/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_surf_treatment/#schema-source","title":"Schema Source","text":""},{"location":"wall_surf_treatment/#linkml-source","title":"LinkML Source","text":"
name: wall_surf_treatment\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The surface treatment of interior wall\ntitle: wall surface treatment\nexamples:\n- value: paneling\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall surface treatment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000845\nalias: wall_surf_treatment\ndomain_of:\n- Biosample\nrange: wall_surf_treatment_enum\nmultivalued: false\n\n
"},{"location":"wall_texture/","title":"Slot: wall texture (wall_texture)","text":"

The feel, appearance, or consistency of a wall surface

URI: MIXS:0000846

"},{"location":"wall_texture/#inheritance","title":"Inheritance","text":""},{"location":"wall_texture/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_texture/#properties","title":"Properties","text":""},{"location":"wall_texture/#aliases","title":"Aliases","text":""},{"location":"wall_texture/#examples","title":"Examples","text":"Value popcorn"},{"location":"wall_texture/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_texture/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_texture/#schema-source","title":"Schema Source","text":""},{"location":"wall_texture/#linkml-source","title":"LinkML Source","text":"
name: wall_texture\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The feel, appearance, or consistency of a wall surface\ntitle: wall texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000846\nalias: wall_texture\ndomain_of:\n- Biosample\nrange: wall_texture_enum\nmultivalued: false\n\n
"},{"location":"wall_thermal_mass/","title":"Slot: wall thermal mass (wall_thermal_mass)","text":"

The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint

URI: MIXS:0000222

"},{"location":"wall_thermal_mass/#inheritance","title":"Inheritance","text":""},{"location":"wall_thermal_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_thermal_mass/#properties","title":"Properties","text":""},{"location":"wall_thermal_mass/#aliases","title":"Aliases","text":""},{"location":"wall_thermal_mass/#examples","title":"Examples","text":"Value"},{"location":"wall_thermal_mass/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_thermal_mass/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"wall_thermal_mass/#schema-source","title":"Schema Source","text":""},{"location":"wall_thermal_mass/#linkml-source","title":"LinkML Source","text":"
name: wall_thermal_mass\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: joule per degree Celsius\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The ability of the wall to provide inertia against temperature fluctuations.\n  Generally this means concrete or concrete block that is either exposed or covered\n  only with paint\ntitle: wall thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000222\nalias: wall_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"wall_water_mold/","title":"Slot: wall signs of water/mold (wall_water_mold)","text":"

Signs of the presence of mold or mildew on a wall

URI: MIXS:0000844

"},{"location":"wall_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"wall_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wall_water_mold/#properties","title":"Properties","text":""},{"location":"wall_water_mold/#aliases","title":"Aliases","text":""},{"location":"wall_water_mold/#examples","title":"Examples","text":"Value no presence of mold visible"},{"location":"wall_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wall_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"wall_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"wall_water_mold/#linkml-source","title":"LinkML Source","text":"
name: wall_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on a wall\ntitle: wall signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000844\nalias: wall_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"was_generated_by/","title":"Slot: was_generated_by","text":"

URI: nmdc:was_generated_by

"},{"location":"was_generated_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e yes DataObject An object that primarily consists of symbols that represent information yes"},{"location":"was_generated_by/#properties","title":"Properties","text":""},{"location":"was_generated_by/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"was_generated_by/#schema-source","title":"Schema Source","text":""},{"location":"was_generated_by/#linkml-source","title":"LinkML Source","text":"
name: was_generated_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasGeneratedBy\nrank: 1000\nalias: was_generated_by\ndomain_of:\n- FunctionalAnnotation\n- DataObject\nrange: WorkflowExecution\nany_of:\n- range: WorkflowExecution\n- range: DataGeneration\n\n
"},{"location":"was_informed_by/","title":"Slot: was_informed_by","text":"

URI: nmdc:was_informed_by

"},{"location":"was_informed_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecution Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes MetatranscriptomeAnnotation yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes MetatranscriptomeAssembly yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... yes MetagenomeSequencing Initial sequencing activity that precedes any analysis yes MetabolomicsAnalysis yes NomAnalysis yes ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... yes MetaproteomicsAnalysis yes"},{"location":"was_informed_by/#properties","title":"Properties","text":""},{"location":"was_informed_by/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"was_informed_by/#schema-source","title":"Schema Source","text":""},{"location":"was_informed_by/#linkml-source","title":"LinkML Source","text":"
name: was_informed_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasInformedBy\nrank: 1000\nalias: was_informed_by\ndomain_of:\n- WorkflowExecution\nrange: DataGeneration\n\n
"},{"location":"wastewater_type/","title":"Slot: wastewater type (wastewater_type)","text":"

The origin of wastewater such as human waste, rainfall, storm drains, etc.

URI: MIXS:0000353

"},{"location":"wastewater_type/#inheritance","title":"Inheritance","text":""},{"location":"wastewater_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wastewater_type/#properties","title":"Properties","text":""},{"location":"wastewater_type/#aliases","title":"Aliases","text":""},{"location":"wastewater_type/#examples","title":"Examples","text":"Value"},{"location":"wastewater_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wastewater_type/#annotations","title":"Annotations","text":"property value expected_value wastewater type name"},{"location":"wastewater_type/#schema-source","title":"Schema Source","text":""},{"location":"wastewater_type/#linkml-source","title":"LinkML Source","text":"
name: wastewater_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: wastewater type name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The origin of wastewater such as human waste, rainfall, storm drains,\n  etc.\ntitle: wastewater type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wastewater type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000353\nalias: wastewater_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"water_cont_soil_meth/","title":"Slot: water content method (water_cont_soil_meth)","text":"

Reference or method used in determining the water content of soil

URI: MIXS:0000323

"},{"location":"water_cont_soil_meth/#inheritance","title":"Inheritance","text":""},{"location":"water_cont_soil_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"water_cont_soil_meth/#properties","title":"Properties","text":""},{"location":"water_cont_soil_meth/#aliases","title":"Aliases","text":""},{"location":"water_cont_soil_meth/#examples","title":"Examples","text":"Value"},{"location":"water_cont_soil_meth/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_cont_soil_meth/#annotations","title":"Annotations","text":"property value expected_value PMID,DOI or url"},{"location":"water_cont_soil_meth/#schema-source","title":"Schema Source","text":""},{"location":"water_cont_soil_meth/#linkml-source","title":"LinkML Source","text":"
name: water_cont_soil_meth\nannotations:\n  expected_value:\n    tag: expected_value\n    value: PMID,DOI or url\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Reference or method used in determining the water content of soil\ntitle: water content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000323\nalias: water_cont_soil_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"water_content/","title":"Slot: water content (water_content)","text":"

Water content measurement

URI: MIXS:0000185

"},{"location":"water_content/#inheritance","title":"Inheritance","text":""},{"location":"water_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"water_content/#properties","title":"Properties","text":""},{"location":"water_content/#aliases","title":"Aliases","text":""},{"location":"water_content/#examples","title":"Examples","text":"Value"},{"location":"water_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_content/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_content/#schema-source","title":"Schema Source","text":""},{"location":"water_content/#linkml-source","title":"LinkML Source","text":"
name: water_content\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: gram per gram or cubic centimeter per cubic centimeter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Water content measurement\ntitle: water content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000185\nalias: water_content\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\n
"},{"location":"water_current/","title":"Slot: water current (water_current)","text":"

Measurement of magnitude and direction of flow within a fluid

URI: MIXS:0000203

"},{"location":"water_current/#inheritance","title":"Inheritance","text":""},{"location":"water_current/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_current/#properties","title":"Properties","text":""},{"location":"water_current/#aliases","title":"Aliases","text":""},{"location":"water_current/#examples","title":"Examples","text":"Value 10 cubic meter per second"},{"location":"water_current/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_current/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_current/#schema-source","title":"Schema Source","text":""},{"location":"water_current/#linkml-source","title":"LinkML Source","text":"
name: water_current\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic meter per second, knots\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Measurement of magnitude and direction of flow within a fluid\ntitle: water current\nexamples:\n- value: 10 cubic meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water current\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000203\nalias: water_current\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"water_cut/","title":"Slot: water cut (water_cut)","text":"

Current amount of water (%) in a produced fluid stream; or the average of the combined streams

URI: MIXS:0000454

"},{"location":"water_cut/#inheritance","title":"Inheritance","text":""},{"location":"water_cut/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_cut/#properties","title":"Properties","text":""},{"location":"water_cut/#aliases","title":"Aliases","text":""},{"location":"water_cut/#examples","title":"Examples","text":"Value"},{"location":"water_cut/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_cut/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_cut/#schema-source","title":"Schema Source","text":""},{"location":"water_cut/#linkml-source","title":"LinkML Source","text":"
name: water_cut\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: percent\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Current amount of water (%) in a produced fluid stream; or the average\n  of the combined streams\ntitle: water cut\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water cut\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000454\nalias: water_cut\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"water_feat_size/","title":"Slot: water feature size (water_feat_size)","text":"

The size of the water feature

URI: MIXS:0000223

"},{"location":"water_feat_size/#inheritance","title":"Inheritance","text":""},{"location":"water_feat_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_feat_size/#properties","title":"Properties","text":""},{"location":"water_feat_size/#aliases","title":"Aliases","text":""},{"location":"water_feat_size/#examples","title":"Examples","text":"Value"},{"location":"water_feat_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_feat_size/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_feat_size/#schema-source","title":"Schema Source","text":""},{"location":"water_feat_size/#linkml-source","title":"LinkML Source","text":"
name: water_feat_size\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: square meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The size of the water feature\ntitle: water feature size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000223\nalias: water_feat_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"water_feat_type/","title":"Slot: water feature type (water_feat_type)","text":"

The type of water feature present within the building being sampled

URI: MIXS:0000847

"},{"location":"water_feat_type/#inheritance","title":"Inheritance","text":""},{"location":"water_feat_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_feat_type/#properties","title":"Properties","text":""},{"location":"water_feat_type/#aliases","title":"Aliases","text":""},{"location":"water_feat_type/#examples","title":"Examples","text":"Value stream"},{"location":"water_feat_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_feat_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"water_feat_type/#schema-source","title":"Schema Source","text":""},{"location":"water_feat_type/#linkml-source","title":"LinkML Source","text":"
name: water_feat_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of water feature present within the building being sampled\ntitle: water feature type\nexamples:\n- value: stream\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000847\nalias: water_feat_type\ndomain_of:\n- Biosample\nrange: water_feat_type_enum\nmultivalued: false\n\n
"},{"location":"water_prod_rate/","title":"Slot: water production rate (water_prod_rate)","text":"

Water production rates per well (e.g. 987 m3 / day)

URI: MIXS:0000453

"},{"location":"water_prod_rate/#inheritance","title":"Inheritance","text":""},{"location":"water_prod_rate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_prod_rate/#properties","title":"Properties","text":""},{"location":"water_prod_rate/#aliases","title":"Aliases","text":""},{"location":"water_prod_rate/#examples","title":"Examples","text":"Value"},{"location":"water_prod_rate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_prod_rate/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"water_prod_rate/#schema-source","title":"Schema Source","text":""},{"location":"water_prod_rate/#linkml-source","title":"LinkML Source","text":"
name: water_prod_rate\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: cubic meter per day\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Water production rates per well (e.g. 987 m3 / day)\ntitle: water production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000453\nalias: water_prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"water_temp_regm/","title":"Slot: water temperature regimen (water_temp_regm)","text":"

Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000590

"},{"location":"water_temp_regm/#inheritance","title":"Inheritance","text":""},{"location":"water_temp_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"water_temp_regm/#properties","title":"Properties","text":""},{"location":"water_temp_regm/#aliases","title":"Aliases","text":""},{"location":"water_temp_regm/#examples","title":"Examples","text":"Value 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"water_temp_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"water_temp_regm/#annotations","title":"Annotations","text":"property value expected_value measurement value;treatment interval and duration"},{"location":"water_temp_regm/#schema-source","title":"Schema Source","text":""},{"location":"water_temp_regm/#linkml-source","title":"LinkML Source","text":"
name: water_temp_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: degree Celsius\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to water with varying\n  degree of temperature, treatment regimen including how many times the treatment\n  was repeated, how long each treatment lasted, and the start and end time of the\n  entire treatment; can include multiple regimens\ntitle: water temperature regimen\nexamples:\n- value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000590\nalias: water_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"watering_regm/","title":"Slot: watering regimen (watering_regm)","text":"

Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens

URI: MIXS:0000591

"},{"location":"watering_regm/#inheritance","title":"Inheritance","text":""},{"location":"watering_regm/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"watering_regm/#properties","title":"Properties","text":""},{"location":"watering_regm/#aliases","title":"Aliases","text":""},{"location":"watering_regm/#examples","title":"Examples","text":"Value 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M"},{"location":"watering_regm/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"watering_regm/#annotations","title":"Annotations","text":"property value expected_value measurement value;treatment interval and duration"},{"location":"watering_regm/#schema-source","title":"Schema Source","text":""},{"location":"watering_regm/#linkml-source","title":"LinkML Source","text":"
name: watering_regm\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value;treatment interval and duration\n  preferred_unit:\n    tag: preferred_unit\n    value: milliliter, liter\n  occurrence:\n    tag: occurrence\n    value: m\ndescription: Information about treatment involving an exposure to watering frequencies,\n  treatment regimen including how many times the treatment was repeated, how long\n  each treatment lasted, and the start and end time of the entire treatment; can include\n  multiple regimens\ntitle: watering regimen\nexamples:\n- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- watering regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000591\nalias: watering_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"websites/","title":"Slot: websites","text":"

A list of websites that are associated with the entity.

URI: nmdc:websites

"},{"location":"websites/#inheritance","title":"Inheritance","text":""},{"location":"websites/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes PersonValue An attribute value representing a person no"},{"location":"websites/#properties","title":"Properties","text":""},{"location":"websites/#comments","title":"Comments","text":""},{"location":"websites/#see-also","title":"See Also","text":""},{"location":"websites/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"websites/#schema-source","title":"Schema Source","text":""},{"location":"websites/#linkml-source","title":"LinkML Source","text":"
name: websites\ndescription: A list of websites that are associated with the entity.\ncomments:\n- DOIs should not be included as websites. Instead, use the associated_dois slot.\n- A consortium's homepage website should be included in the homepage_website slot,\n  not in websites.\n- consortium is a convenience term for a Study whose study_category value is consortium\n- the website slot and its subproperties are virtually identical to the url slot,\n  except that they are multivalued and url is single-valued.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:url\nrank: 1000\nalias: websites\ndomain_of:\n- PersonValue\n- Study\nrange: string\nmultivalued: true\npattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n\n
"},{"location":"weekday/","title":"Slot: weekday (weekday)","text":"

The day of the week when sampling occurred

URI: MIXS:0000848

"},{"location":"weekday/#inheritance","title":"Inheritance","text":""},{"location":"weekday/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"weekday/#properties","title":"Properties","text":""},{"location":"weekday/#aliases","title":"Aliases","text":""},{"location":"weekday/#examples","title":"Examples","text":"Value Sunday"},{"location":"weekday/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"weekday/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"weekday/#schema-source","title":"Schema Source","text":""},{"location":"weekday/#linkml-source","title":"LinkML Source","text":"
name: weekday\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The day of the week when sampling occurred\ntitle: weekday\nexamples:\n- value: Sunday\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weekday\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000848\nalias: weekday\ndomain_of:\n- Biosample\nrange: weekday_enum\nmultivalued: false\n\n
"},{"location":"win/","title":"Slot: well identification number (win)","text":"

A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)

URI: MIXS:0000297

"},{"location":"win/#inheritance","title":"Inheritance","text":""},{"location":"win/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"win/#properties","title":"Properties","text":""},{"location":"win/#aliases","title":"Aliases","text":""},{"location":"win/#examples","title":"Examples","text":"Value"},{"location":"win/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"win/#annotations","title":"Annotations","text":"property value expected_value text"},{"location":"win/#schema-source","title":"Schema Source","text":""},{"location":"win/#linkml-source","title":"LinkML Source","text":"
name: win\nannotations:\n  expected_value:\n    tag: expected_value\n    value: text\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: 'A unique identifier of a well or wellbore. This is part of the Global\n  Framework for Well Identification initiative which is compiled by the Professional\n  Petroleum Data Management Association (PPDM) in an effort to improve well identification\n  systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\ntitle: well identification number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- well identification number\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000297\nalias: win\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"wind_direction/","title":"Slot: wind direction (wind_direction)","text":"

Wind direction is the direction from which a wind originates

URI: MIXS:0000757

"},{"location":"wind_direction/#inheritance","title":"Inheritance","text":""},{"location":"wind_direction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wind_direction/#properties","title":"Properties","text":""},{"location":"wind_direction/#aliases","title":"Aliases","text":""},{"location":"wind_direction/#examples","title":"Examples","text":"Value Northwest"},{"location":"wind_direction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wind_direction/#annotations","title":"Annotations","text":"property value expected_value wind direction name"},{"location":"wind_direction/#schema-source","title":"Schema Source","text":""},{"location":"wind_direction/#linkml-source","title":"LinkML Source","text":"
name: wind_direction\nannotations:\n  expected_value:\n    tag: expected_value\n    value: wind direction name\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Wind direction is the direction from which a wind originates\ntitle: wind direction\nexamples:\n- value: Northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind direction\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000757\nalias: wind_direction\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"wind_speed/","title":"Slot: wind speed (wind_speed)","text":"

Speed of wind measured at the time of sampling

URI: MIXS:0000118

"},{"location":"wind_speed/#inheritance","title":"Inheritance","text":""},{"location":"wind_speed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"wind_speed/#properties","title":"Properties","text":""},{"location":"wind_speed/#aliases","title":"Aliases","text":""},{"location":"wind_speed/#examples","title":"Examples","text":"Value 21 kilometer per hour"},{"location":"wind_speed/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"wind_speed/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"wind_speed/#schema-source","title":"Schema Source","text":""},{"location":"wind_speed/#linkml-source","title":"LinkML Source","text":"
name: wind_speed\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: meter per second, kilometer per hour\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Speed of wind measured at the time of sampling\ntitle: wind speed\nexamples:\n- value: 21 kilometer per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind speed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000118\nalias: wind_speed\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"window_cond/","title":"Slot: window condition (window_cond)","text":"

The physical condition of the window at the time of sampling

URI: MIXS:0000849

"},{"location":"window_cond/#inheritance","title":"Inheritance","text":""},{"location":"window_cond/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_cond/#properties","title":"Properties","text":""},{"location":"window_cond/#aliases","title":"Aliases","text":""},{"location":"window_cond/#examples","title":"Examples","text":"Value rupture"},{"location":"window_cond/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_cond/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_cond/#schema-source","title":"Schema Source","text":""},{"location":"window_cond/#linkml-source","title":"LinkML Source","text":"
name: window_cond\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The physical condition of the window at the time of sampling\ntitle: window condition\nexamples:\n- value: rupture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000849\nalias: window_cond\ndomain_of:\n- Biosample\nrange: window_cond_enum\nmultivalued: false\n\n
"},{"location":"window_cover/","title":"Slot: window covering (window_cover)","text":"

The type of window covering

URI: MIXS:0000850

"},{"location":"window_cover/#inheritance","title":"Inheritance","text":""},{"location":"window_cover/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_cover/#properties","title":"Properties","text":""},{"location":"window_cover/#aliases","title":"Aliases","text":""},{"location":"window_cover/#examples","title":"Examples","text":"Value curtains"},{"location":"window_cover/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_cover/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_cover/#schema-source","title":"Schema Source","text":""},{"location":"window_cover/#linkml-source","title":"LinkML Source","text":"
name: window_cover\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of window covering\ntitle: window covering\nexamples:\n- value: curtains\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window covering\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000850\nalias: window_cover\ndomain_of:\n- Biosample\nrange: window_cover_enum\nmultivalued: false\n\n
"},{"location":"window_horiz_pos/","title":"Slot: window horizontal position (window_horiz_pos)","text":"

The horizontal position of the window on the wall

URI: MIXS:0000851

"},{"location":"window_horiz_pos/#inheritance","title":"Inheritance","text":""},{"location":"window_horiz_pos/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_horiz_pos/#properties","title":"Properties","text":""},{"location":"window_horiz_pos/#aliases","title":"Aliases","text":""},{"location":"window_horiz_pos/#examples","title":"Examples","text":"Value middle"},{"location":"window_horiz_pos/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_horiz_pos/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_horiz_pos/#schema-source","title":"Schema Source","text":""},{"location":"window_horiz_pos/#linkml-source","title":"LinkML Source","text":"
name: window_horiz_pos\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The horizontal position of the window on the wall\ntitle: window horizontal position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window horizontal position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000851\nalias: window_horiz_pos\ndomain_of:\n- Biosample\nrange: window_horiz_pos_enum\nmultivalued: false\n\n
"},{"location":"window_loc/","title":"Slot: window location (window_loc)","text":"

The relative location of the window within the room

URI: MIXS:0000852

"},{"location":"window_loc/#inheritance","title":"Inheritance","text":""},{"location":"window_loc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_loc/#properties","title":"Properties","text":""},{"location":"window_loc/#aliases","title":"Aliases","text":""},{"location":"window_loc/#examples","title":"Examples","text":"Value west"},{"location":"window_loc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_loc/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_loc/#schema-source","title":"Schema Source","text":""},{"location":"window_loc/#linkml-source","title":"LinkML Source","text":"
name: window_loc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The relative location of the window within the room\ntitle: window location\nexamples:\n- value: west\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000852\nalias: window_loc\ndomain_of:\n- Biosample\nrange: window_loc_enum\nmultivalued: false\n\n
"},{"location":"window_mat/","title":"Slot: window material (window_mat)","text":"

The type of material used to finish a window

URI: MIXS:0000853

"},{"location":"window_mat/#inheritance","title":"Inheritance","text":""},{"location":"window_mat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_mat/#properties","title":"Properties","text":""},{"location":"window_mat/#aliases","title":"Aliases","text":""},{"location":"window_mat/#examples","title":"Examples","text":"Value wood"},{"location":"window_mat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_mat/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_mat/#schema-source","title":"Schema Source","text":""},{"location":"window_mat/#linkml-source","title":"LinkML Source","text":"
name: window_mat\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of material used to finish a window\ntitle: window material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000853\nalias: window_mat\ndomain_of:\n- Biosample\nrange: window_mat_enum\nmultivalued: false\n\n
"},{"location":"window_open_freq/","title":"Slot: window open frequency (window_open_freq)","text":"

The number of times windows are opened per week

URI: MIXS:0000246

"},{"location":"window_open_freq/#inheritance","title":"Inheritance","text":""},{"location":"window_open_freq/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_open_freq/#properties","title":"Properties","text":""},{"location":"window_open_freq/#aliases","title":"Aliases","text":""},{"location":"window_open_freq/#examples","title":"Examples","text":"Value"},{"location":"window_open_freq/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_open_freq/#annotations","title":"Annotations","text":"property value expected_value value"},{"location":"window_open_freq/#schema-source","title":"Schema Source","text":""},{"location":"window_open_freq/#linkml-source","title":"LinkML Source","text":"
name: window_open_freq\nannotations:\n  expected_value:\n    tag: expected_value\n    value: value\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The number of times windows are opened per week\ntitle: window open frequency\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window open frequency\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000246\nalias: window_open_freq\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"window_size/","title":"Slot: window area/size (window_size)","text":"

The window's length and width

URI: MIXS:0000224

"},{"location":"window_size/#inheritance","title":"Inheritance","text":""},{"location":"window_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_size/#properties","title":"Properties","text":""},{"location":"window_size/#aliases","title":"Aliases","text":""},{"location":"window_size/#examples","title":"Examples","text":"Value"},{"location":"window_size/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_size/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"window_size/#schema-source","title":"Schema Source","text":""},{"location":"window_size/#linkml-source","title":"LinkML Source","text":"
name: window_size\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: inch, meter\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The window's length and width\ntitle: window area/size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window area/size\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit} x {float} {unit}'\nslot_uri: MIXS:0000224\nalias: window_size\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"window_status/","title":"Slot: window status (window_status)","text":"

Defines whether the windows were open or closed during environmental testing

URI: MIXS:0000855

"},{"location":"window_status/#inheritance","title":"Inheritance","text":""},{"location":"window_status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_status/#properties","title":"Properties","text":""},{"location":"window_status/#aliases","title":"Aliases","text":""},{"location":"window_status/#examples","title":"Examples","text":"Value open"},{"location":"window_status/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_status/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_status/#schema-source","title":"Schema Source","text":""},{"location":"window_status/#linkml-source","title":"LinkML Source","text":"
name: window_status\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Defines whether the windows were open or closed during environmental\n  testing\ntitle: window status\nexamples:\n- value: open\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window status\nrank: 1000\nis_a: core field\nstring_serialization: '[closed|open]'\nslot_uri: MIXS:0000855\nalias: window_status\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"window_type/","title":"Slot: window type (window_type)","text":"

The type of windows

URI: MIXS:0000856

"},{"location":"window_type/#inheritance","title":"Inheritance","text":""},{"location":"window_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_type/#properties","title":"Properties","text":""},{"location":"window_type/#aliases","title":"Aliases","text":""},{"location":"window_type/#examples","title":"Examples","text":"Value fixed window"},{"location":"window_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_type/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_type/#schema-source","title":"Schema Source","text":""},{"location":"window_type/#linkml-source","title":"LinkML Source","text":"
name: window_type\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The type of windows\ntitle: window type\nexamples:\n- value: fixed window\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000856\nalias: window_type\ndomain_of:\n- Biosample\nrange: window_type_enum\nmultivalued: false\n\n
"},{"location":"window_vert_pos/","title":"Slot: window vertical position (window_vert_pos)","text":"

The vertical position of the window on the wall

URI: MIXS:0000857

"},{"location":"window_vert_pos/#inheritance","title":"Inheritance","text":""},{"location":"window_vert_pos/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_vert_pos/#properties","title":"Properties","text":""},{"location":"window_vert_pos/#aliases","title":"Aliases","text":""},{"location":"window_vert_pos/#examples","title":"Examples","text":"Value middle"},{"location":"window_vert_pos/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_vert_pos/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_vert_pos/#schema-source","title":"Schema Source","text":""},{"location":"window_vert_pos/#linkml-source","title":"LinkML Source","text":"
name: window_vert_pos\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: The vertical position of the window on the wall\ntitle: window vertical position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window vertical position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000857\nalias: window_vert_pos\ndomain_of:\n- Biosample\nrange: window_vert_pos_enum\nmultivalued: false\n\n
"},{"location":"window_water_mold/","title":"Slot: window signs of water/mold (window_water_mold)","text":"

Signs of the presence of mold or mildew on the window.

URI: MIXS:0000854

"},{"location":"window_water_mold/#inheritance","title":"Inheritance","text":""},{"location":"window_water_mold/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"window_water_mold/#properties","title":"Properties","text":""},{"location":"window_water_mold/#aliases","title":"Aliases","text":""},{"location":"window_water_mold/#examples","title":"Examples","text":"Value no presence of mold visible"},{"location":"window_water_mold/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"window_water_mold/#annotations","title":"Annotations","text":"property value expected_value enumeration"},{"location":"window_water_mold/#schema-source","title":"Schema Source","text":""},{"location":"window_water_mold/#linkml-source","title":"LinkML Source","text":"
name: window_water_mold\nannotations:\n  expected_value:\n    tag: expected_value\n    value: enumeration\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Signs of the presence of mold or mildew on the window.\ntitle: window signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000854\nalias: window_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\n
"},{"location":"workflow_execution_set/","title":"Slot: workflow_execution_set","text":"

This property links a database object to the set of workflow executions.

URI: nmdc:workflow_execution_set

"},{"location":"workflow_execution_set/#inheritance","title":"Inheritance","text":""},{"location":"workflow_execution_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"workflow_execution_set/#properties","title":"Properties","text":""},{"location":"workflow_execution_set/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"workflow_execution_set/#schema-source","title":"Schema Source","text":""},{"location":"workflow_execution_set/#linkml-source","title":"LinkML Source","text":"
name: workflow_execution_set\ndescription: This property links a database object to the set of workflow executions.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: workflow_execution_set\ndomain_of:\n- Database\nrange: WorkflowExecution\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\n
"},{"location":"xylene/","title":"Slot: xylene (xylene)","text":"

Concentration of xylene in the sample

URI: MIXS:0000156

"},{"location":"xylene/#inheritance","title":"Inheritance","text":""},{"location":"xylene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"xylene/#properties","title":"Properties","text":""},{"location":"xylene/#aliases","title":"Aliases","text":""},{"location":"xylene/#examples","title":"Examples","text":"Value"},{"location":"xylene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"xylene/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"xylene/#schema-source","title":"Schema Source","text":""},{"location":"xylene/#linkml-source","title":"LinkML Source","text":"
name: xylene\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: milligram per liter, parts per million\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of xylene in the sample\ntitle: xylene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- xylene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000156\nalias: xylene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n
"},{"location":"zinc/","title":"Slot: zinc (zinc)","text":"

Concentration of zinc in the sample

URI: nmdc:zinc

"},{"location":"zinc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"zinc/#properties","title":"Properties","text":""},{"location":"zinc/#aliases","title":"Aliases","text":""},{"location":"zinc/#examples","title":"Examples","text":"Value 2.5 mg/kg"},{"location":"zinc/#see-also","title":"See Also","text":""},{"location":"zinc/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"zinc/#annotations","title":"Annotations","text":"property value expected_value measurement value"},{"location":"zinc/#schema-source","title":"Schema Source","text":""},{"location":"zinc/#linkml-source","title":"LinkML Source","text":"
name: zinc\nannotations:\n  expected_value:\n    tag: expected_value\n    value: measurement value\n  preferred_unit:\n    tag: preferred_unit\n    value: mg/kg (ppm)\n  occurrence:\n    tag: occurrence\n    value: '1'\ndescription: Concentration of zinc in the sample\ntitle: zinc\nexamples:\n- value: 2.5 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- zinc\nrank: 1000\nalias: zinc\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n
"}]} \ No newline at end of file diff --git a/pr-preview/pr-2230/soil_type/index.html b/pr-preview/pr-2230/soil_type/index.html index 383533a353..1b7672c462 100644 --- a/pr-preview/pr-2230/soil_type/index.html +++ b/pr-preview/pr-2230/soil_type/index.html @@ -538,13 +538,13 @@

Applicable Classes

-FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected +Biosample +Biological source material which can be characterized by an experiment no -Biosample -Biological source material which can be characterized by an experiment +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected no diff --git a/pr-preview/pr-2230/start_date/index.html b/pr-preview/pr-2230/start_date/index.html index 3a73910313..edb77d6f68 100644 --- a/pr-preview/pr-2230/start_date/index.html +++ b/pr-preview/pr-2230/start_date/index.html @@ -515,58 +515,58 @@

Applicable Classes

-MetaproteomicsAnalysis - +WorkflowExecution +Represents an instance of an execution of a particular workflow no -Extraction -A material separation in which a desired component of an input material is se... +MetatranscriptomeAnnotation + no -WorkflowExecution -Represents an instance of an execution of a particular workflow +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +MetatranscriptomeAssembly + no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +PlannedProcess + no -MetatranscriptomeAnnotation - +MixingProcess +The combining of components, particles or layers into a more homogeneous stat... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -NomAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no @@ -575,43 +575,43 @@

Applicable Classes

no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -MixingProcess -The combining of components, particles or layers into a more homogeneous stat... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetabolomicsAnalysis - +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +NomAnalysis + no -MetatranscriptomeAssembly - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -FiltrationProcess -The process of segregation of phases; e +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -LibraryPreparation - +Extraction +A material separation in which a desired component of an input material is se... no @@ -625,43 +625,43 @@

Applicable Classes

no -PlannedProcess - +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +DataGeneration +The methods and processes used to generate omics data from a biosample or org... no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetaproteomicsAnalysis + no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +FiltrationProcess +The process of segregation of phases; e no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +MetabolomicsAnalysis + no -DataGeneration -The methods and processes used to generate omics data from a biosample or org... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + no diff --git a/pr-preview/pr-2230/started_at_time/index.html b/pr-preview/pr-2230/started_at_time/index.html index 700e8c3991..089ff6c81a 100644 --- a/pr-preview/pr-2230/started_at_time/index.html +++ b/pr-preview/pr-2230/started_at_time/index.html @@ -496,67 +496,67 @@

Applicable Classes

-MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... -no +WorkflowExecution +Represents an instance of an execution of a particular workflow +yes -MetaproteomicsAnalysis - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -NomAnalysis +MetatranscriptomeAnnotation no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -MetabolomicsAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no -WorkflowExecution -Represents an instance of an execution of a particular workflow -yes +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... +no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +MetatranscriptomeAssembly + no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +MetabolomicsAnalysis + no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +NomAnalysis + no -MetatranscriptomeAnnotation - +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetatranscriptomeAssembly +MetaproteomicsAnalysis no diff --git a/pr-preview/pr-2230/substances_used/index.html b/pr-preview/pr-2230/substances_used/index.html index cb295a0952..7115f74c4f 100644 --- a/pr-preview/pr-2230/substances_used/index.html +++ b/pr-preview/pr-2230/substances_used/index.html @@ -512,13 +512,13 @@

Applicable Classes

yes -MobilePhaseSegment -A fluid mixture of substances that flow though a chromatographic stationary p... +DissolvingProcess +A mixing step where a soluble component is mixed with a liquid component no -DissolvingProcess -A mixing step where a soluble component is mixed with a liquid component +MobilePhaseSegment +A fluid mixture of substances that flow though a chromatographic stationary p... no diff --git a/pr-preview/pr-2230/temperature/index.html b/pr-preview/pr-2230/temperature/index.html index e28f3cd858..91e263f3b8 100644 --- a/pr-preview/pr-2230/temperature/index.html +++ b/pr-preview/pr-2230/temperature/index.html @@ -497,13 +497,13 @@

Applicable Classes

-ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no @@ -512,18 +512,18 @@

Applicable Classes

no -DissolvingProcess -A mixing step where a soluble component is mixed with a liquid component +ChromatographyConfiguration +A set of parameters that define and control the actions of a chromatography p... no -ChromatographyConfiguration -A set of parameters that define and control the actions of a chromatography p... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... +DissolvingProcess +A mixing step where a soluble component is mixed with a liquid component no diff --git a/pr-preview/pr-2230/type/index.html b/pr-preview/pr-2230/type/index.html index 1cbbb7b522..67dc86e6f3 100644 --- a/pr-preview/pr-2230/type/index.html +++ b/pr-preview/pr-2230/type/index.html @@ -515,138 +515,123 @@

Applicable Classes

-TimestampValue -A value that is a timestamp +WorkflowExecution +Represents an instance of an execution of a particular workflow no -PortionOfSubstance -A portion of any matter of defined composition that has discrete existence, w... +QuantityValue +A simple quantity, e no -MetaproteomicsAnalysis +MetatranscriptomeAnnotation no -ImageValue -An attribute value representing an image -no - - -EukEval -This class contains information pertaining to evaluating if a Metagenome-Asse... +PersonValue +An attribute value representing a person no -MetaboliteIdentification -This is used to link a metabolomics analysis workflow to a specific metabolit... +GenomeFeature +A feature localized to an interval along a genome no -NamedThing -a databased entity or concept/class +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... no -Extraction -A material separation in which a desired component of an input material is se... +FunctionalAnnotation +An assignment of a function term (e no -AttributeValue -The value for any value of a attribute for a sample +CreditAssociation +This class supports binding associated researchers to studies no -FieldResearchSite -A site, outside of a laboratory, from which biosamples may be collected +Site + no -WorkflowExecution -Represents an instance of an execution of a particular workflow +ChromatographicSeparationProcess +The process of using a selective partitioning of the analyte or interferent b... no -Biosample -Biological source material which can be characterized by an experiment +FailureCategorization + no -NucleotideSequencing -A DataGeneration in which the sequence of DNA or RNA molecules is generated +MaterialEntity + no -MobilePhaseSegment -A fluid mixture of substances that flow though a chromatographic stationary p... +MetatranscriptomeAssembly + no -ProtocolExecution -A PlannedProces that has PlannedProcess parts +Configuration +A set of parameters that define the actions of a process and is shared among ... no -ChromatographicSeparationProcess -The process of using a selective partitioning of the analyte or interferent b... +EukEval +This class contains information pertaining to evaluating if a Metagenome-Asse... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +PortionOfSubstance +A portion of any matter of defined composition that has discrete existence, w... no -PeptideQuantification -This is used to link a metaproteomics analysis workflow to a specific peptide... +StorageProcess +A planned process with the objective to preserve and protect material entitie... no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -Configuration -A set of parameters that define the actions of a process and is shared among ... +Pathway +A pathway is a sequence of steps/reactions carried out by an organism or comm... no -PersonValue -An attribute value representing a person +DataObject +An object that primarily consists of symbols that represent information no -MetatranscriptomeAnnotation +PlannedProcess no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... -no - - -FunctionalAnnotation -An assignment of a function term (e -no - - -CreditAssociation -This class supports binding associated researchers to studies +ControlledTermValue +A controlled term or class from an ontology no -CollectingBiosamplesFromSite +EnvironmentalMaterialTerm no -ChemicalConversionProcess -A process that results in the interconversion of chemical species by a reacti... +NamedThing +a databased entity or concept/class no @@ -655,143 +640,148 @@

Applicable Classes

no -Site +ProcessedSample no -TextValue -A basic string value +TimestampValue +A value that is a timestamp no -ControlledTermValue -A controlled term or class from an ontology +ChemicalEntity +An atom or molecule that can be represented with a chemical formula no -NomAnalysis - +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -MassSpectrometryConfiguration -A set of parameters that define and control the actions of a mass spectrometr... +FieldResearchSite +A site, outside of a laboratory, from which biosamples may be collected no -MetabolomicsAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no -ProcessedSample +CollectingBiosamplesFromSite no -OntologyClass - +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -ControlledIdentifiedTermValue -A controlled term or class from an ontology, requiring the presence of term w... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MagBin +MetagenomeSequencing +Initial sequencing activity that precedes any analysis +no + + +NomAnalysis no -Pathway -A pathway is a sequence of steps/reactions carried out by an organism or comm... +Instrument +A material entity that is designed to perform a function in a scientific inve... no -Doi -A centrally registered identifier symbol used to uniquely identify objects gi... +TextValue +A basic string value no -ProteinQuantification -This is used to link a metaproteomics analysis workflow to a specific protein +InformationObject +Any data or knowledge that reduces uncertainty or enhances understanding abou... no -GeneProduct -A molecule encoded by a gene that has an evolved function +MetaboliteIdentification +This is used to link a metabolomics analysis workflow to a specific metabolit... no -FailureCategorization +MagBin no -DataObject -An object that primarily consists of symbols that represent information +MaterialProcessing +A process that takes one or more samples as inputs and generates one or more ... no -FunctionalAnnotationAggMember - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +GeneProduct +A molecule encoded by a gene that has an evolved function no -QuantityValue -A simple quantity, e +ChemicalConversionProcess +A process that results in the interconversion of chemical species by a reacti... no -Instrument -A material entity that is designed to perform a function in a scientific inve... +ProteinQuantification +This is used to link a metaproteomics analysis workflow to a specific protein no -ChemicalEntity -An atom or molecule that can be represented with a chemical formula +MassSpectrometryConfiguration +A set of parameters that define and control the actions of a mass spectrometr... no -FiltrationProcess -The process of segregation of phases; e +Study +A study summarizes the overall goal of a research initiative and outlines the... no -MetatranscriptomeAssembly - +PeptideQuantification +This is used to link a metaproteomics analysis workflow to a specific peptide... no -EnvironmentalMaterialTerm - +Extraction +A material separation in which a desired component of an input material is se... no -GenomeFeature -A feature localized to an interval along a genome +ImageValue +An attribute value representing an image no -LibraryPreparation - +CalibrationInformation +A calibration object that is associated with a process no -GeolocationValue -A normalized value for a location on the earth's surface +FunctionalAnnotationTerm +Abstract grouping class for any term/descriptor that can be applied to a func... no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +Protocol + no @@ -800,18 +790,23 @@

Applicable Classes

no -MaterialEntity +DissolvingProcess +A mixing step where a soluble component is mixed with a liquid component +no + + +OntologyClass no -CalibrationInformation -A calibration object that is associated with a process +MassSpectrometry +Spectrometry where the sample is converted into gaseous ions which are charac... no -DissolvingProcess -A mixing step where a soluble component is mixed with a liquid component +MobilePhaseSegment +A fluid mixture of substances that flow though a chromatographic stationary p... no @@ -820,48 +815,48 @@

Applicable Classes

no -FunctionalAnnotationTerm -Abstract grouping class for any term/descriptor that can be applied to a func... +GeolocationValue +A normalized value for a location on the earth's surface no -OrthologyGroup -A set of genes or gene products in which all members are orthologous +NucleotideSequencing +A DataGeneration in which the sequence of DNA or RNA molecules is generated no -PlannedProcess +MetaproteomicsAnalysis no -Protocol +FunctionalAnnotationAggMember no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +FiltrationProcess +The process of segregation of phases; e no -MaterialProcessing -A process that takes one or more samples as inputs and generates one or more ... +Doi +A centrally registered identifier symbol used to uniquely identify objects gi... no -StorageProcess -A planned process with the objective to preserve and protect material entitie... +MetabolomicsAnalysis + no -Study -A study summarizes the overall goal of a research initiative and outlines the... +ChromatographyConfiguration +A set of parameters that define and control the actions of a chromatography p... no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +ProtocolExecution +A PlannedProces that has PlannedProcess parts no @@ -870,23 +865,28 @@

Applicable Classes

no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +OrthologyGroup +A set of genes or gene products in which all members are orthologous no -InformationObject -Any data or knowledge that reduces uncertainty or enhances understanding abou... +AttributeValue +The value for any value of a attribute for a sample no -ChromatographyConfiguration -A set of parameters that define and control the actions of a chromatography p... +Biosample +Biological source material which can be characterized by an experiment no -MassSpectrometry -Spectrometry where the sample is converted into gaseous ions which are charac... +LibraryPreparation + +no + + +ControlledIdentifiedTermValue +A controlled term or class from an ontology, requiring the presence of term w... no diff --git a/pr-preview/pr-2230/url/index.html b/pr-preview/pr-2230/url/index.html index 3de4aba556..dc109de351 100644 --- a/pr-preview/pr-2230/url/index.html +++ b/pr-preview/pr-2230/url/index.html @@ -496,11 +496,6 @@

Applicable Classes

-Protocol - -no - - ImageValue An attribute value representing an image no @@ -510,6 +505,11 @@

Applicable Classes

An object that primarily consists of symbols that represent information no + +Protocol + +no +

Properties

diff --git a/pr-preview/pr-2230/version/index.html b/pr-preview/pr-2230/version/index.html index b40e6fb45d..20c9e5a59f 100644 --- a/pr-preview/pr-2230/version/index.html +++ b/pr-preview/pr-2230/version/index.html @@ -496,67 +496,67 @@

Applicable Classes

-MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +WorkflowExecution +Represents an instance of an execution of a particular workflow no -MetaproteomicsAnalysis - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... no -NomAnalysis +MetatranscriptomeAnnotation no -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... no -MetabolomicsAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... no -WorkflowExecution -Represents an instance of an execution of a particular workflow +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... no -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +MetatranscriptomeAssembly + no -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... no -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MetagenomeSequencing +Initial sequencing activity that precedes any analysis no -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +MetabolomicsAnalysis + no -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +NomAnalysis + no -MetatranscriptomeAnnotation - +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... no -MetatranscriptomeAssembly +MetaproteomicsAnalysis no diff --git a/pr-preview/pr-2230/volume/index.html b/pr-preview/pr-2230/volume/index.html index d845454e99..ffdcab4a29 100644 --- a/pr-preview/pr-2230/volume/index.html +++ b/pr-preview/pr-2230/volume/index.html @@ -497,14 +497,14 @@

Applicable Classes

-FiltrationProcess -The process of segregation of phases; e +SubSamplingProcess +Separating a sample aliquot from the starting material for downstream activit... yes -PortionOfSubstance -A portion of any matter of defined composition that has discrete existence, w... -no +FiltrationProcess +The process of segregation of phases; e +yes Extraction @@ -512,14 +512,14 @@

Applicable Classes

yes -MobilePhaseSegment -A fluid mixture of substances that flow though a chromatographic stationary p... +PortionOfSubstance +A portion of any matter of defined composition that has discrete existence, w... no -SubSamplingProcess -Separating a sample aliquot from the starting material for downstream activit... -yes +MobilePhaseSegment +A fluid mixture of substances that flow though a chromatographic stationary p... +no diff --git a/pr-preview/pr-2230/was_informed_by/index.html b/pr-preview/pr-2230/was_informed_by/index.html index 1a58b9b594..214b34625b 100644 --- a/pr-preview/pr-2230/was_informed_by/index.html +++ b/pr-preview/pr-2230/was_informed_by/index.html @@ -496,67 +496,67 @@

Applicable Classes

-MagsAnalysis -A workflow execution activity that uses computational binning tools to group ... +WorkflowExecution +Represents an instance of an execution of a particular workflow yes -MetaproteomicsAnalysis - +MetagenomeAssembly +A workflow execution activity that converts sequencing reads into an assemble... yes -NomAnalysis +MetatranscriptomeAnnotation yes -ReadBasedTaxonomyAnalysis -A workflow execution activity that performs taxonomy classification using seq... +MagsAnalysis +A workflow execution activity that uses computational binning tools to group ... yes -MetabolomicsAnalysis - +MetagenomeAnnotation +A workflow execution activity that provides functional and structural annotat... yes -WorkflowExecution -Represents an instance of an execution of a particular workflow +MetatranscriptomeExpressionAnalysis +A workflow process that provides expression values and read counts for gene f... yes -ReadQcAnalysis -A workflow execution activity that performs quality control on raw Illumina r... +MetatranscriptomeAssembly + yes -MetagenomeAssembly -A workflow execution activity that converts sequencing reads into an assemble... +ReadQcAnalysis +A workflow execution activity that performs quality control on raw Illumina r... yes -MetatranscriptomeExpressionAnalysis -A workflow process that provides expression values and read counts for gene f... +MetagenomeSequencing +Initial sequencing activity that precedes any analysis yes -MetagenomeAnnotation -A workflow execution activity that provides functional and structural annotat... +MetabolomicsAnalysis + yes -MetagenomeSequencing -Initial sequencing activity that precedes any analysis +NomAnalysis + yes -MetatranscriptomeAnnotation - +ReadBasedTaxonomyAnalysis +A workflow execution activity that performs taxonomy classification using seq... yes -MetatranscriptomeAssembly +MetaproteomicsAnalysis yes